Source: UNIVERSITY OF ARIZONA submitted to NRP
DEVELOPMENT AND EXPLOITATION OF GENUS LEVEL COMPARATIVE GENOMICS SYSTEMS TO EMPOWER AGRICULTURAL RESEARCH
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0231997
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2012
Project End Date
Sep 30, 2017
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF ARIZONA
888 N EUCLID AVE
TUCSON,AZ 85719-4824
Performing Department
Plant Science
Non Technical Summary
In 2011, the Economist magazine published an issue entitled "The 9-billion People Question" which addressed a world-wide dilemma that is central to most if not all plant scientists - How can our society grow enough food to feed 2 billion additional human beings in less than 40 years Rice (Oryza sativa) will play a key role in solving the 9BPQ as rice feeds half the world and it is that half that will double in size in the foreseeable future. One of the most important resources that can be utilized to improve cultivated rice is the virtually untapped reservoir of genetic variation hidden within the wild relatives of Oryza. The genus Oryza spans approximately 15 MY of evolutionary history and is composed of 21 wild and 2 domesticated species, 10 distinct genome types, and a 3.6 genome size variation. Wild Oryza species have a broad habitat distribution, including Asia, Australia, Africa, South and Central America, and many novel biotic/abiotic resistances have been identified. This project will help to lay the foundation for a complete genomic interrogation of the wild relatives of rice. Here we propose to generate: 1) Genome Framework Datasets (physical maps) for O. glumaepatula, O. meridionalis, and L. perrieri; 2) Chromsome 3 short arm sequences for the same 3 species, plus O. granulata; 3) Reference Sequences for O. barthii and O. punctata; 4) baseline transcriptome/small RNA datasets for 11 diploid Oryza species, plus L. perrieri; and 5) population datasets for the same set of 12 species in #4. These primary datasets will first be baseline annotated, and then used to address a number of fundamental areas in comparative genomics including: 1) Structural Variation; 2) Phylogenomics; 3) Population Genomics; 4) Genome Evolution & New Gene Origination; and 5) the Role of Transposable Elements in Genome Evolution. All of this data and analysis will be used in support of an international effort to generate reference genome sequences for the all 23 species of the genus Oryza under the rubric - the International Oryza Map Alignment Project (I-OMAP). This information will in turn be used to gain biological insights and to identify agriculturally important genes and can be used to help solve the 9 billion-people question. Additionally, this Hatch Project will be used to support the Arizona Genomics Institute by: 1) continuing to maintain and strengthen AGI's capabilities to remain a competitive world class plant genome center; 2) continuing to develop BAC-based fingerprint/BES framework physical maps for important crop plants; 3) developing and implementing methods to rapidly and cost effectively sequence plant genomes utilizing next generation sequencing; and 4) developing and implementing robust informatics pipelines to efficiently and effectively process next generation sequence data.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011530108050%
2021530104050%
Knowledge Area
202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1530 - Rice;

Field Of Science
1040 - Molecular biology; 1080 - Genetics;
Goals / Objectives
The goal of our research is to establish Oryza as a key biological system to address fundamental questions in genome biology. To accomplish this goal we will: A) generate 5 primary datasets/resources for the genus; B) perform baseline annotation on all sequence datasets; and C) perform computational/experimental analyses to address fundamental questions in comparative genomics. A) Data and resource generation, specifically we will produce: 1) Genome Frameworks: BAC end sequence/fingerprint physical maps for O. glumaepatula, O. meridionalis, and L. perrieri. The AA genome physical maps will complete the framework datasets for all AA genome species, and will provide the resources necessary to generate RefSeqs for these genomes. 2) Vertical Chr3S Datasets: RefSeqs for Chr3S of O. glumaepatula, O. meridionalis, O. granulata and L. perrieri. These RefSeqs will complete a vertical dataset of 14 Chr3 short arm sequences for 7 AA, 1 each of the BB, CC, BBCC, FF, & GG genome types, and L. perrieri. 3) Horizontal Datasets: O. barthii and O. punctata whole genome RefSeqs. 4) Whole Transcriptome Datasets: Deep sequencing of mRNA and small RNAs for 11 Oryza species and L. perrieri. This resource will be used to enhance the comparative annotation and analyses of transcripts and small RNAs across the Oryza. 5) Population Datasets: 15X whole genome sequencing data for 77-140 AA genome accessions. This resource will be used to add statistical power to all proposed analyses. B) Baseline Annotations: We will use automated methods to annotate the genomic and transcriptome resources described above. C) Data analyses: The goal of our analyses will be to discover the major evolutionary events and forces that led to the formation of 22 wild and 2 domesticated Oryza species, and 10 distinct genome types. Specifically, we will focus on: 1) Structural Variation: Identify major structural variations across the Vertical/Horizontal datasets in comparison to the rice RefSeq. These data will allow us to explore the role of genome flux in the Oryza. 2) Phylogenomics: Infer gene trees across the Oryza to address the problem of how to integrate discordant phylogenies from different genomic regions. 3) Population Genomics: Infer historical levels of introgression among AA genome species, and conduct genome-wide population genetic analyses. 4) Genome Evolution & New Gene Origination: Determine genomic features, content of new genes, and their distribution across Oryza. 5) Role of Transposable Elements in Genome Evolution: Characterize TE families in all Oryza species to unravel their impact on genome dynamics during the evolution of the genus. D) Additional General Aims for AGI 1) Continue to maintain and strengthen AGI's capabilities to remain a competitive world class plant genome center. 2) Continue to develop BAC-based fingerprint/BES framework physical maps for important crop and model plants. 3) Develop and implement methods to rapidly and cost effectively sequence plant genomes utilizing next generation sequencing. 4) Develop and implement robust informatics pipelines to efficiently and effectively process next generation sequence data.
