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Proteogenomic analysis of pitaya reveals cold stress-related molecular signature
Pitayas (Hylocereus spp.) is an attractive, highly nutritious and commercially valuable tropical fruit. However, low-temperature damage limits crop production. Genome of pitaya has not been sequenced yet. In this study, we sequenced the transcriptome of pitaya as the reference and further investigat...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7020823/ https://www.ncbi.nlm.nih.gov/pubmed/32095361 http://dx.doi.org/10.7717/peerj.8540 |
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author | Zhou, Junliang Wang, Zhuang Mao, Yongya Wang, Lijuan Xiao, Tujian Hu, Yang Zhang, Yang Ma, Yuhua |
author_facet | Zhou, Junliang Wang, Zhuang Mao, Yongya Wang, Lijuan Xiao, Tujian Hu, Yang Zhang, Yang Ma, Yuhua |
author_sort | Zhou, Junliang |
collection | PubMed |
description | Pitayas (Hylocereus spp.) is an attractive, highly nutritious and commercially valuable tropical fruit. However, low-temperature damage limits crop production. Genome of pitaya has not been sequenced yet. In this study, we sequenced the transcriptome of pitaya as the reference and further investigated the proteome under low temperature. By RNAseq technique, approximately 25.3 million reads were obtained, and further trimmed and assembled into 81,252 unigene sequences. The unigenes were searched against UniProt, NR and COGs at NCBI, Pfam, InterPro and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and 57,905 unigenes were retrieved annotations. Among them, 44,337 coding sequences were predicted by Trandecoder (v2.0.1), which served as the reference database for label-free proteomic analysis study of pitaya. Here, we identified 116 Differentially Abundant Proteins (DAPs) associated with the cold stress in pitaya, of which 18 proteins were up-regulated and 98 proteins were down-regulated. KEGG analysis and other results showed that these DAPs mainly related to chloroplasts and mitochondria metabolism. In summary, chloroplasts and mitochondria metabolism-related proteins may play an important role in response to cold stress in pitayas. |
format | Online Article Text |
id | pubmed-7020823 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-70208232020-02-24 Proteogenomic analysis of pitaya reveals cold stress-related molecular signature Zhou, Junliang Wang, Zhuang Mao, Yongya Wang, Lijuan Xiao, Tujian Hu, Yang Zhang, Yang Ma, Yuhua PeerJ Bioinformatics Pitayas (Hylocereus spp.) is an attractive, highly nutritious and commercially valuable tropical fruit. However, low-temperature damage limits crop production. Genome of pitaya has not been sequenced yet. In this study, we sequenced the transcriptome of pitaya as the reference and further investigated the proteome under low temperature. By RNAseq technique, approximately 25.3 million reads were obtained, and further trimmed and assembled into 81,252 unigene sequences. The unigenes were searched against UniProt, NR and COGs at NCBI, Pfam, InterPro and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and 57,905 unigenes were retrieved annotations. Among them, 44,337 coding sequences were predicted by Trandecoder (v2.0.1), which served as the reference database for label-free proteomic analysis study of pitaya. Here, we identified 116 Differentially Abundant Proteins (DAPs) associated with the cold stress in pitaya, of which 18 proteins were up-regulated and 98 proteins were down-regulated. KEGG analysis and other results showed that these DAPs mainly related to chloroplasts and mitochondria metabolism. In summary, chloroplasts and mitochondria metabolism-related proteins may play an important role in response to cold stress in pitayas. PeerJ Inc. 2020-02-11 /pmc/articles/PMC7020823/ /pubmed/32095361 http://dx.doi.org/10.7717/peerj.8540 Text en © 2020 Zhou et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Bioinformatics Zhou, Junliang Wang, Zhuang Mao, Yongya Wang, Lijuan Xiao, Tujian Hu, Yang Zhang, Yang Ma, Yuhua Proteogenomic analysis of pitaya reveals cold stress-related molecular signature |
title | Proteogenomic analysis of pitaya reveals cold stress-related molecular signature |
title_full | Proteogenomic analysis of pitaya reveals cold stress-related molecular signature |
title_fullStr | Proteogenomic analysis of pitaya reveals cold stress-related molecular signature |
title_full_unstemmed | Proteogenomic analysis of pitaya reveals cold stress-related molecular signature |
title_short | Proteogenomic analysis of pitaya reveals cold stress-related molecular signature |
title_sort | proteogenomic analysis of pitaya reveals cold stress-related molecular signature |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7020823/ https://www.ncbi.nlm.nih.gov/pubmed/32095361 http://dx.doi.org/10.7717/peerj.8540 |
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