Cargando…

A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause

SIMPLE SUMMARY: 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 adaptati...

Descripción completa

Detalles Bibliográficos
Autores principales: Boyle, John H., Rastas, Pasi M. A., Huang, Xin, Garner, Austin G., Vythilingam, Indra, Armbruster, Peter A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919801/
https://www.ncbi.nlm.nih.gov/pubmed/33669192
http://dx.doi.org/10.3390/insects12020167
_version_ 1783658184878063616
author Boyle, John H.
Rastas, Pasi M. A.
Huang, Xin
Garner, Austin G.
Vythilingam, Indra
Armbruster, Peter A.
author_facet Boyle, John H.
Rastas, Pasi M. A.
Huang, Xin
Garner, Austin G.
Vythilingam, Indra
Armbruster, Peter A.
author_sort Boyle, John H.
collection PubMed
description SIMPLE SUMMARY: 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. ABSTRACT: 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.
format Online
Article
Text
id pubmed-7919801
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-79198012021-03-02 A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause Boyle, John H. Rastas, Pasi M. A. Huang, Xin Garner, Austin G. Vythilingam, Indra Armbruster, Peter A. Insects Article SIMPLE SUMMARY: 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. ABSTRACT: 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. MDPI 2021-02-16 /pmc/articles/PMC7919801/ /pubmed/33669192 http://dx.doi.org/10.3390/insects12020167 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Boyle, John H.
Rastas, Pasi M. A.
Huang, Xin
Garner, Austin G.
Vythilingam, Indra
Armbruster, Peter A.
A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause
title A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause
title_full A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause
title_fullStr A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause
title_full_unstemmed A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause
title_short A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause
title_sort linkage-based genome assembly for the mosquito aedes albopictus and identification of chromosomal regions affecting diapause
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919801/
https://www.ncbi.nlm.nih.gov/pubmed/33669192
http://dx.doi.org/10.3390/insects12020167
work_keys_str_mv AT boylejohnh alinkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT rastaspasima alinkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT huangxin alinkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT garnerausting alinkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT vythilingamindra alinkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT armbrusterpetera alinkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT boylejohnh linkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT rastaspasima linkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT huangxin linkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT garnerausting linkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT vythilingamindra linkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause
AT armbrusterpetera linkagebasedgenomeassemblyforthemosquitoaedesalbopictusandidentificationofchromosomalregionsaffectingdiapause