Project Methods
1) Continue to maintain and strengthen AGI's capabilities to remain a competitive and world class plant genome center. Objective 1) really does not have a "procedure". Essentially we will continue to work as hard as possible to maintain a competitive edge in the field of plant genomics. One major focus will be to establish robust protocols and informatics pipelines for next generation sequencing technologies. 2)Continue to develop BAC-based fingerprint/BES framework physical maps for important crop and model plants. My lab was the first lab in the world to construct a plant BAC library in 1994. We have continued to make high-quality BAC libraries for our own research as well as to support the research of others. We will continue to produce BAC libraries in this way and have a proposal pending with the NSF to make approximately 60 new libraries from crop plants and wild species that yet to have libraries. AGI is also one of the best labs in the world to generate BAC-based physical maps and we will continue to perform this activity for the foreseeable future. In fact we already have funded research projects to generate such frameworks for coffee (diploid and polyploid), cucumber, barley, eucalyptus, avocado, and Amborella (a model plant at the base of the angiosperm tree of life). 3)Develop and implement methods to rapidly and cost effectively sequence plant genome utilizing next generation sequencing technologies coupled with BAC-based physical maps. AGI currently supports two next generation sequencing platforms - Roche's GSFLX and Illumina's HiSeq2000. These short read platforms are ideal for re-sequencing applications where a reference genome sequence is already available or for de novo sequencing of small bacterial genomes (~2-4 Mb). Our lab is interested in using these technologies to sequence large eukaryotic genomes de novo by taking advantage of our ability to construct and integrate high-quality BAC-based physical maps with next generation genome assemblies. Our estimate is that we can de novo sequence an entire wild Oryza genome (~ 400 Mb) in less than two months for about $100,000 or less. This is a far cry from the $200,000,000 that was used to sequence the cultivated rice genomel!!!! We now have a NSF grant funded to de novo sequence three wild Oryza genomes in this manner. We are also developing collaborations to generate ~150 reference genomes across the Brassicales family in a similar way. It should be noted that next generation sequencing technologies are changing and improving at an enormous pace. Our lab is constantly updating and optimizing protocols to more cost effectively sequence plant genomes and will continue to take this path for the foreseeable future.

Progress 10/01/15 to 09/30/16

Outputs
Target Audience:1) Academic and industry academic community with a focus on plant genomics and evolutionary biology 2) Community outreach through the public school system, FFA events and public lectures Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Postdocs, graduate students and staff attended national and international scientific meeting and presented their work, either in oral or poster. How have the results been disseminated to communities of interest?Since our last report AGI has published 12peer review manuscripts and gave 9oral presentations. On the outreach side I participated in the Curry Farm FFA Chile Field day, gave 5 lectures in an 8th grade science class on genetics/genomics and feeding the worldat Esperero Middle School. What do you plan to do during the next reporting period to accomplish the goals?1) Finish assembly and annotation of Oryza coarctata genome. 2) Perform GWAS analysis of drought tolerance screen of O. glumatatula accessions. 3) Participate in filed phenotyping of 3K rice genomes at IRRI. 4) Sequence, assembly and annotation 20-30 additional Oryza sative genomes covering all 15 subgroups for pan-genome and natural variation analysis 5) Write several manuscripts. 6) Write a NSF Plant Genome grant on Agroecosystems Genomics to study rice and microbiome genotypes and methane emissions. 7) Work toward sequencing and assembling the 5 remaining species of the genus Oryza for which we do not have any assemblies.

Impacts
What was accomplished under these goals? 1) From our last report I provided the following summary:Summary: The majority of primary analyses C1-5 have been completed, many of which have been published, and the remaining publications will be submitted as the Oryza Nature Package of 9 manuscripts in February 2016. Additional grant proposals are in preparation for continued work on these data sets and for the generation of similar data sets for the remaining species in the genus Oryza. D1) Continue to maintain and strengthen AGI's capabilities to remain a competitive world class plant genome center. Ongoing. Summary: AGI has developed new assembly, annotation and assembly editing pipelines based on PacBio's long read sequencing technology. We are now in the process of negotiation for the purchase of PacBio's new SEQUEL sequencing instrument that has 7X the sequencing capacity as the RSII. On April 15th, 2016 I coordinate the submission of 19 manuscripts to the Nature Family of Journals. A majority of these manuscripts were published as demonstrated in the list of citations. I still have two remaining articles that are in their 2nd revision at Nature - One on a deep analysis of the 3K rice genomes data set for which I am a co-senior author, and one on a deep analysis of 13 Oryza genomes that traverse the Oryza genus. These 2nd revisions will be submitted by May 1st, 2017. 2) In addition the work described above, my laboratory has developed and implemented a number of new protocols for the isolation of high-quality high-molecluar weight DNA for PacBio and 10X genome sequencing. 3) We utilized these protocols to PacBio sequence and assemble two high-quality whole genome shotgun assemblies for IR8 (known as miracle rice) and N22 (an important Aus subgroup). These genomes have been publicly released and have been incorporated into the two Nature manuscripts under revision. 4) AGI is now transferring it PacBio RSII sequencing skill and knowhow to PacBio's new sequencing platform - Sequel. AGI recently completed the production sequencing of Oryza coarctata, a salt loving relative of rice with a polyploid genome. 5) Lastly, AGI streamlined it computational infrastructure so we can now run PacBio assemblies and MAKER annotations on our own servers.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang, J., Y. Yu, F. Tao, J. Zhang, D. Copetti, D. Kudrna, J. Talag, S. Lee, R.A. Wing, C. Fan. DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. 2016. Genome Biology 17:92
