NATIONAL ANIMAL GENOME RESEARCH PROGRAM

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 0219958
• Multistate No.: NRSP-_OLD8
• Project Start Date: Jul 1, 2009
• Project End Date: Sep 30, 2013
• Program Code: [(N/A)]- (N/A)

Recipient Organization
MISSISSIPPI STATE UNIV
(N/A)
MISSISSIPPI STATE,MS 39762

Performing Department
Biochemistry & Molecular Biology

Non Technical Summary
Transposable elements (TEs) are common components of eukaryotic genomes. We work to identify, characterize and utilize TEs in a variety of model and non-model organisms. As part of our work, we examine the genomes of representative crocodilians to identify the impact of TEs on genome evolution, structure and function. Because crocodilians are one of the major vertebrate groups a basic grasp of the structure and function of their genomes is essential. This is especially true given that these animals represent are the closest living relatives of birds - another major group and a significant source of agricultural products (chickens, ducks, turkeys, etc.). To facilitate comparative genomics and test a hypotheses within Crocodylia and between crocodilians and other vertebrate groups we will: 1) provide fundamental information about genome organization and gene synteny in three crocodilian species and, 2) provide information about crocodilian genome diversity and evolution through detailed analysis of TEs. The proposed research will complement and enhance international efforts to understand crocodilians as keystone predators, model organisms, and agricultural products by generating key genomic data and by providing key molecular resources to the vertebrate genome community. It will also provide tools that will advance understanding of the genome dynamics that serve to differentiate archosaurs (crocodilians and birds) from other vertebrates. In other research we study similar aspects of mammalian genomes. Chiropterans represent a unique order within Mammalia. However, one bat genus in particular, Myotis (Vespertilionidae), has demonstrated itself to be extraordinary even among bats. It has been the subject of intense study due to unprecedented observations of multiple recent Class II transposable element (DNA transposon) expansions. Given that no other such expansions are evident in other mammals for the past 40 million years; these bats represent a unique opportunity to study the impact of Class II elements on mammalian genomes. Conversely, they also represent a system through which to examine the influence of genome/organism characteristics on the success of TEs. In the course of the project, we will experimentally determine the taxonomic limits of DNA transposon invasion/expansion in bats, investigate patterns of activity as they relate to species diversity within the family, and perform preliminary analyses of potential TE interactions within these genomes. The research will complement and enhance international efforts to understand the impact of TEs as factors in mammalian genome evolution and diversification and to provide additional TE-derived tools for genetic manipulation in mammalian model systems. These TE-derived tools discovered in both projects will serve as novel mechanisms for the genetic manipulation of agricultural products including mammals (cattle, sheep, etc.) and poultry.

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
304	0830	1040	100%

Knowledge Area
304 - Animal Genome;

Subject Of Investigation
0830 - Wild animals;

Field Of Science
1040 - Molecular biology;

Keywords

genomics

transposable element

mammals

birds

Goals / Objectives
Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest.

Project Methods
We will 1) generate a 5X BAC library for Gavialis gangeticus to complement the existing BAC libraries for Crocodylus porosus and Alligator mississippiensis; 2) use 454 sequencing to sequence eleven targeted gene-rich regions from each library; 3) perform analyses of these regions with birds, reptiles and mammals; 4) create annotated interactive databases based on GBrowse and GO annotation; 5) create HRCot libraries for three representative taxa; 6) sequence (to 10X coverage) the HRCot libraries and; 7) characterize the TE portion of the crocodilian genomes and determine the evolutionary contributions of TEs to crocodilian genome evolution. We will determine aspects of gene synteny, genome structure, rates of molecular evolution and the specific TE contribution to representatives of all extant families of Crocodylia. Through these efforts will build critical resources and knowledge required to facilitate meaningful hypothesis driven studies about amniote genome structure and evolution. While a number of broad impacts are anticipated to come from this work, some specific outcomes of significance to the scientific community are as follows: 1) Genomic resources for crocodilian researchers will be developed to address current questions in crocodilian biology and genomics; and 2) We will achieve an increased understanding of the place of crocodilians in vertebrate evolution and contribute resources critical for addressing questions about other amniotes. We will also utilize a combination of traditional and next-generation sequencing techniques (454 pyrosequencing) to address hypotheses related to the distribution and impact of TEs in vespertilionid bats. We will follow the protocol developed by Macas et al. (2007) in their examination of repetitive DNA in the pea genome. Recent research has suggested that Class II elements may be extremely useful tools for the introduction/modification of genes in mammalian cells. Human and model organism applications are innumerable, but we also consider agricultural applications in the form of transgenic cows, sheep, goats, etc. A limiting factor in developing Class II elements as tools for genetic manipulation has been a lack of information on the behavior and impact of these elements in mammalian systems. Class II activity in Vespertilionidae represents a natural experiment through which we can identify the impacts of Class II TEs on mammalian genomes. These bats also represent a repository of native mammalian DNA transposons that must be investigated by biochemists interested in mammalian cell line transformation. The particular elements to be characterized have demonstrated their ability to succeed in mammalian cells and could therefore be more efficient than the TE-based vectors currently available, which are derived from fish, frogs and insects. Furthermore, as part of this project and in future research, we will identify additional factors impacting the success and/or suppression of TEs in mammalian genomes (e.g., endogenous microRNAs, invasion mechanisms, TE interactions, etc.) and thereby inform scientists hoping to use these tools for gene therapy and the production of transgenic mammals.

