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...
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PeerJ Inc.
2020-02-01
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| Online Access: | https://peerj.com/articles/8540.pdf |
| _version_ | 1827608233349480448 |
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| author | Junliang Zhou Zhuang Wang Yongya Mao Lijuan Wang Tujian Xiao Yang Hu Yang Zhang Yuhua Ma |
| author_facet | Junliang Zhou Zhuang Wang Yongya Mao Lijuan Wang Tujian Xiao Yang Hu Yang Zhang Yuhua Ma |
| author_sort | Junliang Zhou |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T07:08:07Z |
| format | Article |
| id | doaj.art-3352e21e6c6343b19ee7f8acd2843b9e |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:08:07Z |
| publishDate | 2020-02-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-3352e21e6c6343b19ee7f8acd2843b9e2023-12-03T09:20:52ZengPeerJ Inc.PeerJ2167-83592020-02-018e854010.7717/peerj.8540Proteogenomic analysis of pitaya reveals cold stress-related molecular signatureJunliang Zhou0Zhuang Wang1Yongya Mao2Lijuan Wang3Tujian Xiao4Yang Hu5Yang Zhang6Yuhua Ma7Guizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, ChinaGuizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, ChinaGuizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, ChinaGuizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, ChinaGuizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, ChinaZhejiang Academy of Forestry, Hangzhou, Zhejiang, ChinaFudan University, Institutes of Biomedical Sciences, Shanghai, Shanghai, ChinaGuizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, ChinaPitayas (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.https://peerj.com/articles/8540.pdfTranscriptomeShotgun label-free ProteomicPitayaCold stressProteins expression |
| spellingShingle | Junliang Zhou Zhuang Wang Yongya Mao Lijuan Wang Tujian Xiao Yang Hu Yang Zhang Yuhua Ma Proteogenomic analysis of pitaya reveals cold stress-related molecular signature PeerJ Transcriptome Shotgun label-free Proteomic Pitaya Cold stress Proteins expression |
| 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 | Transcriptome Shotgun label-free Proteomic Pitaya Cold stress Proteins expression |
| url | https://peerj.com/articles/8540.pdf |
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