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhang, J. D. Kudrna, T. Ming, W. Li, D. Copetti, Y. Yu, J.L. Goicoechea, Y. Lei, R.A. Wing. Genome Puzzle Master (GPM) - An integrated pipeline for building and editing pseudomolecules from fragmented sequences. 2016. Bioinformatics doi: 10.1093/bioinformatics/btw370.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: van Andel, T.R., R.S. Meyer, S.A. Afllitos, J.A. Carney, M.A. Veltman, D. Copetti, J.M. Flowers, R.M. Havinga, H. Maat, M.D. Purugganan, R.A. Wing, M.E. Schranz. Ancestor rice of Suriname Maroons traced back to its African origin. 2016 Nature Plants doi: 10.1038/NPLANTS.2016.149.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ray, S., L.K. Bose, J. Ray, U. Ngangkham, J.L. Katara, S. Samantaray, L. Behera, M. Anumalla, O.N. Singh, M. Chen, R.A. Wing, T. Mohapatra. Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha. 2016. MGG 291:1783-1794.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhang, J., L.-L. Chen, S. Sun, D. Kudrna, D. Copetti, W. Li, T. Mu, W.-B. Jiao, F. Xing, S. Lee, J. Talag, J.-M. Song, B. Du, W. Xie, M. Luo, C.E. Maldonado, J.L. Goicoechea, L. Xiong, C. Wu, Y. Xing, D. Zhou, S. Yu, Y. Zhao, G. Wang, Y. Yu, Y. Luo, B.E.P. Hurtado, A. Danowitz, R.A. Wing* & Q. Zhang* (*Co-corresponding Authors). Building two reference-quality indica rice genomes with clone-based PacBio long-read and Illumina paired-end sequencing data. 2016. Scientific Data doi:10.1038/sdata.2016.76.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhang, J., L.L. Chen, F. Xing, D. Kudrna, W. Yao, D. Copetti, T. Mua, W. Lia, J.-M. Song, W. Xie, S. Lee, J. Talag, L. Shao, Y. An, C.-L. Zhang, Y. Ouyang, S. Sun, W.-B. Jiao, F. Lv, B. Du, M. Luo, C.E. Maldonado, J.L. Goicoechea, L. Xiong, C. Wu, Y. Xing, D. Zhou, S. Yu, Y. Zhao, G. Wanga, Y. Yu, Y. Luo, Z.W. Zhou, B.E.P. Hurtado, A. Danowitz, R.A. Wing*, & Q. Zhang* (*Co-corresponding Authors). Extensive complementarity of two indica rice reference genomes. 2016. PNAS USA 113: E5163-E5171, doi:10.1073/pnas.1611012113.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wicker, T., Y. Yu, G. Haberer, K.F.X. Mayer, P.R. Marri, S. Rounsley, M. Chen, A. Zuccolo, O. Panaud, R.A Wing, S. Roffler. DNA transposons specifically accelerate evolution of genes in rice and other grasses. 2016. Nature Communications 7:12790, doi:10.1038/ncomms12790.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Copetti, D., R.A. Wing. The dark side of the genome: revealing the native transposable element/repeat content of eukaryotic genomes. 2016. Molecular Plant doi:10.1016/j.molp.2016.09.006.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gan, X., A. Hay, M. Kwantes, G. Haberer, A. Hallab, R. Dello loio, H. Hofhuis, B. Pieper, M. Cartolano, U. Neumann, L. Nikolov, B. Song, M. Hajheidari, R. Briskine, E. Kougioumoutzi, D. Vlad, S. Broholm, J. Hein, K. Meksem, D. Lightfoot, K.K. Shimizu, R. Shimizu-Inatsugi, M. Imprialou, D. Kudrna, R.A. Wing, S. Sato, P. Huijser, D. Filatov, K. Mayer, R. Mott, & M. Tsiantis. The Cardamine hirsuta genome highlights the pervasive role of transcription factors and tandem gene duplications in morphological diversity. 2016. Nature Plants 2:16167, doi:10.1038/nplants.2016.167.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mansueto, L., R.R. Fuentes, F.N. Borja, J. Detras, J.M. Abriol-Santos, D. Chebotarov, M. Sanciangco, K. Palis, D. Copetti, A. Poliakov, I. Dubchak, V. Solovyev, R.A. Wing, R.S. Hamilton, R. Mauleon, K.L. McNally, N. Alexandrov. Rice SNP-seek database update: new SNPs, indels, and queries. 2016. Nucleic Acids Research, doi:10.1093/nar/gkw1135.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Brozynska, M., D. Copetti, A. Furtado, R.A. Wing, D. Crayn, G. Fox, R. Ishikawa, R. Henry. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. 2017. Plant Biotec. J., doi:10.1111/pbi.12674.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Choi, J.Y., A.E. Platts, D.Q. Fuller, Y.I. Hsing, R.A. Wing, M.D. Purugganan. The rice paradox: Multiple origins but single domestication in Asian rice. 2017. Mol. Biol. Evol. doi:10.1093/molbev/msx049


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:1) Academic and industry academic community with a focus on plant genomics and evolutionary biology 2) Community outreach through the public school system, FFA events and public lectures Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?1) Postdocs, graduate students and staff attended national and international scientific meeting and presented their work, either in oral or poster. How have the results been disseminated to communities of interest?Since our last report AGI has published 11 peer review manuscripts and gave 16 oral presentations. On the outreach side I participated in the Curry Farm FFA Chile Field day, gave 5 lectures in my daughter's 8th grade science class on genetics/genomics and feeding the world, and ran the 6th annual Plant Science Family Night at Ventana Vista Elementary School. What do you plan to do during the next reporting period to accomplish the goals?1) Submit our Oryza Nature Package for publication to the Nature family of journals in February 2016. 2) Write and submit several additional manuscripts of plant genomics. 3) Submit 2-3 grant proposals to the NSF, USDA, DOE to continue our work on rice and it's wild relatives. 4) Continue to maintain and strengthen AGI's capabilities to remain a competitive world class plant genome center. 5) Develop and implement methods to rapidly and cost effectively sequence plant genomes utilizing next generation sequencing. Ongoing. See D2 Summary. 6) Continue to Develop and implement robust informatics pipelines to efficiently and effectively process next generation sequence data.

