Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.)
The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, an...
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PeerJ Inc.
2020-07-01
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| author | Min Yang Chenping Zhou Hu Yang Ruibin Kuang Bingxiong Huang Yuerong Wei |
| author_facet | Min Yang Chenping Zhou Hu Yang Ruibin Kuang Bingxiong Huang Yuerong Wei |
| author_sort | Min Yang |
| collection | DOAJ |
| description | The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene structures and protein motifs according to analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLHs varied from one to 10 with an average of five. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of CpbHLHs. |
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| last_indexed | 2024-03-09T07:29:07Z |
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| spelling | doaj.art-4b06b0a98aef4a04ad5b1560691936bc2023-12-03T06:47:12ZengPeerJ Inc.PeerJ2167-83592020-07-018e931910.7717/peerj.9319Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.)Min Yang0Chenping Zhou1Hu Yang2Ruibin Kuang3Bingxiong Huang4Yuerong Wei5Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, ChinaGuangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, ChinaGuangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, ChinaGuangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, ChinaGuangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, ChinaGuangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, ChinaThe basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene structures and protein motifs according to analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLHs varied from one to 10 with an average of five. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of CpbHLHs.https://peerj.com/articles/9319.pdfPapaya Genome-wide analysis bHLH transcription factors Abiotic stress Expression analysis |
| spellingShingle | Min Yang Chenping Zhou Hu Yang Ruibin Kuang Bingxiong Huang Yuerong Wei Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.) PeerJ Papaya Genome-wide analysis bHLH transcription factors Abiotic stress Expression analysis |
| title | Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.) |
| title_full | Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.) |
| title_fullStr | Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.) |
| title_full_unstemmed | Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.) |
| title_short | Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.) |
| title_sort | genome wide analysis of basic helix loop helix transcription factors in papaya carica papaya l |
| topic | Papaya Genome-wide analysis bHLH transcription factors Abiotic stress Expression analysis |
| url | https://peerj.com/articles/9319.pdf |
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