Progress 07/01/09 to 09/30/13

Outputs
Target Audience: Transposable elements (TEs) are common components of eukaryotic genomes. We work to identify, characterize and utilize TEs in a variety of model and non-model organisms. We also work to identify mechanisms used to control them. As part of our work, we examine the genomes of representative crocodilians to identify the impact of TEs on genome evolution, structure and function. Because crocodilians are one of the major vertebrate groups a basic grasp of the structure and function of their genomes is essential. This is especially true given that these animals represent are the closest living relatives of birds - another major group and a significant source of agricultural products (chickens, ducks, turkeys, etc.). To facilitate comparative genomics and test a hypotheses within Crocodylia and between crocodilians and other vertebrate groups we will: 1) provide fundamental information about genome organization and gene synteny in three crocodilian species and, 2) provide information about crocodilian genome diversity and evolution through detailed analysis of TEs. The proposed research will complement and enhance international efforts to understand crocodilians as keystone predators, model organisms, and agricultural products by generating key genomic data and by providing key molecular resources to the vertebrate genome community. It will also provide tools that will advance understanding of the genome dynamics that serve to differentiate archosaurs (crocodilians and birds) from other vertebrates. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? I served as major advisor to three PhD students at MSU during 2012-2013. Each is conducting research into the nature and application of transposable elements in either bats, crocodilians and insects. Finally, I mentored a postdoctoral researcher, Meganathan Ramakodi, during 2012. His efforts were focused on mitogenomics of crocodilians, bats, and insects. How have the results been disseminated to communities of interest? Members of the laboratory attended and presented at the following meetings and/or conferences: Ray, DA. Transposable Element Analyses in Non-Model Animals. Mobile DNA in Mammalian Genomes, Big Sky MT, June 2013. Invited Presentation. Ray, DA. Genome Analyses in Non-Traditional Model Animals. Texas Tech University, Lubbock, TX, April 2013. Invited Presentation. Ray, DA. Genomic Analyses in Non-Traditional Model Animals. Rutgers University, Piscataway, NJ, March 2013. Invited Presenation. Platt, RN, MW Vandewege, C Kern, CJ Schmidt, FG Hoffmann, DA Ray. Large number of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Mobile DNA in Mammalian genomes, Big Sky MT, June 2013. Oral Presentation. Vandewege, MW, RN Platt, DA Ray, FG Hoffmann. piRNA isolation and characterization from horse and dog. Mississippi EPSCoR 2012, University of Mississippi, Oxford, MS, April 2012. Poster Presentation. What do you plan to do during the next reporting period to accomplish the goals? I have left Mississippi State University for a new position and will no longer be reporting.

Impacts
What was accomplished under these goals? The International Crocodilian Genomes Working Group (ICGWG) continues to be a force in the genomics community. The group itself has swelled to over 60 members and our genome drafts are being accessed and utilized by dozens of laboratories. The Heliconius work had led us to devlop a project more broadly targeted among insects to investifate TE evolution. Our bat research has expanded into the world of small RNA regulation of genes and transposable elements, with two manuscript either in preparation or under review.