Impacts
What was accomplished under these goals? To follow is a list of accomplishments by objectives: A 1) Genome Frameworks: BAC end sequence/fingerprint physical maps for O. glumaepatula, O. meridionalis, and L. perrieri. DONE A 2) Vertical Chr3S Datasets: RefSeqs for Chr3S of O. glumaepatula, O. meridionalis, O. granulata and L. perrieri. These RefSeqs will complete a vertical dataset of 14 Chr3 short arm sequences for 7 AA, 1 each of the BB, CC, BBCC, FF, & GG genome types, and L. perrieri. DONE A 3) Horizontal Datasets: O. barthii and O. punctata whole genome RefSeqs. DONE A 4) Whole Transcriptome Datasets: Deep sequencing of mRNA and small RNAs for 11 Oryza species and L. perrieri. This resource will be used to enhance the comparative annotation and analyses of transcripts and small RNAs across the Oryza. DONE A 5) Population Datasets: 15X whole genome sequencing data for 77-140 AA genome accessions. This resource will be used to add statistical power to all proposed analyses. DONE Summary: All primary data sets have been generated and deposited in the appropriate public data bases (i.e. Genbank, Gramene, ENSEMBL-Plants) B) Baseline Annotations: We will use automated methods to annotate the genomic and transcriptome resources described above. DONE Summary: All annotations have been completed and deposited in the appropriate public data bases (i.e. Genbank, Gramene, ENSEMBL-Plants) C1) Structural Variation: Identify major structural variations across the Vertical/Horizontal datasets in comparison to the rice RefSeq. These data will allow us to explore the role of genome flux in the Oryza. DONE. C2) Phylogenomics: Infer gene trees across the Oryza to address the problem of how to integrate discordant phylogenies from different genomic regions. DONE. C3) Population Genomics: Infer historical levels of introgression among AA genome species, and conduct genome-wide population genetic analyses. DONE. C4) Genome Evolution & New Gene Origination: Determine genomic features, content of new genes, and their distribution across Oryza. DONE. C5) Role of Transposable Elements in Genome Evolution: Characterize TE families in all Oryza species to unravel their impact on genome dynamics during the evolution of the genus. DONE. Summary: The majority of primary analyses C1-5 have been completed, many of which have been published, and the remaining publications will be submitted as the Oryza Nature Package of 9 manuscripts in February 2016. Additional grant proposals are in preparation for continued work on these data sets and for the generation of similar data sets for the remaining species in the genus Oryza. D1) Continue to maintain and strengthen AGI's capabilities to remain a competitive world class plant genome center. Ongoing. Summary: AGI has developed new assembly, annotation and assembly editing pipelines based on PacBio's long read sequencing technology. We are now in the process of negotiation for the purchase of PacBio's new SEQUEL sequencing instrument that has 7X the sequencing capacity as the RSII. D2) Continue to develop BAC-based fingerprint/BES framework physical maps for important crop and model plants. Ongoing. Summary: AGI has one grant pending to generation a WGP physical map for a European maize accession. Other than this we will likely be phasing out whole genome BAC-based physical maps over the next year. D3) Develop and implement methods to rapidly and cost effectively sequence plant genomes utilizing next generation sequencing. Ongoing. See D2 Summary. D4) Develop and implement robust informatics pipelines to efficiently and effectively process next generation sequence data. Ongoing. See D2 Summary.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gerring, A.D.W., F. Maumus, D. Copetti, N. Choisne, D. Zwickl, M. Zytnicki, A.R. McTaggart, S. Scalabrin, S. Vezzulli, R.A.Wing, H. Quesneville, & P.Y. Teycheney. 2014. Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nature Communications 5: Article number 5269.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Gao, D., N. Jiang, R.A. Wing, J. Jiang, S.A. Jackson. 2015. Transposons play an important role in the evolution and diversification of centromeres among closely related species. Frontiers in Plant Sci. 6:216.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sanderson, M.J., D. Copetti, A. B�rquez, E. Bustamante, J. Charboneau, L. Eguiarte, S. Kumar, H.O. Lee, J. Lee, M. McMahon, K. Steele., R.A. Wing, T.J. Yang, D. Zwick, M.F. Wojciechowski. 2015. Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea, Cactaceae): Loss of the NDH gene suite and inverted repeat. American J. Botany 102:1115-1127.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Copetti, D., J. Zhang, M. El Badouri, D. Gao, J. Wang, E. Barghini, R. Cossu, A. Angelova, C.E. Maldonado, S. Roffler, H. Ohyanagi, T. Wicker, C. Fan, A. Zuccolo, M. Chen, A.C. de Oliveira, B. Han, R. Henry, Y.I. Hsing, N. Kurata, W. Wang, S. Jackson, O. Panaud, R.A. Wing. 2015. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 16:538.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mu�oz-Amatria�n, M., S. Lonardi, M.C. Luo, K. Madishetty, J. Svensson, M. Moscou, S. Wanamaker, T. Jiang, A. Kleinhofs, G. Muehlbauer, R. Wise, N. Stein, Y. Ma, E. Rodriguez, D. Kudrna, P. Bhat, S. Chao, P. Condamine, S. Heinen, J. Resnik, R.A. Wing, H. Witt, M. Alpert, M. Beccuti, S. Bozdag, F. Cordero, H. Mirebrahim, R. Ounit, Y. Wu, F. You, J. Zheng, H. Simkova, J. Dolezel, J. Grimwood, J. Schmutz, D. Duma, L. Altschmied, T. Blake, P. Bregitzer, L. Cooper, M. Dilbirligi, A. Falk, L. Feiz, A. Graner, P. Gustafson, P. Hayes, P. Lemaux, J. Mammadov, T. Close. 2015. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. The Plant Journal 84:216227.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kim, K., S.C. Lee, J. Lee, Y. Yu, K. Yang, B.S. Choi, H.J. Koh, N.E. Waminal, H.I. Choi, N.H. Kim, W. Jang, H.S. Park, J. Lee, H.O. Lee, H.J. Joh, H.J. Lee, J.Y. Park, S. Perumal, M. Jayakodi, Y.S. Lee, B. Kim, D. Copetti, S. Kim, S. Kim, K.B. Lim, Y.D. Kim, J. Lee, K.S. Cho, B.S. Park, R.A. Wing, T.J. Yang. 2015. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. 2015. Scientific Reports 5:15655.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Zhang, Y., S. Zhang2, H. Liu, B. Fu, L. Li, M. Xie, Y. Song, X. Li, J. Cai, W. Wan, L. Kui, H. Huang, J. Lyu, Y. Dong, W. Wang, L. Huang, J. Zhang, Q. Yang, Q. Shan, Q. Li, W. Huang, D. Tao, M. Wang, M. Chen, Y. Yu, R.A. Wing*, W. Wang*, F. Hu* (*co-corresponding authors). 2015. Genome and comparative transcriptomics of African wild rice Oryza longistaminata provide insights into molecular mechanism of rhizomatousness and self-incompatibility. Molecular Plant 8:16831686.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wing, R.A. 2015. Research Highlight - Harvesting rices dispensable genome. 2015. Genome Biology 16: 217.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wicker, T., R.A. Wing, I. Schubert. Inter-chromosomal sequence exchange in a peculiar group of grass chromosomes. 2015. The Plant Journal 84:747-759.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: De Vega, J.J., S. Ayling, M. Hegarty, D. Kudrna, J.L. Goicoechea, A. Ergon, O.A. Rognli, C. Jones, M. Swain, R. Geurts, C. Lang, K.F.X. Mayer, S. R�ssner, S. Yates, K.J. Webb, I.S. Donnison, G.E.D. Oldroyd, R.A. Wing, M. Caccamo, W. Powell, M.T. Abberton, L. Sk�tb. Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific Reports 5:17394.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Wendel, J.F., S.A. Jackson, B.C. Meyers, R.A. Wing. Game of omes: The kingdom of DNA reflects a complex, episodic history of upheaval, recovery, and survival. 2016. Genome Biology (in press).


