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按蚊斯蒂芬斯，城市疟疾媒介的基因组三部曲揭示了与适应环境异质性相关的基因座结构。

The genome trilogy of Anopheles stephensi, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity.

机构信息

Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bangalore, 560100, India.

Tata Institute for Genetics and Society, Center at inStem - GKVK campus, Bellary Road, Bangalore, 560065, India.

出版信息

Sci Rep. 2022 Mar 4;12(1):3610. doi: 10.1038/s41598-022-07462-3.

DOI:10.1038/s41598-022-07462-3
PMID:35246568
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8897464/
Abstract

Anopheles stephensi is the most menacing malaria vector to watch for in newly urbanising parts of the world. Its fitness is reported to be a direct consequence of the vector adapting to laying eggs in over-head water tanks with street-side water puddles polluted by oil and sewage. Large frequent inversions in the genome of malaria vectors are implicated in adaptation. We report the genome assembly of a strain of An. stephensi of the type-form, collected from a construction site from Chennai (IndCh) in 2016. The genome reported here with a L50 of 4, completes the trilogy of high-resolution genomes of strains with respect to a 16.5 Mbp 2Rb genotype in An. stephensi known to be associated with adaptation to environmental heterogeneity. Unlike the reported genomes of two other strains, STE2 (2R+/2Rb) and UCI (2Rb/2Rb), IndCh is found to be homozygous for the standard form (2R+/2R+). Comparative genome analysis revealed base-level details of the breakpoints and allowed extraction of 22,650 segregating SNPs for typing this inversion in populations. Whole genome sequencing of 82 individual mosquitoes from diverse geographical locations reveal that one third of both wild and laboratory populations maintain the heterozygous genotype of 2Rb. The large number of SNPs can be tailored to 1740 exonic SNPs enabling genotyping directly from transcriptome sequencing. The genome trilogy approach accelerated the study of fine structure and typing of an important inversion in An. stephensi, putting the genome resources for this understudied species on par with the extensively studied malaria vector, Anopheles gambiae. We argue that the IndCh genome is relevant for field translation work compared to those reported earlier by showing that individuals from diverse geographical locations cluster with IndCh, pointing to significant convergence resulting from travel and commerce between cities, perhaps, contributing to the survival of the fittest strain.

摘要

致倦库蚊是世界新城市化地区最令人担忧的疟疾传播媒介。据报道，这种媒介的适应性导致其在头顶水箱中产卵，而这些水箱中的水则受到了石油和污水的污染。疟疾媒介基因组的大规模频繁倒位与适应有关。我们报告了 2016 年从钦奈（IndCh）建筑工地收集的致倦库蚊标准型的基因组组装。与已知与环境异质性适应相关的 16.5 Mbp 2Rb 基因型的致倦库蚊菌株的高分辨率基因组三部曲相比，这里报道的基因组具有 L50 为 4 的特点。与报告的两个其他菌株（STE2（2R+/2Rb）和 UCI（2Rb/2Rb））的基因组不同，IndCh 被发现是标准型（2R+/2R+）的纯合子。比较基因组分析揭示了断点的碱基水平细节，并允许提取 22650 个分离 SNP 用于对该反转进行种群分型。来自不同地理区域的 82 只个体的全基因组测序显示，三分之一的野生和实验室种群都保持 2Rb 的杂合基因型。大量的 SNP 可以定制为 1740 个外显子 SNP，从而能够直接从转录组测序中进行基因分型。全基因组测序三部曲加速了致倦库蚊重要反转的精细结构和分型研究，使这个研究较少的物种的基因组资源与广泛研究的疟疾媒介冈比亚按蚊相媲美。我们认为，与之前报道的相比，IndCh 基因组与来自不同地理区域的个体聚类，这表明由于城市之间的旅行和商业往来导致了显著的趋同，这可能有助于最适应环境的菌株的生存，因此 IndCh 基因组与现场翻译工作更相关。

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