Publications

• Type: Journal Articles Status: Published Year Published: 2013 Citation: Ge, R-L, Q Cai, Y-Y Shen, A San, L Ma, Y Zhang, X Yi, Y Chen, L Yang, R He, Y Hui, M Hao, Y Li, B Wang, X Ou, Y Zhang, K Wu, C Geng, W Zhoa, Y Zhou, DM Irwin, Y Yang, L Ying, L Ying, H Bao, J Kim, DM Larkin, J Ma, HA Lewin, J Xing, RN Platt, DA Ray, L Auvil, B Capitanu, X Zhang, RW Murphy, J Wang, Y-P Zhang, and J Wang (2013) Draft genome sequence of the Tibetan antelope, Nature Communications 4:1858.
• Type: Journal Articles Status: Published Year Published: 2013 Citation: Supple, M, H Hines, C Lavoie, DA Ray, D Nielson, D Dasmahapatra, WO McMillan and B Counterman (2013) Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Research 2013 23:1248-1257.
• Type: Journal Articles Status: Published Year Published: 2013 Citation: Lavoie, CA, RN Platt, PA Novick, BA Counterman and DA Ray (2013) Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera. Mobile DNA 2013 4:21.
• Type: Journal Articles Status: Published Year Published: 2013 Citation: Castoe, TA< APJ de Koning, KT Hall, DC Card, DR Schield, MK Fujita, RP Ruggiero, JF Degner, JM Daza, W Gu, J Reyes-Velasco, KJ Shaney, JM Castoe, SE Fox, AW Poole, D Polanco, J Dobry, MW Vandewege, Q Li, R Schott, A Kapusta, P Minx, C Feschotte, P Uetz, DA Ray, FG Hoffman, R Bogden, EN Smith, BSW Chang, F Vonk, NR Casewell, CV Henkel, MK Richardson, SP Mackessy, AM Bronikowski, M Yandell, WC Warren, SM Secor, and DD Pollock (2013) The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Science, USA.
• Type: Journal Articles Status: Submitted Year Published: 2013 Citation: Platt, RN, MW Vandewege, C Kern, CJ Schmidt, FG Hoffmann, DA RAy (Under revision) Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Molecular Biology and Evolution.
• Type: Theses/Dissertations Status: Other Year Published: 2011 Citation: A STUDY OF MOBILE DNA CONTENT AND ACTIVITY IN NON-MODEL MAMMALIAN ORGANISMS
• Type: Journal Articles Status: Published Year Published: 2009 Citation: Ray, DA, RN Platt and MA Batzer (2009) Reading between the LINEs to see into the past. Trends in Genetics 25(11):475-479.
• Type: Journal Articles Status: Published Year Published: 2010 Citation: Novick, P, JD Smith, DA Ray and S Boissinot (2010) Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene 449:85-94
• Type: Book Chapters Status: Published Year Published: 2010 Citation: Ray, DA, K Han, JA Walker and MA Batzer (2010) Laboratory methods for the analysis of primate mobile elements. Pp 153-179 in "Genetic Variation: Methods and Protocols (Methods in Molecular Biology)", MR Barnes and G Breen (Eds.), Humana Press Inc., Totowa, NJ.
• Type: Journal Articles Status: Published Year Published: 2010 Citation: Pegan, HJT, JD Smith, RM Hubley and DA Ray (2010) PiggyBac-ing on primate genome: Novel elements, recent activity and horizontal transfer. Genome Biology and Evolution 2:293-303
• Type: Journal Articles Status: Published Year Published: 2010 Citation: Meganathan, PR, B Dubey, MA Batzer, DA Ray and I Haque (2010) Molecular phylogenetic analyses of Genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus. Molecular Phylogenetics and Evolution 57:393-402.
• Type: Journal Articles Status: Published Year Published: 2011 Citation: Novick, P, JD Smith, M Floumanhaft, DA Ray and S Boissinot (2011) The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. Genome Biology and Evolution 3:1-14
• Type: Journal Articles Status: Published Year Published: 2011 Citation: Alfoldi, J, F Di Palma, M Grabherr, C Williams, L Kong, E Mauceli, P Russell, CB Lowe, R Glor, JD Jaffe, DA Ray, S Boissinot, AM Shedlock, C Botka, TA Castoe, JK Colbourne, MK Fujita, RG Moreno, BF ten Hallers, D Haussler, A Heger, D Heiman, DE Janes, J Johnson, PJ de Jong, MY Koriabine, P Novick, CL Organ, SE Peach, S Poe, DD Pollock, K de Queiroz, T Sanger, S Searle, JD Smith, Z Smith, R Swofford, J Turner-Maier, J Wade, S Young, A Zadissa, Genome Sequencing Platform and Whole Genome Assembly Team, SV Edwards, TC Gleen, CJ Schneider, JB Losos, ES Lander, M Breen, CP Ponting, and K Lindblad-Toh (2011) The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals. Nature 477:587-591.
• Type: Journal Articles Status: Published Year Published: 2011 Citation: Smith, JD and DA Ray (2011) Expedited batch processing and analysis of transposon insertions. BMC Research Notes 4:482.
• Type: Journal Articles Status: Published Year Published: 2012 Citation: Meganathan, PR, HJT Pagan, ES McColloch, RD Stevens and DA Ray (2012) Complete mitochondiral genome sequences of three bat species and whole genome mitochonrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera. Gene 492:121-129.
• Type: Journal Articles Status: Published Year Published: 2012 Citation: Chouvarine, P, AM Cooksey, FM McCarthy, DA Ray, BB Baldwin, SC Burgess, and DG Peterson (2012) Transcriptome-based differentiation of closely-related Miscanthus lines. PLoS ONE 7 (1): e29850.
• Type: Journal Articles Status: Published Year Published: 2011 Citation: Ray, DA and MA Batzer (2011) Reading TE leaves: New approaches to the identification of transposable element insertions. Genome Research 21:813-820.
• Type: Journal Articles Status: Published Year Published: 2011 Citation: Thomas, J, M Sorourian, D Ray, RJ Baker and EJ Pritham (2011) The limited distribution of Helitrons to vesper bats supports horizontal transfer. Gene 474:52-58.
• Type: Journal Articles Status: Published Year Published: 2011 Citation: Meganathan, PR, B Dubey, MA Batzer, DA Ray and I Haque (2011) Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the order Crocodylia. gene 478:35-41.
• Type: Journal Articles Status: Published Year Published: 2011 Citation: Castoe, TA, APJ de Koning, KT Hall, KD Yokoyama, W Gu, EN Smith, C Feschotte, P Uetz, DA Ray, J Dobry, R Bogden, SP Mackessy, AM Bronikowski, WC Warren, SM Secor and DD Pollock (2011) Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biology 12:406
• Type: Journal Articles Status: Published Year Published: 2012 Citation: Stevens, RD, MM Gavilanez, JS Tello and DA Ray (2012) Phylogenetic structure illuminates mechanistic role of environmental heterogeneity on community organization. Journal of Animal Ecology 81(2) 455-462.
• Type: Journal Articles Status: Published Year Published: 2012 Citation: St. John, JA, EL Braun, SR Isberg, LG Miles, AY Chong, J Gongora, P Dalzell, B Bed'Horn, A Abzhanov, SC Burgess, AM Cooksey, TA Castoe, NG Crawford, LD Densmore, JC Drew, SV Edwards, BC Faircloth, MK Fujita, MJ Greenwold, FG Hoffmann, JM Howard, T Iguchi, DE Janes, SY Khan, K Kohno, APJ de Koning, SL Lance, FM McCarthy, JE McCormack, ME Merchant, DG Peterson, DD Pollock, N Pourmand, BJ Raney, KA Roessler, JR Sanford, RH Sawyer, CJ Schmidt, EW Triplett, TD Tuberville, M Venegas-Anaya, JT Howard, ED Jarvis, LG Guillette, TC Glenn, RE Green, DA Ray (2012) Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology 13:415.
• Type: Journal Articles Status: Published Year Published: 2012 Citation: Pagan, HJT, J Macas, P Novak, ES McColloch, RD Stevens, and DA Ray (2012) Survery sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among bats. Genome Biology and Evolution 4(4):575-585.
• Type: Journal Articles Status: Published Year Published: 2012 Citation: Platt, RN and DA Ray (2012) A non-LTR retroelement extinction in Spermophilus tridecemlinetus. Gene 500:47-53.
• Type: Journal Articles Status: Published Year Published: 2012 Citation: The Heliconius Genome Consortium (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487:94-98.

Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: Activities: Experiments: We continued work to sequence three crocodilian genomes for publication in 2013. By the end of 2012, we had assembled all three genomes (Alligator mississippiensis, Crocodylus porosus, and Gavialis gangeticus) and preliminary annotations were available for all three. A website was developed for dissemination of the data and results to the public (www.crocgenomes.org). We continued our collaboration with researchers at the University of Utah (and one collaborator has moved to Rutgers) to continue our work in developing a novel method of inferring phylogenies using transposable elements. Toward that goal, we have collected data for one third of the target taxa and are continuing to collect data for the remaining organisms. Seven manuscripts from our laboratory were published during 2012. Teaching: I taught two classroom courses at MSU during 2012 - Molecular Biology (BCH 4713/6713) and Graduate Seminar (BCH 8101). Mentoring: I served as major advisor to three PhD students at MSU during 2012. Each is conducting research into the nature and application of transposable elements in either bats, crocodilians and insects. I also served as a research mentor to one undergraduate. Kacy Mobley (MUW)joined our laboratory for ten weeks as part of the NSF funded summer REU program. She performed research related to transposable element biology in crocodilians and presented her research at a poster session hosted by the Honors College in July. Finally, I mentored a postdoctoral researcher, Meganathan Ramakodi, during 2012. His efforts were focused on mitogenomics of crocodilians, bats, and insects. Events: Members of the laboratory attended and presented at the following meetings and/or conferences: Genomic Impact of Eukaryotic Transposable Elements (1), February 2012; MCBIOS (3), February 2012; EPSCoR (1); Undergraduate Research Symposium (1), July 2012; 4th International Workshop on Crocodylian Genetics and Genomics (2), May 2012; 63rd Fujihara Seminar, August 2012. Products: The laboratory continues to maintain a website to disseminate our work. http://crocoduck.bch.msstate.edu/ as well as information related to crocodilian genomics. www.crocgenomes.org. PARTICIPANTS: Graduate Students Supported: Roy Platt (PhD student), Jeremy Smith (PhD student), Christine Lavoie (PhD student) Undergraduate Students Supported: Kacy Mobley (Mississippi University for Women) Partner Organizations and Collaborators: Jaime Gongora, Chris Moran, Sally Isberg - University of Sydney, R. E. Green - University of California at Santa Cruz, Erich Jarvis - Duke University, Travis Glenn - University of Georgia, Toni Gabaldon - Centre de Regulacio Genomica, Lynn Jorde, David Witherspoon - University of Utah, Jinchuan Xing - Rutgers University, Jiri Macas - Biology Centre of the Academy of Sciences of the Czech Republic, Richard Stevens - Louisiana State University, Fiona McCarthy, Eric Lyons - University of Arizona. TARGET AUDIENCES: Our target audience is broad and ranges from early childhood to the academy. We have given educational presentations about our work with bats to elementary school students and lectures on molecular biology techniques to high school students. Finally, research presentations have been given a multiple conferences and meetings internationally. PROJECT MODIFICATIONS: We have now added insect genomes to our list of model taxa. These organisms include agricultural pests and organisms of interest to human health. Their genomes are small and readily amenable to the analyses we typically perform and they represent excellent models for transposable element evolution.

