Carlos Congrains, Sheina B Sim, Daniel F Paulo, Renee L Corpuz, Angela N Kauwe, Tyler J Simmonds, Sheron A Simpson, Brian E Scheffler, Scott M Geib
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引用次数: 0
摘要
墨西哥果蝇(Anastrepha ludens)是一种多食性真果蝇(双翅目:Tephritidae),被认为是中美洲和北美洲危害各种经济相关水果的最严重害虫之一。尽管它与农业息息相关,但高质量的基因组组装尚未见报道。在此,我们结合 PacBio 高保真长读数和染色质构象捕获测序数据,描述了 A. ludens 染色体级基因组的生成过程。最终的组装包括 140 个支架(821 Mb,N50 = 131 Mb),其中包含 99.27% 的双翅目完整保守直向同源物(BUSCO)。我们使用三种策略确定了性染色体:1) 利用 HiFi 读数目测 Hi-C 接触图和覆盖率分析;2) 与黑腹果蝇的同源关系;3) 常染色体与性染色体支架平均读数深度的差异。在一个大支架(100 Mb)和八个较小的等位组(1.8 Mb)中发现了 X 染色体,在一个大支架(6.1 Mb)和 35 个较小的等位组(4.3 Mb)中发现了 Y 染色体。性染色体和常染色体在转座元件和基因含量方面存在很大差异。此外,A. ludens 和 Anastrepha obliqua 的直向同源物的进化速度表明,与常染色体连锁基因相比,X 连锁基因的进化速度更快,这与快速 X 效应一致,从而使我们对这一多样性蝇类群中性染色体的进化有了新的认识。该基因组组装为未来的进化、遗传和基因组转化研究提供了宝贵的资源,有助于管理这种重要的农业害虫。
Chromosome-scale genome of the polyphagous pest Anastrepha ludens (Diptera: Tephritidae) provides insights on sex chromosome evolution in Anastrepha.
The Mexican fruit fly, Anastrepha ludens, is a polyphagous true fruit fly (Diptera: Tephritidae) considered one of the most serious insect pests in Central and North America to various economically relevant fruits. Despite its agricultural relevance, a high-quality genome assembly has not been reported. Here, we described the generation of a chromosome-level genome for the A. ludens using a combination of PacBio high fidelity long-reads and chromatin conformation capture sequencing data. The final assembly consisted of 140 scaffolds (821 Mb, N50 = 131 Mb), containing 99.27% complete conserved orthologs (BUSCO) for Diptera. We identified the sex chromosomes using three strategies: 1) visual inspection of Hi-C contact map and coverage analysis using the HiFi reads, 2) synteny with Drosophila melanogaster, and 3) the difference in the average read depth of autosomal versus sex chromosomal scaffolds. The X chromosome was found in one major scaffold (100 Mb) and eight smaller contigs (1.8 Mb), and the Y chromosome was recovered in one large scaffold (6.1 Mb) and 35 smaller contigs (4.3 Mb). Sex chromosomes and autosomes showed considerable differences of transposable elements and gene content. Moreover, evolutionary rates of orthologs of A. ludens and Anastrepha obliqua revealed a faster evolution of X-linked, compared to autosome-linked, genes, consistent with the faster-X effect, leading us to new insights on the evolution of sex chromosomes in this diverse group of flies. This genome assembly provides a valuable resource for future evolutionary, genetic, and genomic translational research supporting the management of this important agricultural pest.
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.