Progress 10/01/13 to 09/30/14

Outputs
Target Audience:1) Academic and industry academic community with a focus on plant genomics and evolutionary biology 2) Community outreach through the public school system, FFA events and public lectures Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?1) Postdocs and graduate students attended international scientific meeting and presented their work, either in oral or poster form. 2) AGI hosted the 12th International Symposium on Rice Functional Genomics and AGI Postdocs & graduate students served on the local organizing committee to provide input on speakers, topics, and workshops. Of note NIFA provided $10,000 in support of this meeting. How have the results been disseminated to communities of interest?Peer review publications, database submissions, seminar and poster presentations, and public outreach activities such as our annual Plant Science Family Nights held at Ventana Vista Elementary School, Tucson, AZ. What do you plan to do during the next reporting period to accomplish the goals?C) Continues our analyses, manuscript writing and submissions. D, E) Continue to explore new methods and strategies to create the highest quality reference genoms available for crop genomes and their wild relatives. F) Continue our education and outreach activities as we have in the past. In addition - AGI will continue to write for grant support to NIFA, NSF and the NIH as well have operate our PacBio service center for collaborative and service based research.

Impacts
What was accomplished under these goals? A) All resources and data sets listed under Goal A have been achieved, the majority of which have been deposited into public data bases B) All base line annotation data has been completed, and deposited in Gramene (gramene.org) & Ensenbl plants (plants.ensembl.org) C) Data analysis is still in progress. Several manuscripts have already been published (see publications), and several more are being written or have been submitted, or are under peer review. Our main Oryza paper describing the evolutionary analysis of 11 Oryza genome and the outgroup L. perrieri will be submitted to Nature/Nature Genetics before the end of 2015. D) AGI acquired a PacBio RSII high throughput genome and RNA sequencing machine which will help to keep AGI at the cutting edge of agricultural genomics for the near future. E) We developed two high-quality indica rice physical maps using KeyGene's whole genome profiling method, that was licensed to AGI F) AGI continues on the informatice front to support all of our sequencing and analysis pipelines. On this front AGI developed an Oryza specific repeat database www.RiTE.org and a PacBio sequence and assembly tracking pipeline in order to manage all of our long-read sequencing projects.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: C. Wang, X. Shi, L. Liu, H. Li, J.S.S. Ammiraju, D.A. Kudrna, W Xiong, H. Wang, Z. Dai, Y. Zheng, J. Lai, W. Jin., J. Messing, J.L. Bennetzen, R.A. Wing, & M. Luo. 2013. Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives. Genetics 195:723-737.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Jacquemin, J., J.S.S. Ammiraju, G. Haberer2, D.D. Billheimer, Y. Yu., L.C. Liu, L.F. Rivera, K. Mayer, M. Chen, & R.A. Wing. 2013. 15 MYA of evolution in the Oryza genus shows extensive gene family expansion. Molecular Plant (10.1093/mp/sst149).
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Chamala, S., A.S. Chanderbali, J.P. Der, T. Lan, B. Walts, V.A. Albert, C.W. dePamphilis, J. Leebens-Mack, S. Rounsley, S. Schuster, R.A. Wing, N. Xiao, R. Moore, P.S. Soltis, D.E. Soltis, & W. Barbazuk.2013. Assembly and validation of the complete nuclear genome sequence of the basal angiosperm Amborella, a non-model species. Science 342:1516-1517
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Amborella Genome Project. 2013. The Amborella genome and the evolution of flowering plants. Science 342:1241084.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wang, X., D.A. Kudrna, Y. Pan, H. Wang, L.L., H. Lin, J. Zhang, X. Song, J.L. Goicoechea, R.A. Wing, Q. Zhang, & M. Luo. 2014. Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping. Genetics 196:937-949.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Pan Y., Y. Deng, H. Lin, D.A. Kudrna, R.A Wing, L. Li, Q. Zhang, & M. Luo. 2014. Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 9311 and evaluation of the two rice reference sequence assemblies. The Plant Journal 77:795805.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zwickl D., J. Stein, R.A. Wing, D. Ware, & M. Sanderson. 2014. Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Systematic Biology doi: 10.1093/sysbio/syu027.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Schmutz, J., P. McClean, S. Mamidi, G.A. Wu,, S.B. Cannon, J Grimwood, J. Jenkins, S. Shu, Q. Song, C. Chavarro, M. Torres-Torres, V. Geffroy, S.M. Moghaddam, D. Gao, B. Abernathy, K. Barry, M. Blair, M.A. Brick, M. Chovatia, P. Gepts, D.M Goodstein, M. Gonzales, U. Hellsten, D.L. Hyten, G. Jia, JD. Kelly, D. Kudrna, R. Lee, M.M.S. Richard, P.N. Miklas, JM. Osorno, J Rodrigues, V. Thareau, C.A. Urrea, M. Wang, Y. Yu, M. Zhang, R.A. Wing, P.B. Cregan, D.S. Rokhsar, & SA. Jackson. 2014. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics 46: 707713.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Wang, M., Y. Yu, G. Haberer, P. Marri, C. Fan, J.L. Goicoechea, A. Zuccolo, X. Song, D. Kudrna, S.A. Jetty, R. Cossu , C. Maldonado, J. Chen , S. Lee, N. Sisneros, K. de Baynast , W. Golser, M. Wissotski, W. Kim , P. Sanchez, M.N. Ndjiondjop, K. Sanni , M. Long, J. Carney, O. Panaud, T. Wicker, C. Machado, M. Chen, K. Mayer, S. Rounsley, & R.A. Wing. 2014. The genome of African rice (Oryza glaberrima): Evidence for independent domestication. Nature Genetics 46:982-988.