Impacts
The International Crocodilian Genomes Working Group (ICGWG) continues to be a force in the genomics community. The group itself has swelled to over 60 members and our genome drafts are being accessed and utilized by dozens of laboratories. Our examination of the Heliconius genome has resulted in one manuscript that was published in Nature and a second manuscript is in preparation. The Heliconius work has led us to develop a project more broadly targeted among insects to investigate TE evolution.

Publications

• The Heliconius Genome Consortium (2012) Genomic evidence for promiscuous exchange of adaptations among Heliconius butterfly species. Nature 487:94-98.
• Platt, RN and DA Ray (2012) A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 500:47-53.
• Pagan, HJT, J Macas, P Novak, ES McCulloch, RD Stevens, and DA Ray (2012) Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among bats. Genome Biology and Evolution 4(4):575-585.
• Stevens, RD, MM Gavilanez, JS Tello and DA Ray (2012) Phylogenetic structure illuminates mechanistic role of environmental heterogeneity on community organization. Journal of Animal Ecology 81(2) 455-462. St. John, JA, EL Braun, SR Isberg, LG Miles, AY Chong, J Gongora, P Dalzell, C Moran, B Bedhom, A Abzhanov, SC Burgess, AM Cooksey, TA Castoe, NG Crawford, LD Densmore, JC Drew, SV Edwards, BC Faircloth, MK Fujita, MJ Greenwold, FG Hoffmann, JM Howard, T Iguchi, DE Janes, SY Khan, S Kohno, AJ de Koning, SL Lance, FM McCarthy, JE McCormack, ME Merchant, DG Peterson, DD Pollock, N Pourmand, BJ Raney, KA Roessler, JR Sanford, RH Sawyer, CJ Schmidt, EW Triplett, TD Tuberville, M Venegas-Anaya, JT Howard, ED Jarvis, LJ-Jr Guillette, TC Glenn, RE Green, DA Ray (2012) Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology 13:415.
• Chouvarine, P, AM Cooksey, FM McCarthy, DA Ray, BB Baldwin, SC Burgess, and DG Peterson (2012) Transcriptome-based differentiation of closely-related Miscanthus lines. PLoS ONE 7(1): e29850.
• Meganathan, PR, HJT Pagan, ES McCulloch, RD Stevens and DA Ray (2012) Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera. Gene 492:121-129.

Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: Activities: Experiments: We continued work to sequence three crocodilian genomes for publication in 2013. By the end of 2011, we had collected all data for assembly of the three genomes (Alligator mississippiensis, Crocodylus porosus, and Gavialis gangeticus) and preliminary assemblies were available for the first two. A website was developed for dissemination of the data and results to the public. As part of the efforts associated with this project, we received NSF funding to sequence and assemble the G. gangeticus genome. We entered a collaboration with researchers at the University of Utah to continue our work in developing a novel method of inferring phylogenies using transposable elements. Toward that goal, we began constructing Illumina sequencing libraries using novel TE-based techniques. Teaching: I taught two classroom courses at MSU during 2011 - Molecular Biology (BCH 4713/6713) and Senior Seminar (BCH 3901/8101). Mentoring: I served as major advisor to four PhD students at MSU. Three students, Heidi Pagan, Jeremy Smith, and Roy Platt began their studies at West Virginia University and transferred when I accepted my position in the Department of Biochemistry and Molecular Biology at MSU. The fourth, Christine Lavoie joined the laboratory in early 2011. Each is conducting research into the nature and application of transposable elements in either bats or crocodilians. I also served as a research mentor to two undergraduates. The first of these, Jungyeon Kim, is acting as a student worker in the laboratory. She is funded by a Strategic Research Initiative grant funded by MAFES. Miss Kim presented her research as part of the Undergraduate Research Symposium at MSU on April 22, 2010 (see section B1h for the title). In addition, Jordan Hawkins (MUW)joined our laboratory for ten weeks as part of the NSF funded summer REU program. Sheperformed research related to transposable element biology in bats and presented her research at a poster session hosted by the Honors College in July. Events: Members of the laboratory attended and presented at the following meetings and/or conferences: Mobile DNA in Mammalian Genomes, August 2011; Evolution, June 2011, Plant and Animal Genomes IXX, January 2011. Products: The laboratory continues to maintain a website to disseminate our work. http://crocoduck.bch.msstate.edu/. A second website was established related to crocodilian genomics. www.crocgenomes.org. PARTICIPANTS: Individuals: David Ray (PI), Meganathan Ramakodi (postdoctoral researcher), Roy Platt (graduate student), Heidi Pagan (graduate student), Jeremy Smith (graduate student), Christine Lavoie (graduate student). Partner Institutions and collaborators: Jaime Gongora (University of Sydney), Chris Moran (University of Sydney), Travis Glenn (University of Georgia), Ed Green (University of California, Santa Cruz), Llewellyn Densmore (Texas Tech University), Robert Bradley (Texas Tech University), Ellen Pritham (University of Texas), Ed Braun (University of Florida), Daniel Peterson (Mississippi State University), Brian Counterman (Mississippi State University, Federico Hoffmann (Mississippi State University), Jordan Hawkins (Mississippi University for Women) TARGET AUDIENCES: Efforts were made to disseminate information to several Target Audiences. Teaching and lectures were delivered at Mississippi State University, and at several regional, national and international meetings. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
The International Crocodilians Genome Working Group (ICGWG) continues to be a force in the genomics community. We held our first meeting at Mississippi State University in August 2011 and 20 members attended. The group itself has swelled to over 40 members. Amanda Chong, a graduate student from the University of Sydney visited the laboratory for six months to participate in the project. Our examination of the Heliconius genome has resulted in one manuscript that has been submitted and accepted at Nature. to the Heliconius Genome Consortium and the TE library produced is informing the assembly process for that genome. Our efforts to catalog the TEs in the Anolis carolinensis genome have resulted in one publication at Nature.

