Cargando…
The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution
Trichoptera is a highly adapted group of freshwater insects. They are generally more sensitive to dissolved oxygen and water quality than most freshwater organisms, and this sensitivity allows them to be used as reliable biological indicators of water quality. At present, there exists no chromosome-...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9539401/ https://www.ncbi.nlm.nih.gov/pubmed/36073551 http://dx.doi.org/10.1093/gbe/evac136 |
_version_ | 1784803476258160640 |
---|---|
author | Ge, Xinyu Jin, Jianfeng Peng, Lang Zang, Haoming Wang, Beixin Sun, Changhai |
author_facet | Ge, Xinyu Jin, Jianfeng Peng, Lang Zang, Haoming Wang, Beixin Sun, Changhai |
author_sort | Ge, Xinyu |
collection | PubMed |
description | Trichoptera is a highly adapted group of freshwater insects. They are generally more sensitive to dissolved oxygen and water quality than most freshwater organisms, and this sensitivity allows them to be used as reliable biological indicators of water quality. At present, there exists no chromosome-level genome of a hydropsychid species. Cheumatopsyche charites Malicky & Chantaramongkol, 1997 can successfully survive and thrive in polluted streams where other caddisflies are infrequent, suggesting that they are tolerant to latent contamination. Here we report a high-quality chromosome-level genome assembly of C. charites generated combining PacBio long reads and Hi-C reads. We obtained a genome assembly of 223.23 Mb, containing 68 scaffolds with an N50 length of 13.97 Mb, and 155 contigs (99.67%) anchored into 16 pseudochromosomes. We identified 36.12 Mb (16.18%) of the genome as being composed of repetitive elements, identified 369 noncoding RNAs, and predicted 8,772 protein-coding genes (96.80% BUSCO completeness). Gene family evolution analyses identified 7,148 gene families, of which 41 experienced rapid evolution. The expanded gene families were shown to be involved in detoxification metabolism, digestive absorption, and resistance to viruses or bacteria. This high-quality genome provides a valuable genomic basis for the study of trichopteran evolution. |
format | Online Article Text |
id | pubmed-9539401 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-95394012022-10-07 The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution Ge, Xinyu Jin, Jianfeng Peng, Lang Zang, Haoming Wang, Beixin Sun, Changhai Genome Biol Evol Genome Report Trichoptera is a highly adapted group of freshwater insects. They are generally more sensitive to dissolved oxygen and water quality than most freshwater organisms, and this sensitivity allows them to be used as reliable biological indicators of water quality. At present, there exists no chromosome-level genome of a hydropsychid species. Cheumatopsyche charites Malicky & Chantaramongkol, 1997 can successfully survive and thrive in polluted streams where other caddisflies are infrequent, suggesting that they are tolerant to latent contamination. Here we report a high-quality chromosome-level genome assembly of C. charites generated combining PacBio long reads and Hi-C reads. We obtained a genome assembly of 223.23 Mb, containing 68 scaffolds with an N50 length of 13.97 Mb, and 155 contigs (99.67%) anchored into 16 pseudochromosomes. We identified 36.12 Mb (16.18%) of the genome as being composed of repetitive elements, identified 369 noncoding RNAs, and predicted 8,772 protein-coding genes (96.80% BUSCO completeness). Gene family evolution analyses identified 7,148 gene families, of which 41 experienced rapid evolution. The expanded gene families were shown to be involved in detoxification metabolism, digestive absorption, and resistance to viruses or bacteria. This high-quality genome provides a valuable genomic basis for the study of trichopteran evolution. Oxford University Press 2022-09-08 /pmc/articles/PMC9539401/ /pubmed/36073551 http://dx.doi.org/10.1093/gbe/evac136 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Genome Report Ge, Xinyu Jin, Jianfeng Peng, Lang Zang, Haoming Wang, Beixin Sun, Changhai The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution |
title | The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution |
title_full | The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution |
title_fullStr | The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution |
title_full_unstemmed | The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution |
title_short | The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution |
title_sort | first chromosome-level genome assembly of cheumatopsyche charites malicky and chantaramongkol, 1997 (trichoptera: hydropsychidae) reveals how it responds to pollution |
topic | Genome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9539401/ https://www.ncbi.nlm.nih.gov/pubmed/36073551 http://dx.doi.org/10.1093/gbe/evac136 |
work_keys_str_mv | AT gexinyu thefirstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT jinjianfeng thefirstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT penglang thefirstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT zanghaoming thefirstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT wangbeixin thefirstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT sunchanghai thefirstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT gexinyu firstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT jinjianfeng firstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT penglang firstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT zanghaoming firstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT wangbeixin firstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution AT sunchanghai firstchromosomelevelgenomeassemblyofcheumatopsychecharitesmalickyandchantaramongkol1997trichopterahydropsychidaerevealshowitrespondstopollution |