Progress 10/01/12 to 09/30/13

Outputs
Target Audience: The target audience for our research are: 1) basic scientists working on the genomics of crop plants and their wild relative; 2) breeders working on the use of genomics to improve crops; and 3) the general public in the form of outreach. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project offers many opportunities for training and professional development from the profession staff level down to the high school level. Our undergraduate training has been one of the cornerstones of our wet lab and plant growth systems operations. We trained/mentored a high school student, undergraduates, and graduate students this past year working on everything from genome sequencing, data analysis, bioinformatics, plant phenotyping and growth systems. For Post-Docs, graduate students and other professionals, we provided ongoing mentoring and professional development in the following: lab and project management, paper writing, report writing, grant writing, seminars and poster presentations, training and workshops in analytical methods, programming/bioinformatics, statistics, career advancement, independent research development, Responsible Conduct of Research, and so forth. For this reporting period this project 29 training and professional development opportunities were accomplished by project participants (listed below) Dr. Julie Jacquemin (AGI, Postdoctoral Scientist). Training opportunity: Julie will talk the “Population Genetics and Association Mapping” course at the 18th Summer Institute in Statistical Genetics, University of Washington in July 2013. Course Description: Hardy-Weinberg equilibrium, population structure, haplotype frequency, linkage disequilibrium, genetic association testing. Outreach opportunity: Julie participated in Plant Science Family Night and the Math and Science Fun Fest during year 3. She created a hands-on phylogentic tree module in collaboration with D. Zwickl and M. Sanderson, where kids investigated which plants are closely related to each other and which ones are distantly related to each other. Mentoring opportunity: Julie is mentoring a UA Junior, Ms. Naomi Rhodes, this summer in the areas of evolutionary genomics and bioinformatics. Dr. Paul Sanchez (AGI Postdoctoral Scientist). Outreach opportunity: Paul participated in Plant Science Family Night and the Math and Science Fun Fest. He created a hands-on activity called: The Art & Science of Producing New Rice Plants. Dave Kudrna. (AGI, Group Leader, OGE Project Manager). Outreach opportunity: Dave participated Plant Sciences Family Night, BIO5 Chess Club Science Lecture and this summer’s USDA Ag Discovery Camp in year-3 and created a hands on activity to explain “What is the meaning of a DNA sequence?”. The purpose of this center was to introduce to the student that a DNA sequence is represented by four letters (A, T, G, C) and that they look just like letters of the alphabet. But importantly, where do sequences come from, what do they do and/or mean, what do they tell us and how do we figure out what they tell us. Since much DNA work is done with computers we ran this Center live --via the internet. We allowed each student to sit at the keyboard; they were introduced to a DNA sequence, blast, NCBI, simple data analysis. We used agricultural and domestication/evolutionary significant genes of rice as the basis and involved other organism’s DNA sequences and also human. Dr. Jose Luis Goicoechea (AGI, Postdoctoral Scientist). Teaching opportunity. He was part of the Winter Breeding Institute (January 6th – 10th 2013), Jose Luis gave one lecture entitled “Physical Mapping” (1hr30’) - within the module “Introduction to plant genomics”, coordinated by R. Wing. Outreach opportunity. He participated in the Plant Sciences Family Night. He was involved with the phylogenetic tree module where children and parents investigated the relation of plants to each other, and which are more distantly related. Carlos Maldonado (AGI, Graduate Student) Outreach opportunity. Carlos participated in Plant Science Family Night in year-3 where he designed a puzzle game to show some basic features of the molecular biology central dogma and how a deletion in a specific gene changes the encoded protein and the phenotype. Using a fraction of the red pericarp gene of rice (Rc) the kids built the complementary strands of the wild type gene and a mutated one, comparing the sequences they were able to find a deletion, then using the genetic code to translate the gene and pseudogene proteins they were able to see the difference that makes rice grains white or red. This activity will be written up as a chapter of his dissertation. Dr. Dario Copetti (AGI Postdoctoral Scientist). Mentoring opportunity: In June and July 2012 Dario mentored Mr. William George, a junior high school student participating in the KEYS program. During a 6-week period he developed an assay to quantify repeated sequences by means of a RT-PCR assay. Teaching opportunity: Dario prepared and gave a lecture (1 h 30') for the UA Winter Breeding Institute (January 6th – 10th 2013) on repeat annotation and transposable elements within the module “Introduction to plant genomics”, coordinated by R. Wing. Outreach Opportunity: Dario participated in the DNA candy center at AGI’s Plant Sciences Family Night by teaching and helping students understand the structure of DNA using candy to construct a DNA model. Muhua Wang (AGI Graduate Student) Training opportunity: To improve his mastery of evolutionary biology, Muhua attended the University of Chicago as a visitor to work in Manyuan Long’s lab and learned in-depth analysis methodologies in population genetics. While there, he audited 2 graduate courses: Population Genetics- taught by Dr. Richard Hudson, and Molecular Evolution taught by Dr. Martin Kreitman; Jan. 8, 2103 to Mar. 21 2013. Teaching opportunity: Muhua prepared and gave one lecture (1hr30’) for the UA Winter Breeding Institute (January 6th – 10th 2013), entitled “How to Deal with a Lane of Illumina Data – Resequencing/ SNP calling”, within the module “Introduction to plant genomics”, coordinated by R. Wing. Dr. Yeisoo Yu (AGI, Sequencing Group Leader). Teaching opportunity: Yeisoo prepared and presented two lectures for the UA Winter Breeding Institute (January 6th – 10th 2013) entitled “Plant Genomes and Genome Sequencing” (1hr30’), and “Genome Assembly and Editing” (1hr30’) - within the module “Introduction to plant genomics”, coordinated by R. Wing. Outreach opportunity: Yeisoo created