Cargando…
Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti
BACKGROUND: Aedes aegypti is the principal mosquito vector of Zika, dengue, and yellow fever viruses. Two subspecies of Ae. aegypti exhibit phenotypic divergence with regard to habitat, host preference, and vectorial capacity. Chromosomal inversions have been shown to play a major role in adaptation...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068900/ https://www.ncbi.nlm.nih.gov/pubmed/32164699 http://dx.doi.org/10.1186/s12915-020-0757-y |
_version_ | 1783505667291611136 |
---|---|
author | Redmond, Seth N. Sharma, Atashi Sharakhov, Igor Tu, Zhijian Sharakhova, Maria Neafsey, Daniel E. |
author_facet | Redmond, Seth N. Sharma, Atashi Sharakhov, Igor Tu, Zhijian Sharakhova, Maria Neafsey, Daniel E. |
author_sort | Redmond, Seth N. |
collection | PubMed |
description | BACKGROUND: Aedes aegypti is the principal mosquito vector of Zika, dengue, and yellow fever viruses. Two subspecies of Ae. aegypti exhibit phenotypic divergence with regard to habitat, host preference, and vectorial capacity. Chromosomal inversions have been shown to play a major role in adaptation and speciation in dipteran insects and would be of great utility for studies of Ae. aegypti. However, the large and highly repetitive genome of Ae. aegypti makes it difficult to detect inversions with paired-end short-read sequencing data, and polytene chromosome analysis does not provide sufficient resolution to detect chromosome banding patterns indicative of inversions. RESULTS: To characterize chromosomal diversity in this species, we have carried out deep Illumina sequencing of linked-read (10X Genomics) libraries in order to discover inversion loci as well as SNPs. We analyzed individuals from colonies representing the geographic limits of each subspecies, one contact zone between subspecies, and a closely related sister species. Despite genome-wide SNP divergence and abundant microinversions, we do not find any inversions occurring as fixed differences between subspecies. Many microinversions are found in regions that have introgressed and have captured genes that could impact behavior, such as a cluster of odorant-binding proteins that may play a role in host feeding preference. CONCLUSIONS: Our study shows that inversions are abundant and widely shared among subspecies of Aedes aegypti and that introgression has occurred in regions of secondary contact. This library of 32 novel chromosomal inversions demonstrates the capacity for linked-read sequencing to identify previously intractable genomic rearrangements and provides a foundation for future population genetics studies in this species. |
format | Online Article Text |
id | pubmed-7068900 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-70689002020-03-18 Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti Redmond, Seth N. Sharma, Atashi Sharakhov, Igor Tu, Zhijian Sharakhova, Maria Neafsey, Daniel E. BMC Biol Research Article BACKGROUND: Aedes aegypti is the principal mosquito vector of Zika, dengue, and yellow fever viruses. Two subspecies of Ae. aegypti exhibit phenotypic divergence with regard to habitat, host preference, and vectorial capacity. Chromosomal inversions have been shown to play a major role in adaptation and speciation in dipteran insects and would be of great utility for studies of Ae. aegypti. However, the large and highly repetitive genome of Ae. aegypti makes it difficult to detect inversions with paired-end short-read sequencing data, and polytene chromosome analysis does not provide sufficient resolution to detect chromosome banding patterns indicative of inversions. RESULTS: To characterize chromosomal diversity in this species, we have carried out deep Illumina sequencing of linked-read (10X Genomics) libraries in order to discover inversion loci as well as SNPs. We analyzed individuals from colonies representing the geographic limits of each subspecies, one contact zone between subspecies, and a closely related sister species. Despite genome-wide SNP divergence and abundant microinversions, we do not find any inversions occurring as fixed differences between subspecies. Many microinversions are found in regions that have introgressed and have captured genes that could impact behavior, such as a cluster of odorant-binding proteins that may play a role in host feeding preference. CONCLUSIONS: Our study shows that inversions are abundant and widely shared among subspecies of Aedes aegypti and that introgression has occurred in regions of secondary contact. This library of 32 novel chromosomal inversions demonstrates the capacity for linked-read sequencing to identify previously intractable genomic rearrangements and provides a foundation for future population genetics studies in this species. BioMed Central 2020-03-12 /pmc/articles/PMC7068900/ /pubmed/32164699 http://dx.doi.org/10.1186/s12915-020-0757-y Text en © The Author(s). 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Redmond, Seth N. Sharma, Atashi Sharakhov, Igor Tu, Zhijian Sharakhova, Maria Neafsey, Daniel E. Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti |
title | Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti |
title_full | Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti |
title_fullStr | Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti |
title_full_unstemmed | Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti |
title_short | Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti |
title_sort | linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector aedes aegypti |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068900/ https://www.ncbi.nlm.nih.gov/pubmed/32164699 http://dx.doi.org/10.1186/s12915-020-0757-y |
work_keys_str_mv | AT redmondsethn linkedreadsequencingidentifiesabundantmicroinversionsandintrogressioninthearboviralvectoraedesaegypti AT sharmaatashi linkedreadsequencingidentifiesabundantmicroinversionsandintrogressioninthearboviralvectoraedesaegypti AT sharakhovigor linkedreadsequencingidentifiesabundantmicroinversionsandintrogressioninthearboviralvectoraedesaegypti AT tuzhijian linkedreadsequencingidentifiesabundantmicroinversionsandintrogressioninthearboviralvectoraedesaegypti AT sharakhovamaria linkedreadsequencingidentifiesabundantmicroinversionsandintrogressioninthearboviralvectoraedesaegypti AT neafseydaniele linkedreadsequencingidentifiesabundantmicroinversionsandintrogressioninthearboviralvectoraedesaegypti |