CHROMOSOME REARRANGEMENTS IN EVOLUTION OF MALARIA MOSQUITOES

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1012754
• Project Start Date: Jul 1, 2017
• Project End Date: Jun 30, 2022
• Program Code: [(N/A)]- (N/A)

Recipient Organization
VIRGINIA POLYTECHNIC INSTITUTE
(N/A)
BLACKSBURG,VA 24061

Performing Department
Entomology

Non Technical Summary
The major goal of this HATCH project is to develop chromosome-based high-quality genome assemblies for species that belong to different subgenera of Anopheles. We will use these assemblies to explore phylogenetic relationships and to determine the pattern and mechanisms of chromosome evolution in malaria mosquitoes. The project is timely and innovative because it will create genomic tools for the newly sequenced Anopheles species cluster using the multicolor fluorescent in situ hybridization and microscopic analysis. We will, for the first time, perform phylogenetic analysis of anopheline mosquitoes by genome-wide gene order analysis, and provide a theoretical framework for the development of innovative approaches for manipulating chromosomal rearrangements. Public welfare will be advanced to a new level because instead of using common insecticides from all mosquito species, it will become possible to design species-specific insecticides and other novel tools using genomic information. The availability of state-of-the-art equipment and the expertise of the PI in cytogenetics and comparative genomic analysis will ensure the successful achievement of the project's goal.

Animal Health Component

0%

Research Effort Categories

Basic

100%

Applied

0%

Developmental

0%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
721	7010	1080	100%

Knowledge Area
721 - Insects and Other Pests Affecting Humans;

Subject Of Investigation
7010 - Biological Cell Systems;

Field Of Science
1080 - Genetics;

