Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii)
The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich i...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2022-09-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/13981.pdf |
| _version_ | 1797425607880998912 |
|---|---|
| author | Wenjuan Liu Yaqi Yi Jingyi Zhuang Chang Ge Yunpeng Cao Lin Zhang Meilan Liu |
| author_facet | Wenjuan Liu Yaqi Yi Jingyi Zhuang Chang Ge Yunpeng Cao Lin Zhang Meilan Liu |
| author_sort | Wenjuan Liu |
| collection | DOAJ |
| description | The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms. |
| first_indexed | 2024-03-09T08:18:33Z |
| format | Article |
| id | doaj.art-61f1f8b5f1724b26a17befe2942d3e61 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:18:33Z |
| publishDate | 2022-09-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-61f1f8b5f1724b26a17befe2942d3e612023-12-02T21:55:27ZengPeerJ Inc.PeerJ2167-83592022-09-0110e1398110.7717/peerj.13981Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii)Wenjuan Liu0Yaqi Yi1Jingyi Zhuang2Chang Ge3Yunpeng Cao4Lin Zhang5Meilan Liu6Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, ChinaKey Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, ChinaKey Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, ChinaSchool of Urban Design, Wuhan University, Wuhan, Hubei, ChinaKey Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, ChinaKey Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, ChinaKey Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, ChinaThe basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms.https://peerj.com/articles/13981.pdfVfbHLHsTung treeTissue-specific expressionFlower and seed developmentLow temperature |
| spellingShingle | Wenjuan Liu Yaqi Yi Jingyi Zhuang Chang Ge Yunpeng Cao Lin Zhang Meilan Liu Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii) PeerJ VfbHLHs Tung tree Tissue-specific expression Flower and seed development Low temperature |
| title | Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii) |
| title_full | Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii) |
| title_fullStr | Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii) |
| title_full_unstemmed | Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii) |
| title_short | Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii) |
| title_sort | genome wide identification and transcriptional profiling of the basic helix loop helix gene family in tung tree vernicia fordii |
| topic | VfbHLHs Tung tree Tissue-specific expression Flower and seed development Low temperature |
| url | https://peerj.com/articles/13981.pdf |
| work_keys_str_mv | AT wenjuanliu genomewideidentificationandtranscriptionalprofilingofthebasichelixloophelixgenefamilyintungtreeverniciafordii AT yaqiyi genomewideidentificationandtranscriptionalprofilingofthebasichelixloophelixgenefamilyintungtreeverniciafordii AT jingyizhuang genomewideidentificationandtranscriptionalprofilingofthebasichelixloophelixgenefamilyintungtreeverniciafordii AT changge genomewideidentificationandtranscriptionalprofilingofthebasichelixloophelixgenefamilyintungtreeverniciafordii AT yunpengcao genomewideidentificationandtranscriptionalprofilingofthebasichelixloophelixgenefamilyintungtreeverniciafordii AT linzhang genomewideidentificationandtranscriptionalprofilingofthebasichelixloophelixgenefamilyintungtreeverniciafordii AT meilanliu genomewideidentificationandtranscriptionalprofilingofthebasichelixloophelixgenefamilyintungtreeverniciafordii |