a center for Plant Science Family Night where the chemical structure of the DNA molecule was explained by building a candy model. Kids could build a small double helix using candies as proxies for the four bases and the sugar-phosphate backbone. The goal of this booth was to teach kids about how plant genomes are sequenced, and the importance of genome information to help solve world hunger. Dr. Jianwei Zhang (AGI, Bioinformatics Group Leader). Teaching opportunity: Jianwei prepared and gave two lectures for the UA Winter Breeding Institute (January 6th – 10th 2013) entitled “Genome Assembly Editing” (1hr30’), and “Genes and Databases” (1hr30’) - within the module “Introduction to plant genomics”, coordinated by R. Wing. Outreach opportunity: Jianwei participated in our 2012 Plant Science Family Night and created a rice tasting activity whereby attendees could taste 12 different rice varieties from around the world and vote for their favorite one. We were able to obtain rice verities from many of our collaborators from around the world including O. glaberrima from the Africa Rice Center in Benin. How have the results been disseminated to communities of interest? Project staff disseminated results in various ways including invited lectures, talks, posters at meetings, publications and via the World Wide Web. Our group participated in major scientific meetings by attending and presenting data and findings. Major meetings attended include: The International Symposium on Rice Functional Genomics (November 2012, Chen Mai, Thailand); the International Plant and Animal Genome Conference (January 2013, San Diego, CA), and the Annual Meeting of the Society for Molecular Biology and Evolution (July 2013, Chicago, IL). Our data and results have been disseminated in 25 publications to date and in 36 invited lectures given. Websites that provide the major releases of OGE data and results are: Gramene: (http://www.gramene.org/) and OMAP: (http://www.omap.org/cgi-bin/status/status.cgi). Our project has a strong outreach component that include 1) Outreach to Elementary Students and their Families, 2) Outreach to Underrepresented students, 3) Outreach to Broad U.S. and International Rice Communities. AGI organized it's 3rd Plant Science Family Nights (PSFN) at Ventana Vista Elementary School in Tucson AZ on Oct. 5 2012. We had more than 400 attendees, we featured over 30 activities covering diverse plant-related topics and the reviews from attendees were overwhelmingly positive. A detailed overview of PSFN is included in the supporting pdf files. Our involvement with students is a cornerstone to our wetlab activities and we have about 6 undergraduate students in the AGI labs where they work on cutting edge molecular DNA technology. Additionally, we hosted two high school students in the Keep Engaging Youth in Science (KEYS) summer education program. We also participated in the USDA Ag Discovery Camp, in 2012 and 2013, where we provided workshop style introductions to the 9 billion people question, useful crop alleles and functional genes. The highlight was hands-on activities, with OGE and rice gene sequences and functional gene annotations, where we used bioinformatics tools, ie BLAST, via NCBI databases to discover connections to useful agricultural traits. This project’s involvement with the US and International Rice communities was evident by involvement in several diverse topics: 1) Conference Proceedings and Invited lectures (see invited lectures presented in the supporting pdf files); 2) Winter Breeding Institute which was composed of four 2½ day modules, of which 1 was taught by AGI entitled “Introduction to Plant Genomics”; 3) we hosted an International Oryza Map Alignment Meeting at the Plant and Animal Genome Conference in San Diego, Jan. 2013.; 4) due to so many requests for bioinformatics support, we have started to develop training modules for teaching basic and advanced bioinformatics techniques. To make it easier to understand for the user, and to save time for teaching and understanding, we have initiated a series of YouTube bioinformatics videos on the AGI youtube channel; 5) PI Wing participated with the Lifelong Learning group at the Highlands Dove Mountain, Tucson AZ, where he presented part of his lecture on “Genomics Now- The 9 Billion People Question” that outlines his research with the eventual goal of helping to solve the 9-billion people question. What do you plan to do during the next reporting period to accomplish the goals? AGI - Wing: By the beginning of Year-4 (August 2013) of the NSF OGE grant, AGI will have completed essentially all production, assembly, annotation, and sequence submission objectives. The entire year 4 will be devoted to data analysis, manuscript writing, and publication in collaboration with OGE and IOMAP PIs, and outreach. Data analysis and manuscript submission: The OGE consortia along with the IOMAP has now assembled and annotated 11 Oryza genomes and 1 outgroup genome (L. perrieri). Our collective goal is to analyze these data sets in earnest with the plan of submitting a major paper describing the resource and a subset of analyses by the end of 2013, followed by a series of companion papers. (see main and companion paper outlines in the supporting pdf files). Below is a brief outline of some of the topics that AGI will be pursuing over the next year of the: 1) Oryza Repeat annotation will be more fully analyzed given the enhanced data sets. Using repeatExplorer, we have developed a more comprehensive custom repeat database of all Oryza genomes at both the nucleotidic and protein levels; we also included the outgroup Leersia. 2) Oryza Gene Index – Now that we have generated base-line transcriptome data, assemblies and annotations for 11 Oryza species and L. perrieri, we are planning to release a new database called the Oryza Gene Index (OGI). The OGI will serve as an invaluable tool for comparative analysis of transcriptome data covering 15 MY of evolutionary history. We are presently using the OGI to explore transcription factor evolution across the Oryza and we have already identified and mapped 81 conserved TF families thus far. 3) AGI is exploring gene family evolution within a phylogenetics context. These analyses make use of variations in gene family size, gene amplifications, gene losses and purifying selections and will openly move to in-depth studies on these gene functions. This work will be expanded. 4) A comprehensive analysis of structural variation across the 11 genomes of Oryza and Leersia will be completed.