Keywords

health

malaria

mosquitoes

genomes

Goals / Objectives
1. Importance to agricultural life of Virginia. Mosquitoes are a growing problem in Virginia at this time. Most of the time when Virginia citizens complain about being bitten by daytime biting mosquitoes, Asian tiger mosquitoes are to blame. The Asian tiger mosquito Aedes albopictus is an invasive species and is one of the most common and widespread mosquitoes in Virginia. It is also a potential vector of Zika virus and other arboviruses in Virginia. Other medically important Culicine mosquitoes in Virginia are Aedes triseriatus (the primary vector of La Crosse virus) and Culex pipiens (the major vector of the West Nile virus). The Centers for Disease Control and Prevention (CDC) also report about local transmission of Plasmodium vivax malaria in Virginia [2]. This case underscores the need to consider the possibility of malaria in patients with fever of unknown origin. Malaria vector An. quadrimaculatus is local to Virginia and is susceptible to Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae. Because of the opportunistic feeding behavior, wide distribution, and variety of transmitting pathogens, mosquitoes are significant pests of people and livestock. Moreover, mosquitoes are potential vectors for agents used in bioterrorist attacks. For example, the introduction of Rift Valley fever virus would have a devastating impact on the U.S. livestock industry both by direct loss from induced disease and from a loss of export market. We must be ready to meet the challenges within the state to address the concerns of the general public about these potential risks associated with dealing with mosquito-borne disease epidemics. Successful vector control is needed to reduce the threat to human health in rural and urban communities and to leverage the decrease of animal production in agriculture. Genomic information will help to control better this vector of infectious diseases. The Virginia vector An. quadrimaculatus is a close relative to An. atroparvus for which genomic information already exists [6]. Knowledge obtained in this research can be used for better understanding of genome rearrangements, which are crucial for mosquito rapid adaptation to environment. This work will be informative about genome rearrangements in Culicine mosquitoes such as Aedes albopictus and Culex pipiens, which do not have polytene chromosome and therefore are less suitable for such study. The proposed work fits well with the emphasis on infectious diseases research at Virginia Tech.2. What are the important gaps that this project will fill and why is it necessary to do this project now? Targeting genes responsible for vectorial capacity is a novel approach to controlling infectious diseases. Chromosomal inversions contribute to the increase of vectorial capacity in major malaria vectors such as An. gambiae and An. funestus [7-9]. Therefore genes responsible for high vectorial capacity must be located within historic and present genome rearrangements. If they are found, these genes can be targeted to reduce vector potential. However, the patterns and mechanisms of chromosomal evolution in mosquitoes are not well understood. The main reason for this gap is the lack of chromosome-based genome assemblies for the majority of malaria mosquitoes. To develop a better understanding of genetic determinants of vectorial capacity and with support from vector biologists and members of the malaria community, NHGRI and NIAID funded sequencing of the genomes and transcriptomes of 16 Anopheles species [6]. When these multiple genome sequences became available, researchers had the unique opportunity to perform comparative analysis for inferring rapid and gradual evolutionary changes relevant to vector ability. However, success of these comparative genomic analyses will be limited, and inferences about evolution of the vectorial capacity traits will be less informative if researchers deal with numerous sequencing contigs rather than with chromosome-based genome assemblies. Fragmented unmapped sequences create serious problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. A timely investment in producing reliable genome assemblies for major vectors will enable researchers to perform comprehensive comparative genomic analyses, to study chromosome evolution and will maximize investments in whole-genome resequencing of individual genomes from natural populations.3. How will public welfare and scientific knowledge be advanced? The major goal of this HATCH project is to develop chromosome-based high-quality genome assemblies for species that belong to different subgenera of Anopheles. We will use these assemblies to explore phylogenetic relationships and to determine the pattern and mechanisms of chromosome evolution in malaria mosquitoes. The project is timely and innovative because it will create genomic tools for the newly sequenced Anopheles species cluster using the multicolor fluorescent in situ hybridization and microscopic analysis. We will, for the first time, perform phylogenetic analysis of anopheline mosquitoes by genome-wide gene order analysis, and provide a theoretical framework for the development of innovative approaches for manipulating chromosomal rearrangements. Public welfare will be advanced to a new level because instead of using common insecticides from all mosquito species, it will become possible to design species-specific insecticides and other novel tools using genomic information. The availability of state-of-the-art equipment and the expertise of the PI in cytogenetics and comparative genomic analysis [3, 12-15] will ensure the successful achievement of the project's goal.The proposal has three objectives.Objective 1. Physically map sequencing contigs to chromosomes of An. albimanus, An. atroparvus, and An. funestus. We will place and orient contigs to polytene chromosomes by fluorescence in situ hybridization (FISH), thus, creating chromosome-based genome assemblies for the species belonging to the subgenera Anopheles and Cellia. We will use these maps and earlier developed physical maps for An. gambiae and An. stephensi from subgenus Cellia to achieve Objectives 2 and 3.Objective 2. Reconstruct genome-scale rearrangement phylogeny of genus Anopheles. We will test the monophyly of three Anopheles subgenera, determine sister-group relationships among subgenera and different series within Cellia, and identify the ancestral group in anopheline mosquitoes. The phylogenetic analyses of gene order will be done using powerful bioinformatic tools: the Multiple Genome Rearrangements (MGR) [16], Sorting Permutation by Reversals and block-INterchanGes (SPRING) [17], and Neighboring Gene Pair (NGP) [18] algorithms. Given the abundance and uniqueness of fixed inversions in the evolution of Anopheles [12, 15], this approach should produce a reliable phylogenetic framework for comparative genomics studies of vectorial capacity.Objective 3. Determine the pattern and mechanisms of chromosome evolution in genus Anopheles. Using paired-read sequences for the Anopheles species cluster and a combination of cytogenetic and bioinformatic approaches, we will test the hypotheses that (i) the X chromosome has the highest rate of inversion fixation despite the paucity of inversion polymorphisms, (ii) inversions have chromosome-specific and species-specific mechanisms of origin and rates of fixation, and (iii) polymorphic inversions in multiple species of Anopheles nonrandomly capture similar sets of genes.

