A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira.

IF 2.1 3区生物学 Q3 GENETICS & HEREDITY G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI:10.1093/g3journal/jkae167

Kenta Tomihara, Ana Llopart, Daisuke Yamamoto

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Abstract

Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, Drosophila madeirensis, is endemic to the island of Madeira in the Atlantic Ocean. D. subobscura is known for its strict light-dependence in mating and its unique courtship displays, including nuptial gift-giving. D. subobscura has also attracted the interest of researchers because of its abundant variations in chromosomal polymorphisms correlated to the latitude and season, which have been used as a tool to track global climate warming. Although D. madeirensis can be an important resource for understanding the evolutionary underpinning of these genetic characteristics of D. subobscura, little work has been done on the biology of this species. Here, we used a HiFi long-read sequencing data set to produce a de novo genome assembly for D. madeirensis. This assembly comprises a total of 111 contigs spanning 135.5 Mb and has an N50 of 24.2 Mb and a BUSCO completeness score of 98.6%. Each of the 6 chromosomes of D. madeirensis consisted of a single contig except for some centromeric regions. Breakpoints of the chromosomal inversions between D. subobscura and D. madeirensis were characterized using this genome assembly, updating some of the previously identified locations.

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马德拉岛特有果蝇 Drosophila madeirensis 的染色体级基因组组装。

subobscura 果蝇分布于欧洲、近东和美洲，而它的姊妹种 D. madeirensis 则是大西洋马德拉岛的特有物种。D.subobscura因其严格的交配光依赖性和独特的求偶表演（包括新婚礼物赠送）而闻名。D.subobscura也引起了研究人员的兴趣，因为它的染色体多态性变化丰富，与纬度和季节相关，被用作追踪全球气候变暖的工具。虽然D. madeirensis是了解D. subobscura这些遗传特征的进化基础的重要资源，但对该物种的生物学研究却很少。在这里，我们使用 HiFi 长线程测序数据集为 D. madeirensis 生成了一个全新的基因组组装。该序列包括 111 个等位基因，跨度 135.5 Mb，N50 为 24.2 Mb，BUSCO 完整性得分 98.6%。除了一些中心区外，D. madeirensis 的六条染色体均由单个等位基因组成。利用该基因组组装鉴定了亚布仓鼠和马迪伦氏鼠之间染色体倒位的断裂点，更新了之前确定的一些位置。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

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.