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Characteristics and potential functional effects of long insertions in Asian butternuts

BACKGROUND: Structural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly de...

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Autores principales: Chen, Yidan, Miao, Yating, Bai, Weining, Lin, Kui, Pang, Erli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9617325/
https://www.ncbi.nlm.nih.gov/pubmed/36307757
http://dx.doi.org/10.1186/s12864-022-08961-3
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author Chen, Yidan
Miao, Yating
Bai, Weining
Lin, Kui
Pang, Erli
author_facet Chen, Yidan
Miao, Yating
Bai, Weining
Lin, Kui
Pang, Erli
author_sort Chen, Yidan
collection PubMed
description BACKGROUND: Structural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly detected and studied in all but model species. RESULTS: We used whole-genome resequencing of paired reads from 80 Asian butternuts to detect long insertions and further analyse their characteristics and potential functional effects. By combining of mapping-based and de novo assembly-based methods, we obtained a multiple related species pangenome representing higher taxonomic groups. We obtained 89,312 distinct contigs totaling 147,773,999 base pair (bp) of new sequences, of which 347 were putative long insertions placed in the reference genome. Most of the putative long insertions appeared in multiple species; in contrast, only 62 putative long insertions appeared in one species, which may be involved in the response to the environment. 65 putative long insertions fell into 61 distinct protein-coding genes involved in plant development, and 105 putative long insertions fell into upstream of 106 distinct protein-coding genes involved in cellular respiration. 3,367 genes were annotated in 2,606 contigs. We propose PLAINS (https://github.com/CMB-BNU/PLAINS.git), a streamlined, comprehensive pipeline for the prediction and analysis of long insertions using whole-genome resequencing. CONCLUSIONS: Our study lays down an important foundation for further whole-genome long insertion studies, allowing the investigation of their effects by experiments. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08961-3.
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spelling pubmed-96173252022-10-30 Characteristics and potential functional effects of long insertions in Asian butternuts Chen, Yidan Miao, Yating Bai, Weining Lin, Kui Pang, Erli BMC Genomics Research BACKGROUND: Structural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly detected and studied in all but model species. RESULTS: We used whole-genome resequencing of paired reads from 80 Asian butternuts to detect long insertions and further analyse their characteristics and potential functional effects. By combining of mapping-based and de novo assembly-based methods, we obtained a multiple related species pangenome representing higher taxonomic groups. We obtained 89,312 distinct contigs totaling 147,773,999 base pair (bp) of new sequences, of which 347 were putative long insertions placed in the reference genome. Most of the putative long insertions appeared in multiple species; in contrast, only 62 putative long insertions appeared in one species, which may be involved in the response to the environment. 65 putative long insertions fell into 61 distinct protein-coding genes involved in plant development, and 105 putative long insertions fell into upstream of 106 distinct protein-coding genes involved in cellular respiration. 3,367 genes were annotated in 2,606 contigs. We propose PLAINS (https://github.com/CMB-BNU/PLAINS.git), a streamlined, comprehensive pipeline for the prediction and analysis of long insertions using whole-genome resequencing. CONCLUSIONS: Our study lays down an important foundation for further whole-genome long insertion studies, allowing the investigation of their effects by experiments. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08961-3. BioMed Central 2022-10-28 /pmc/articles/PMC9617325/ /pubmed/36307757 http://dx.doi.org/10.1186/s12864-022-08961-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://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
Chen, Yidan
Miao, Yating
Bai, Weining
Lin, Kui
Pang, Erli
Characteristics and potential functional effects of long insertions in Asian butternuts
title Characteristics and potential functional effects of long insertions in Asian butternuts
title_full Characteristics and potential functional effects of long insertions in Asian butternuts
title_fullStr Characteristics and potential functional effects of long insertions in Asian butternuts
title_full_unstemmed Characteristics and potential functional effects of long insertions in Asian butternuts
title_short Characteristics and potential functional effects of long insertions in Asian butternuts
title_sort characteristics and potential functional effects of long insertions in asian butternuts
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9617325/
https://www.ncbi.nlm.nih.gov/pubmed/36307757
http://dx.doi.org/10.1186/s12864-022-08961-3
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