Publications

• Smith, JD and DA Ray (2011) Expedited batch processing and analysis of transposon insertions. BMC Research Notes 4:482
• Alfoldi, J + 46 co-authors (2011) The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals. Nature 477:587-591
• Castoe, TA, APJ de Koning, KT Hall, KD Yokoyama, W Gu, EN Smith, C Feschotte, P Uetz, DA Ray, J Dobry, R Bogden, SP Mackessy, AM Bronikowski, WC Warren, SM Secor, and DD Pollock (2011) Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biology 12:406.
• Meganathan, PR, B Dubey, MA Batzer, DA Ray and I Haque (2011) Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia. Gene 478:35-41.
• Thomas, J, M Sorourian, D Ray, RJ Baker and EJ Pritham (2011) The limited distribution of Helitrons to vesper bats supports horizontal transfer. Gene 474:52-58.
• Ray, DA and MA Batzer (2011) Reading TE leaves: New approaches to the identification of transposable element insertions. Genome Research 21:813-820.
• Novick, P, JD Smith, M Floumanhaft, DA Ray and S Boissinot (2011) The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. Genome Biology and Evolution 3:1-14.

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: Activities: Experiments: We began work to sequence three crocodilian genomes for publication in 2012. Thus far, we have collected nearly 200 Gb of data for Crocodylus porosus and nearly the same amount for Alligator mississippiensis. In working toward these goals, we have created a BAC library for a third organism to be sequenced, Gavialis gangeticus. We received funding to develop a novel method of inferring phylogenies using transposable elements. Toward that goal, we have begun constructing Illumina sequencing libraries using novel TE-based techniques. Teaching: I taught one classroom course at MSU during 2010, Molecular Biology (BCH 4713/6713). I also served as Directed Independent Study advisor to one graduate student during the Fall of 2010. Christine Lavoie performed research into the genetics of forensically and agriculturally important flies. She has since joined the laboratory as an M.S. student (January 1, 2011). Mentoring: I served as major advisor to three PhD students at MSU. All three students, Heidi Pagan, Jeremy Smith, and Roy Platt began their studies at West Virginia University and transferred when I accepted my position in the Department of Biochemistry and Molecular Biology at MSU. Each is conducting research into the nature and application of transposable elements in either bats or crocodilians. I also served as a research mentor to three undergraduates. The first of these, Jungyeon Kim, is acting as a student worker in the laboratory. She is funded by a Strategic Research Initiative grant funded by MAFES. Miss Kim presented her research as part of the Undergraduate Research Symposium at MSU on April 22, 2010 (see section B1h for the title). In addition, Tiffany Cromity (MUW) and Janice Okeke (Millsaps College) joined our laboratory for ten weeks as part of the NSF funded summer REU program. Both performed research related to transposable element biology in bats and fish. Both students presented their research at a poster session hosted by the Honors College on July 29th, 2010 (see section B1h for the titles). I served as a member of the graduate committees of the 13 students. Events: The laboratory attended and presented at the following meetings and/or conferences: Biology of Genomes, Cold Spring Harbor, NY, May 2010. MidSouth Computational Biology and Bioinformatics Society (MCBIOS), Arkansas State University, Jonesboro, AR, February 2010. NSF REU poster presentation, Mississippi State, MS July, 2010. Heliconius Genome Consortium, University of Cambridge, Cambridge, UK, March, 2010. Undergraduate Research Symposium, Mississippi State, MS, April, 2010. Digital Biology Learning Community Seminar, Mississippi State, MS, April 2010. Individual invited presentations were made at: Michigan State University, East Lansing, MI, October 2010. Invited Presentation. University of South Carolina, Columbia, SC, March 2010. Invited Presentation. Products: The laboratory continues to maintain a website to disseminate our work. http://crocoduck.bch.msstate.edu/ PARTICIPANTS: Individuals: David Ray (PI), Meganathan Ramakodi (postdoctoral researcher), Roy Platt (graduate student), Heidi Pagan (graduate student), Jeremy Smith (graduate student), Christine Lavoie (graduate student). Partner Institutions and collaborators: Jaime Gongora (University of Sydney), Chris Moran (University of Sydney), Travis Glenn (University of Georgia), Ed Green (University of California, Santa Cruz), Llewellyn Densmore (Texas Tech University), Robert Bradley (Texas Tech University), Ellen Pritham (University of Texas), Ed Braun (University of Florida), Daniel Peterson (Mississippi State University), Brian Counterman (Mississippi State University, Federico Hoffmann (Mississippi State University), Tiffany Cromity (Mississippi University for Women), Janice Okeke (Millsaps College). TARGET AUDIENCES: Efforts were made to disseminate information to several Target Audiences. Teaching and lectures were delivered at Mississippi State University, Michigan State University, University of South Carolina. Teaching efforts were targeted at the African American community. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Our work on the Crocodylus porosus genome has resulted in the formation of the Crocodilian Genome Working group. The stated goals of this group are to generate draft genome sequences for three crocodilians by the end of 2012. Twenty researchers representing universities and farms in the US and Australia are active members of the group. One outcome of the formation of this group has been an NSF proposal to sequence the third of the three genomes proposed. These efforts have also resulted in a collaboration with the University of Sydney. A graduate student from that institution is visiting our laboratory during Spring 2011 to participate. Our examination of the Heliconius genome has resulted in one presentation to the Heliconius Genome Consortium and the TE library produced is informing the assembly process for that genome. Our efforts to catalog the TEs in the Anolis carolinensis genome have resulted in two publications and will be presented as part of the upcoming Anolis genome paper to be submitted to Nature in April, 2011.

