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Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance
Crop Brassicas contain monogenomic and digenomic species, with no evidence of a trigenomic Brassica in nature. Through somatic fusion (Sinapis alba + B. juncea), a novel allohexaploid trigenomic Brassica (H1 = AABBSS; 2n = 60) was produced and used for transcriptome analysis to uncover genes for the...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524822/ https://www.ncbi.nlm.nih.gov/pubmed/36186472 http://dx.doi.org/10.3389/fgene.2022.958217 |
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author | Singh, Kaushal Pratap Kumari, Preetesh Yadava, Devendra Kumar |
author_facet | Singh, Kaushal Pratap Kumari, Preetesh Yadava, Devendra Kumar |
author_sort | Singh, Kaushal Pratap |
collection | PubMed |
description | Crop Brassicas contain monogenomic and digenomic species, with no evidence of a trigenomic Brassica in nature. Through somatic fusion (Sinapis alba + B. juncea), a novel allohexaploid trigenomic Brassica (H1 = AABBSS; 2n = 60) was produced and used for transcriptome analysis to uncover genes for thermotolerance, annotations, and microsatellite markers for future molecular breeding. Illumina Novaseq 6000 generated a total of 76,055,546 paired-end raw reads, which were used for de-novo assembly, resulting in the development of 486,066 transcripts. A total of 133,167 coding sequences (CDSs) were predicted from transcripts with a mean length of 507.12 bp and 46.15% GC content. The BLASTX search of CDSs against public protein databases showed a maximum of 126,131 (94.72%) and a minimum of 29,810 (22.39%) positive hits. Furthermore, 953,773 gene ontology (GO) terms were found in 77,613 (58.28%) CDSs, which were divided into biological processes (49.06%), cellular components (31.67%), and molecular functions (19.27%). CDSs were assigned to 144 pathways by a pathway study using the KEGG database and 1,551 pathways by a similar analysis using the Reactome database. Further investigation led to the discovery of genes encoding over 2,000 heat shock proteins (HSPs). The discovery of a large number of HSPs in allohexaploid Brassica validated our earlier findings for heat tolerance at seed maturity. A total of 15,736 SSRs have been found in 13,595 CDSs, with an average of one SSR per 4.29 kb length and an SSR frequency of 11.82%. The first transcriptome assembly of a meiotically stable allohexaploid Brassica has been given in this article, along with functional annotations and the presence of SSRs, which could aid future genetic and genomic studies. |
format | Online Article Text |
id | pubmed-9524822 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95248222022-10-01 Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance Singh, Kaushal Pratap Kumari, Preetesh Yadava, Devendra Kumar Front Genet Genetics Crop Brassicas contain monogenomic and digenomic species, with no evidence of a trigenomic Brassica in nature. Through somatic fusion (Sinapis alba + B. juncea), a novel allohexaploid trigenomic Brassica (H1 = AABBSS; 2n = 60) was produced and used for transcriptome analysis to uncover genes for thermotolerance, annotations, and microsatellite markers for future molecular breeding. Illumina Novaseq 6000 generated a total of 76,055,546 paired-end raw reads, which were used for de-novo assembly, resulting in the development of 486,066 transcripts. A total of 133,167 coding sequences (CDSs) were predicted from transcripts with a mean length of 507.12 bp and 46.15% GC content. The BLASTX search of CDSs against public protein databases showed a maximum of 126,131 (94.72%) and a minimum of 29,810 (22.39%) positive hits. Furthermore, 953,773 gene ontology (GO) terms were found in 77,613 (58.28%) CDSs, which were divided into biological processes (49.06%), cellular components (31.67%), and molecular functions (19.27%). CDSs were assigned to 144 pathways by a pathway study using the KEGG database and 1,551 pathways by a similar analysis using the Reactome database. Further investigation led to the discovery of genes encoding over 2,000 heat shock proteins (HSPs). The discovery of a large number of HSPs in allohexaploid Brassica validated our earlier findings for heat tolerance at seed maturity. A total of 15,736 SSRs have been found in 13,595 CDSs, with an average of one SSR per 4.29 kb length and an SSR frequency of 11.82%. The first transcriptome assembly of a meiotically stable allohexaploid Brassica has been given in this article, along with functional annotations and the presence of SSRs, which could aid future genetic and genomic studies. Frontiers Media S.A. 2022-09-16 /pmc/articles/PMC9524822/ /pubmed/36186472 http://dx.doi.org/10.3389/fgene.2022.958217 Text en Copyright © 2022 Singh, Kumari and Yadava. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Singh, Kaushal Pratap Kumari, Preetesh Yadava, Devendra Kumar Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance |
title | Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance |
title_full | Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance |
title_fullStr | Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance |
title_full_unstemmed | Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance |
title_short | Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance |
title_sort | development of de-novo transcriptome assembly and ssrs in allohexaploid brassica with functional annotations and identification of heat-shock proteins for thermotolerance |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524822/ https://www.ncbi.nlm.nih.gov/pubmed/36186472 http://dx.doi.org/10.3389/fgene.2022.958217 |
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