Project Methods
We anticipate few difficulties with procedures as outlined in our experimental plan. We have considerable previous experience in Anopheles cytogenetics and genomics. Our preliminary studies indicate that polytene chromosome preparations are suitable for high-resolution physical mapping by FISH, which is the most cost-efficient way to obtain a highly finished, predominantly euchromatic genome assembly. The resulting assemblies may miss some parts of heterochromatic sequences. However, this will not be a problem for our analyses because inversions occur mainly in euchromatin. The rearrangement-based phylogeny reconstruction has been successfully conducted using physical maps of the Drosophila species cluster [18, 36]. Using our previous HATCH grant, we performed sequencing, physical chromosome mapping, and bioinformatic analysis of the breakpoint regions of chromosome 2 in ingroup (An. gambiae, An. merus) and outgroup species (An. stephensi, An. nili, An. moucheti, An. sinensis, Aedes aegypti, and Culex pipiens). We have demonstrated that the 2La, 2Ro, 2R+p, and 2R+b arrangements are ancestral indicating that the An. merus-An. gambiae clade is basal in the complex [33]. These data contradict previous views that assumed either An. quadriannulatus [7] or An. arabiensis [47] as the basal species in the An. gambiae complex. The phylogenetic analyses of gene orders will be done using powerful bioinformatic tools: the Multiple Genome Rearrangements (MGR) [16], Sorting Permutation by Reversals and block-INterchanGes (SPRING) [17], and Neighboring Gene Pair (NGP) [18] algorithms. The MGR program works with multiple genomes and implements an algorithm that seeks a tree that minimizes the sum of the rearrangements over all the edges of the tree [16]. The SPRING program computes both the breakpoint and rearrangement distances between any pair of two chromosomes using the Neighbor-Joining method [17]. The important assumptions of the NGP algorithm are that chromosomal inversions result in the disruption of two pairs of neighboring genes and that the likelihood of breakpoint reuse along disjoint lineages is low. Neighboring pairs of homologous genes showing the same pairwise orientation in a pair of species will be considered to have escaped rearrangements [18]. The genome of An. atroparvus will be used to root the phylogenetic tree for species of subgenus Cellia. When possible, we will use gene orders of outgroup species Ae. aegypti and Cx. pipiens for rooting the anopheline tree. Genomes of the malaria mosquitoes encountered in Virginia will also be used for a phylogenomic study in order to understand historic relationships among mosquito species. Our data will be compared with reconstructions obtained earlier. For example, the most recent analysis of complete sequences of the mitochondrial genomes (mtDNA) indicated that subgenus Cellia and subgenus Anopheles are sister taxa that split about 58 MYA [1]. Breakpoint reuse and multiple origin of the same inversion could theoretically confound identification of ancestral arrangements. Although breakpoint reuses occur in evolution, there is no clear evidence for multiple origins of the same inversion [41, 46]. Our multispecies approach will identify instances of breakpoint reuse, and we will take them into consideration. Phylogenies based on inversion data are usually highly congruent with phylogenies based on DNA sequence data and are shown to be more information rich than are nucleotide data [34]. The analysis of genes inside polymorphic inversions will be limited to chromosome arms 2R, 2L, and 3L of An. gambiae and homologous arms in An. funestus and An. stephensi. Also, this analysis will be more relevant to inversions associated with phenotypic variations rather than to neutral rearrangements.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:My target audience included students, faculty, other scientists, stakeholders, and the public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Students have been provided with training opportunities in conducting experiments and writing manuscripts for publication. They had theopportunity to present their work at the international virtual meeting:the Allied Genetics Conference, April 22-25,2020. How have the results been disseminated to communities of interest?I disseminated my work to communities of interest byparticipating inCold Spring Harbor Laboratory meetingGENOME ORGANIZATION & NUCLEAR FUNCTION,April 28 - May 1, 2020; 13th Annual Arthropod Genomics Symposium:July 21-23 2020;American Society of Tropical Medicine and Hygiene meeting, November 15-19, 2020. My outreach activities for the publicwere: Virginia Tech Science Festival on November 16, 2019. What do you plan to do during the next reporting period to accomplish the goals?Anopheles coluzziiandAn. arabiensisbelong to theAn. gambiaecomplex and are among the major malaria vectors in Sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species. We will producede novochromosome-level genome assemblies forAn. coluzziiandAn. arabiensisusing the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. Each assembly will consist of three chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species should demonstrate if we obtained improved reference-quality genomes. The new assemblies will allow us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions inAn. coluzziiandAn. arabiensis.The new chromosome-level assemblies will facilitate functional and population genomic studies inAn. coluzziiandAn. arabiensis. The developed assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.

Impacts
What was accomplished under these goals? Heterochromatin is identified as a potential factor driving the diversification of species. To understand the magnitude of heterochromatin variation within theAnopheles gambiaecomplex of malaria mosquitoes, we analyzed metaphase chromosomes inAn. arabiensis,An. coluzzii,An. gambiae,An. merus, andAn. quadriannulatus. Using fluorescencein situhybridization (FISH) with ribosomal DNA (rDNA), a highly repetitive fraction of DNA, and heterochromatic Bacterial Artificial Chromosome (BAC) clones, we established the correspondence of pericentric heterochromatin between the metaphase and polytene X chromosomes ofAn. gambiae. We then developed chromosome idiograms and demonstrated that the X chromosomes exhibit qualitative differences in their pattern of heterochromatic bands and position of satellite DNA (satDNA) repeats among the sibling species with postzygotic isolation,An. arabiensis,An. merus,An. quadriannulatus, andAn. coluzziiorAn. gambiae. The identified differences in the size and structure of the X chromosome heterochromatin point to a possible role of repetitive DNA in the speciation of mosquitoes. We found thatAn. coluzziiandAn. gambiae, incipient species with prezygotic isolation, share variations in the relative positions of the satDNA repeats and the proximal heterochromatin band on the X chromosomes. This previously unknown genetic polymorphism in malaria mosquitoes may be caused by a differential amplification of DNA repeats or an inversion in the sex chromosome heterochromatin.