Publications

• Novick, P., J. D. Smith, D.A. Ray, S. Boissinot (2010) Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene 449:85-94.
• Pagan, H.J.T., J.D. Smith, R.M. Hubley, and D.A. Ray. (2010) PiggyBac-ing on a primate genome: Novel elements, recent activity and horizontal transfer. Genome Biology and Evolution 2:293-303.
• Meganathan, P.R., B. Dubey, M.A. Batzer, D.A. Ray, and I. Haque (2010) Molecular phylogenetic analyses of Genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus. Molecular Phylogenetics and Evolution 57:393-402.
• Novick, P., J.D. Smith, M. Floumanhaft, D.A. Ray, and S. Boissinot (2011) The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. Genome Biology and Evolution 3:1-14.
• Thomas, J., M. Sorourian, D. Ray, R.J. Baker, and E.J. Pritham (2011) Distribution of Helitrons in different species of bats. Gene 474:52-58

Progress 09/01/09 to 12/31/09

Outputs
OUTPUTS: As part of our efforts, the laboratory created and updated a website detailing all research in which we are participating. We have continued collaborations with the Broad Institute, the Life Sciences and Biotechnology Institute to further our efforts at genome analysis from a transposable element perspective. We have expanded our collaborations with individual researchers including Stephane Boissinot at Queens College, Lou Densmore at Texas Tech University, Travis Glenn at the University of Georgia and Daniel Peterson at Mississippi State University. As part of these efforts, we are generating a proposal to develop the first complete genome sequence for a crocodilian. PARTICIPANTS: David A Ray - PI Heidi JT Pagan - Graduate student at Mississippi State University Roy N Platt - Graduate student at Mississippi State University Jeremy D Smith - Graduate student at Mississippi State University Stephane Boissinot - Collaborator at Queens College Peter Novick - Graduate student at Queens College Travis Glenn - Collaborator/Genomics facility director at University of Georgia Daniel G Peterson - Co-PI Mississippi State University Shane Burgess - Collaborator and Director of the Life Sciences and Biotechnology Institute at Mississippi State University Richard D Stevens - Co-PI Louisiana State University Llewellyn D Densmore - Collaborator at Texas Tech University TARGET AUDIENCES: Classroom instruction in the form of Molecular Biology lectures at Mississippi State University. Laboratory training of graduate and undergraduate students at Mississippi State University. PROJECT MODIFICATIONS: There was a short delay in beginning work on our study of crocodilian genomics as we awaited transfer of NSF funds from WVU to MSU. The transfer was complete as of January 15, 2010. We are now awaiting fresh blood from Gavialis gangeticus to begin work. Three sources have assured us delivery of samples during March, 2010.

Impacts
We have revealed details about the horizontal transfer of transposable elements in bats and primates that has influenced our understanding of primate and bat evolution. We have increased our knowledge of transposable element evolution in rodents that will lead to a broader understanding of the impact of these elements in mammal genomes. We have developed knowledge in the area of fly genomics. In particular, we are focusing on flies of importance to forensics and agriculture. As a result of these studies, we have obtained funding to investigate transposable element activity in a number of additional flies. The picture of genome evolution continues to become more complex as a result of this and other discoveries.

Publications

• Novick, P., J. D. Smith, D.A. Ray, S. Boissinot (2010) Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. GENE 449:85-94.
• Ray, D.A., R.N. Platt, M.A. Batzer (2009) Reading between the LINEs to see into the past. Trends in Genetics 25(11):475-479.
• Thompson, M.L., A.E. Gauna, M.L. Williams, D.A. Ray (2009) Multiple chicken repeat 1 (CR1) lineages in the genomes of oestroid flies. GENE 448:40-45.