Highly contiguous genome assembly of Drosophila prolongata-a model for evolution of sexual dimorphism and male-specific innovations.

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI:10.1093/g3journal/jkae155
David Luecke, Yige Luo, Halina Krzystek, Corbin Jones, Artyom Kopp
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Abstract

Drosophila prolongata is a member of the melanogaster species group and rhopaloa subgroup native to the subtropical highlands of Southeast Asia. This species exhibits an array of recently evolved male-specific morphological, physiological, and behavioral traits that distinguish it from its closest relatives, making it an attractive model for studying the evolution of sexual dimorphism and testing theories of sexual selection. The lack of genomic resources has impeded the dissection of the molecular basis of sex-specific development and behavior in this species. To address this, we assembled the genome of D. prolongata using long-read sequencing and Hi-C scaffolding, resulting in a highly complete and contiguous (scaffold N50 2.2 Mb) genome assembly of 220 Mb. The repetitive content of the genome is 24.6%, the plurality of which are long terminal repeats retrotransposons (33.2%). Annotations based on RNA-seq data and homology to related species revealed a total of 19,330 genes, of which 16,170 are protein-coding. The assembly includes 98.5% of Diptera BUSCO genes, including 93.8% present as a single copy. Despite some likely regional duplications, the completeness of this genome suggests that it can be readily used for gene expression, genome-wide association studies (GWAS), and other genomic analyses.

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长尾果蝇的高度连续基因组组装--性别二形性和雄性特异性创新进化的模型。
延长果蝇(Drosophila prolongata)是原产于东南亚亚热带高原的黑腹果蝇种群和蚱蜢亚群的成员。该物种表现出一系列新近进化的雄性特异性形态、生理和行为特征,使其有别于近亲,成为研究性二形进化和检验性选择理论的极具吸引力的模型。基因组资源的缺乏阻碍了对该物种性别特异性发育和行为的分子基础的研究。为了解决这个问题,我们利用长线程测序和 Hi-C 支架法组装了 D. prolongata 的基因组,得到了 220Mb 的高度完整和连续(支架 N50 2.2Mb)的基因组。该基因组的重复性含量为 24.6%,其中大部分是 LTR 逆转录子(33.2%)。根据 RNA-seq 数据和与相关物种的同源性进行的注释共发现了 19,330 个基因,其中 16,170 个是编码蛋白质的基因。该基因组包括了双翅目 BUSCO 98.5% 的基因,其中 93.8% 的基因为单个拷贝。尽管可能存在一些区域性重复,但该基因组的完整性表明,它可随时用于基因表达、GWAS 和其他基因组分析。
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来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
期刊介绍: G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.
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