Publications

• Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Bondarenko SM, Sharakhov IV. Reorganization of the nuclear architecture in the Drosophila melanogaster Lamin B mutant lacking the CaaX box. Nucleus. 2020 Dec;11(1):283-298.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Sharma A, Kinney NA, Timoshevskiy VA, Sharakhova MV, Sharakhov IV. Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex. Genes (Basel). 2020 Mar 19;11(3):327.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: George P, Kinney NA, Liang J, Onufriev AV, Sharakhov IV. Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes. Cells. 2020 Feb 1;9(2):339.

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:My target audience included students, faculty, other scientists, stakeholders and public. My outreach activities for the public were:Kids' Tech University on March 2, 2019; ICAT Creativity and Innovation Day on May 6, 2019; an exhibit at the Moss Arts Center at Virginia Tech "ICAT: Open (at the) Source" "Perspectives" from April 4 to June 1, 2019; Virginia TechHokie BugFest 2019; Virginia Tech Science Festival 2019. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?My students participated inphysical mapping of mosquito genomes. The project provideddevelopment of students through their involvement in meetings, workshops, including the Eastern Branch ESA meeting in Blacksburg. How have the results been disseminated to communities of interest?The new mosquito assemblies have been submitted to VectorBase. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? New sequencing technologies have lowered financial barriers to whole-genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbors (adjacencies) offers a potentially useful complementary method for improving draft assemblies. We employed three gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: six with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and three with new assemblies based on re-scaffolding or Pacific Biosciences long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: seven for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further seven with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our comparisons show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Liang J, Sharakhov IV. Premeiotic and meiotic failures lead to hybrid male sterility in the Anopheles gambiae complex. Proc Biol Sci. 2019 Jul 10;286(1906):20191080. doi: 10.1098/rspb.2019.1080. Epub 2019 Jul 10. PMID: 31288705
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Robert M. Waterhouse, Sergey Aganezov, Yoann Anselmetti, Jiyoung Lee, Livio Ruzzante, Maarten J. M. F. Reijnders, Romain Feron, S�verine B�rard, Phillip George, Matthew W. Hahn, Paul I. Howell, Maryam Kamali, Sergey Koren, Daniel Lawson, Gareth Maslen, Ashley Peery, Adam M. Phillippy, Maria V. Sharakhova, Eric Tannier, Maria F. Unger, Simo V. Zhang, Max A. Alekseyev, Nora J. Besansky, Cedric Chauve, Scott J. Emrich and Igor V. Sharakhov. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. BMC Biology. 2019.

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:students, faculty, fellow scientists, and researchers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?My PhD students participated with poster presentations at 2 international scientificmeetings. My PhD studentJiang-Tao Liang was awardedfirst place honor for his poster at the ESA meeting. How have the results been disseminated to communities of interest?I presented the results of my work at five international meetings. What do you plan to do during the next reporting period to accomplish the goals?We will develop new assemblies of the genomes of several Anopheles species.

Impacts
What was accomplished under these goals? We leveraged the combined detection power of three such gene synteny-based methods applied to 21 Anopheles mosquito assemblies with variable contiguity levels to produce consensus sets of scaffold adjacency predictions. Three complementary validations were performed on subsets of assemblies with additional supporting data: six with physical mapping data; 13 with paired-end RNA sequencing (RNAseq) data; and three with new assemblies based on re-scaffolding or incorporating Pacific Biosciences (PacBio) sequencing data. Improved assemblies were built by integrating the consensus adjacency predictions with supporting experimental data, resulting in 20 new reference assemblies with improved contiguities. Combined with physical mapping data for six anophelines, chromosomal positioning of scaffolds improved assembly anchoring by 47% for A. funestus and 38% A. stephensi. Reconciling an A. funestus PacBio assembly with synteny-based and RNAseq-based adjacencies and physical mapping data resulted in a new 81.5% chromosomally mapped reference assembly and cytogenetic photomap. While complementary experimental data are clearly key to achieving high-quality chromosomal-level assemblies, our assessments and validations of gene synteny-based computational methods highlight the utility of applying comparative genomics approaches to improve community genomic resources.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Nicholas Allen Kinney1, Igor V. Sharakhov1,2,3* and Alexey V. Onufriev1,4,5,6. Chromosomenuclear envelope attachments affect interphase chromosome territories and entanglement. Epigenetics & Chromatin (2018) 11:3 https://doi.org/10.1186/s13072-018-0173-5
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Lukyanchikova, V., Fishman, V., Nuriddinov, M., Battulin, N., Serov, O. L., & Sharakhov, I. (2018). Improving the accuracy of genome assemblies of Anopheles species and revealing the principles of 3D genome organization in dipteran insects using Hi-C approach. Poster session presented at the meeting of ESA, Vancouver, BC.
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Liang, J., & Sharakhov, I. (2018). A failure of meiosis leads to hybrid male sterility in the Anopheles gambiae complex. Poster session presented at the meeting of ESA, Vancouver, BC.
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Sharakhov, I. (2018). Mechanisms and patterns of chromosome evolution in malaria mosquitoes. In 1st AsiaEvo Conference. Shenzhen, China.
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Sharakhov, I., Lukyanchikova, V., Fishman, V., Nuriddinov, M., Battulin, N., Liang, J., & Serov, O. L. (2018). The Hi-C approach improved genome assemblies and revealed principles of 3D genome organization in malaria vectors. In The 67th annual meeting of the American Society of Tropical Medicine and Hygiene. (Labels: Food, Nutrition, and Health, International activity)
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Sharakhov, I., & Liang, J. (2018). Chromosome organization and dynamics in Anopheles species and their hybrids.. In International Conference "Chromosome-2018". Novosibirsk, Russia.
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Sharakhov, I. (2018). The interplay between chromosome-nuclear envelope attachments and chromosome-chromosome contacts. In Nuclear lamins, nuclear organization and transcription. Riga, Latvia.
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Sharakhov, I., George, P., Kinney, N. A., & Onufriev, A. V. (2018). The interplay between chromosome-nuclear envelope attachments and chromosome-chromosome contacts. Poster session presented at the meeting of 2018 Keystone Symposia Conference X5: Chromatin Architecture and Chromosome Organization.

Progress 07/01/17 to 09/30/17

Outputs
Target Audience:Students, Faculty, and Scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Basic preliminary training of graduate students. How have the results been disseminated to communities of interest?2017 annualASTMH meeting EMBO meeting What do you plan to do during the next reporting period to accomplish the goals?Continue to develop projects and collect data for all objectives.

Impacts
What was accomplished under these goals? Sequencing contigs have beenphysically mapped to chromosomes ofAn. albimanus, An. atroparvus,andAn. funestus.We have placed and oriented contigs to polytene chromosomes by fluorescencein situhybridization (FISH), thus, creating chromosome-based genome assemblies for the species belonging to the subgeneraAnophelesandCellia.Our physical mapping, assisted by an ortholog-based bioinformatics approach,identified and corrected nine misassemblies in five large genomic scaffolds. Misassemblies mostly occurredin junctions between contigs. Our comparative analysis of scaffolds with the An. gambiae genome detectedmultiple genetic exchanges between pericentromeric regions of chromosomal arms caused by partial-arm translocations.The final map consists of 40 ordered genomic scaffolds and corrected fragments of misassembled scaffolds.The An. albimanus physical map comprises 98.2% of the total genome assembly and represents the most completegenome map among mosquito species. This study demonstrates that physical mapping is a powerful tool forcorrecting errors in draft genome assemblies and for creating chromosome-anchored reference genomes.In this study, we developed a physical genome map of Anopheles atroparvus, one of the dominant vectors of malaria in Europe, based on the ovarian nurse cell polytene chromosomes. Using a fluorescence in situ hybridization of genomic scaffolds and synteny information, we anchored 89.6% of the genome to the chromosomes. The final map consists of 56 ordered genomic scaffolds representing the second of the most completely mapped anophelinae assemblies after the An. albimanus genome. Comparison of An. atroparvus genome with genomes of An. albimanus and An. gambiae detected multiple translocations of the genetic material among pericentromeric regions of autosomes that break down the integrity of chromosomal elements in the evolution of Anopheles. We also detected nonrandom distribution of large conserved synteny blocks and confirmed a higher rate of inversion fixation in the X chromosome compared with autosomes.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: The Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles. 2017. Gleb N. Artemov,*,1 Ashley N. Peery,1 Xiaofang Jiang, Zhijian Tu, Vladimir N. Stegniy,* Maria V. Sharakhova*, and Igor V. Sharakhov*.