Impacts
What was accomplished under these goals? A1 Genome Framework Datasets for O. glumaepatula, O. meridionalis, Leersia perrieri (UA). Completed. A2 Vertical datasest: Chromosome 3 short arm sequences for: O. glumaepatula, O. meridionalis, O. granulata, Leersia perrieri. (UA). Completed. A3 Horizontal dataset: Whole genome sequence assemblies for: O. barthii and O. punctata. (UA). Completed. A4 Baseline transcriptome (mRNA and small RNA) datasests for 11 Orya and one out-group species. (UA). Completed. A5 Population re-sequence data sets for: O. barthii, O. glaberrima, O. sativa japonica, O. sativa indica, O. rufipogon, O. nivara, O. longistaminata, O. glumaepatula, O. meridionalis (UA). We completed the re-sequencing for O. barthii, O. glaberrima, O. sativa japonica, O. sativa indica, O. rufipogon, O. nivara, and O. meridionalis and *O. glumaepatula (*7 accessions only). Our collaborator, Bin Han, agreed to provide to us his population of re-sequencing data for a large set of O. rufipogon accessions. We have collected the tissues and isolated DNA from a large accession list of O. longistaminata and O. glumaepatula (see AGI supporting file); those population re-sequencing are scheduled to be completed by mid-summer. This objective will be completed by the end of the reporting period.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Peer reviewed publications during the 2012-2013 reporting period Thais RS Figueira, T.R.S., V. Okura, F.R. Silva, M.J. Silva, D. Kudrna, J.S.S. Ammiraju, J. Talag, R.A. Wing, and P. Arruda. A BAC library of the SP80-3280 sugarcane variety (Saccharum sp.) and its inferred microsynteny with the sorghum genome. 2012. BMC Research Notes 5:185.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Peer reviewed publications during the 2012-2013 reporting period Ortiz M, A. Legatzki, J.W. Neilson, B. Fryslie, W.M Nelson, R.A. Wing, C.A. Soderlund, B.M. Pryor, R.M. Maier. Making a living while starving in the dark metagenomic insights into the energy dynamics of a carbonate cave. 2013. Intl. Soc. Micro. Ecol. 1-14. Singh, R., M. Ong-Abdullah, E.T.L. Low, M.A.A. Manaf, R. Rosli, R. Nookiah, L.C.-L. Ooi, S.E. Ooi, K.L. Chan, M.A. Halim, N. Azizi, J. Nagappan, B. Bacher, N. Lakey, S.W. Smith, D. He, M. Hogan, M.A. Budiman, E.K. Lee, R. DeSalle, D. Kudrna, J.L. Goicoechea, R.A. Wing, R.K. Wilson, R.S. Fulton, J.M. Ordway, R.A. Martienssen, R. Sambanthamurthi. Oil plam genome sequence reveals divergence of interfertile species in old and new worlds. 2013. Nature 500:335-339. Matsuba, Y., T.T.H. Nguyene, K. Wiegertb, V. Falaraa, E. Gonzales-Vigilb, B. Leonga, D. Kundra, W. Golserc, R.A. Wing, A. Bolgerd, B. Usadeld, A.R. Fernied , C.S. Barryb, E. Picherskya. Evolution of a complex locus for terpene biosynthesis in Solanum. 2013. Plant Cell 25:2022203. Zhang, C., J. Wang, N.C. Marowsky, M. Long, R.A. Wing, and C. Fan. High occurrence of functional new chimeric genes in a survey of rice chromosome 3 short arm genome sequences. 2013. Genome Biol. & Evo. 5:1038-1048.. Jacquemin, J., D. Bhatia, K. Singh, and R.A. Wing. The International - Oryza Map Alignment Project: Development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. 2013. Curr. Op. Plant Biol. 16:147-156. Koo, H.J., E.T. McDowell, X. Ma, K.A. Greer, J. Kapteyn, Z. Xie, A. Descour, H. Kim, Y. Yu, D. Kudrna, R.A. Wing, C.A. Soderlund, D.R. Gang. Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. 2013. BMC Plant Biol. 13:27. Chen J, Q. Huang, D. Gao, J. Wang, Y. Lang, T. Liu, B. Li, Z. Bai, J.L. Goicoechea, C. Liang, C. Chen, W. Zhang, S. Sun, Y. Liao, X. Zhang, L. Yang, C. Song, M. Wang, J. Shi, G. Liu, J. Liu, H. Zhou, W. Zhou, Q. Yu, N. An, Y. Chen, Q. Cai, B. Wang, B. Liu, J. Min, Y. Huang, H. Wu, Z. Li, Y. Zhang, Y. Yin, W. Song, J. Jiang, S.A. Jackson, R.A. Wing, J. Wang, M. Chen. (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Commun 4: 1595 Maron, L.G., C.T. Guimar�es, M. Kirst, P.S. Albert, J.A. Birchler, P.J. Bradbury, E.S. Buckler, A.E. Coluccio, T.V. Danilova, D. Kudrna, J.V. Magalhaes, M.A. Pi�eros, M.C. Schatz, R.A. Wing, L.V. Kochian. Aluminum tolerance in maize is associated with higher MATE1 gene copy-number. 2013. PNAS 110:5241-5246. Yang, R., D.E. Jarvis, H. Chen, M.A. Beilstein, J. Grimwood, J. Jenkins, S. Shu, S. Prochnik, M. Xin, C. Ma, J. Schmutz, R.A. Wing, T. Mitchell-Olds, K.S. Schumaker, X. Wang. The Reference Genome of the Halophytic Plant Eutrema salsugineum. 2013. Frontiers in Plant Sci 4:46. Ortiz, M., J.W. Neilson, W.M. Nelson, A. Legatzki, A. Byrne, Y. Yu, R.A. Wing, C.A. Soderlund, B.M. Pryor, L.S. Pierson, R.M. Maier. Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ. 2013. Microbial Ecology 62:371-383. Yang, Lu, T. Liu, B Li, Y. Sui, J. Chen, J. Shi, R.A. Wing, M. Chen. Comparative Sequence Analysis of the Ghd7 Orthologous Regions Revealed Movement of Ghd7 in the Grass Genomes. 2012. PLoS ONE 7: e50236. doi:10.1371/journal.pone.0050236 The International Barley Genome Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. 2012. Nature doi:10.1038/nature11543.