A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause.
A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause.
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基于连锁的白纹伊蚊基因组拼接及滞育影响区域的鉴定
DOI：
10.3390/insects12020167
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发表时间：
2021-02-16
期刊：
影响因子：
3
通讯作者：
Armbruster PA
中科院分区：
文献类型：
--
作者：
Boyle JH;Rastas PMA;Huang X;Garner AG;Vythilingam I;Armbruster PA
基因组序列可以为理解生物体的广泛生物学特性提供基础。对于病媒和害虫物种，这些知识可用于开发基于基因组修饰的新型控制策略，这些基因组修饰破坏了与生态适应和疾病传播相关的性状。在这里，我们使用遗传作图实验，以产生一个改进的版本以前的基因组序列的入侵载体蚊子，白纹伊蚊。然后，我们使用改进的基因组序列来识别基因组中包含候选基因的区域，这些候选基因可能会影响这种蚊子进行越冬休眠的能力，这是一种关键的生态适应。亚洲虎蚊（Aedes albopictus）是一种具有重大公共卫生问题的入侵性病媒蚊。大的基因组大小（约1.19-1.28 Gb的细胞荧光测定法估计），包括约68%的重复DNA序列，使其难以产生高质量的基因组组装该物种。我们构建了一个高密度的连锁图谱。白纹伊蚊基于RNaseq获得的111，328个信息SNP。然后，我们进行了AalbF 2的连锁图锚定重组，Palatini等人（2020）产生的基因组组装。我们重组的基因组序列AalbF 3代表了相对于AalbF 2的几项改进。首先，AalbF 3组件的大小为1.45 Gb，几乎是AalbF 2的一半。此外，相对于AalbF 2，AalbF 3包含更高比例的完整和单拷贝BUSCO基因（84.3%）以及更高比例的对齐RNAseq读数，这些读数一致地映射到基因组的单个位置（46%）。我们证明了AalbF 3的效用，通过使用它作为一个参考的批量分离子为基础的比较基因组学分析，确定染色体区域与候选SNPs簇puppable与光周期滞育，一个关键的生态适应的基础上的快速范围扩张和气候适应的A。白纹伊蚊
A genome sequence can provide the basis for understanding a wide range of biological properties of an organism. For vector and pest species, this knowledge can be used to develop novel control strategies based on genome modifications that disrupt traits related to ecological adaptation and disease transmission. Here, we use a genetic mapping experiment to produce an improved version of a previous genome sequence for the invasive vector mosquito, Aedes albopictus. We then use the improved genome sequence to identify regions of the genome that contain candidate genes that may affect the ability of this mosquito to undergo overwintering dormancy, a crucial ecological adaptation. The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19–1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our reassembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as a reference for a bulk-segregant-based comparative genomics analysis that identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of A. albopictus.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
3.8
作者：
Huang X;Poelchau MF;Armbruster PA
通讯作者：
Armbruster PA
DOI：
10.1093/bioinformatics/btx220
发表时间：
2017-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Huang S;Kang M;Xu A
通讯作者：
Xu A
影响因子：
7.7
作者：
Matthews, Benjamin J.;Younger, Meg A.;Vosshall, Leslie B.
通讯作者：
Vosshall, Leslie B.
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng