Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.)
The most predominant type of resistance (R) genes contain nucleotide-binding sites and leucine-rich repeat (NBS-LRR) domains, characterization of which is helpful for plant resistance improvement. However, the NBS genes of Ipomoea trifida (H.B.K.) remain insufficient to date. In this study, a genome...
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| Format: | Article |
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De Gruyter
2022-05-01
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| Series: | Open Life Sciences |
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| Online Access: | https://doi.org/10.1515/biol-2022-0052 |
| _version_ | 1811203777836875776 |
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| author | Si Zengzhi Qiao Yake Zhang Kai Ji Zhixin Han Jinling |
| author_facet | Si Zengzhi Qiao Yake Zhang Kai Ji Zhixin Han Jinling |
| author_sort | Si Zengzhi |
| collection | DOAJ |
| description | The most predominant type of resistance (R) genes contain nucleotide-binding sites and leucine-rich repeat (NBS-LRR) domains, characterization of which is helpful for plant resistance improvement. However, the NBS genes of Ipomoea trifida (H.B.K.) remain insufficient to date. In this study, a genome-wide analysis of the NBS-encoding gene in I. trifida (H.B.K.) was carried out. A total of 442 NBS encoding genes were identified, amounting to 1.37% of the total genes of I. trifida (H.B.K.). Based on the analysis of the domains, the identified ItfNBS genes were further classified into seven groups: CNL, NL, CN, N, TNL, TN, and RNL. Phylogenetic analysis showed that the I. trifida NBS genes clustered into three independent clades: RNL, TNL, and CNL. Chromosome location analysis revealed that the distribution of ItfNBS genes in chromosomes was uneven, with a number ranging from 3 to 45. Multiple stress-related regulatory elements were detected in the promoters of the NBS-encoding genes, and their expression profiles were obtained. The qRT-PCR analysis revealed that IbNBS10, IbNBS20, IbNBS258, and IbNBS88 responded to stem nematode infection. These results provide critical proof for further characterization and analysis of NBS-encoding genes with important functions. |
| first_indexed | 2024-04-12T03:00:55Z |
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| id | doaj.art-876bd8f7447c48c386abe07a7b66b449 |
| institution | Directory Open Access Journal |
| issn | 2391-5412 |
| language | English |
| last_indexed | 2024-04-12T03:00:55Z |
| publishDate | 2022-05-01 |
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| spelling | doaj.art-876bd8f7447c48c386abe07a7b66b4492022-12-22T03:50:40ZengDe GruyterOpen Life Sciences2391-54122022-05-0117149751110.1515/biol-2022-0052Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.)Si Zengzhi0Qiao Yake1Zhang Kai2Ji Zhixin3Han Jinling4Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinghuangdao, 066000, Hebei Province, ChinaHebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinghuangdao, 066000, Hebei Province, ChinaHebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinghuangdao, 066000, Hebei Province, ChinaHebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinghuangdao, 066000, Hebei Province, ChinaHebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinghuangdao, 066000, Hebei Province, ChinaThe most predominant type of resistance (R) genes contain nucleotide-binding sites and leucine-rich repeat (NBS-LRR) domains, characterization of which is helpful for plant resistance improvement. However, the NBS genes of Ipomoea trifida (H.B.K.) remain insufficient to date. In this study, a genome-wide analysis of the NBS-encoding gene in I. trifida (H.B.K.) was carried out. A total of 442 NBS encoding genes were identified, amounting to 1.37% of the total genes of I. trifida (H.B.K.). Based on the analysis of the domains, the identified ItfNBS genes were further classified into seven groups: CNL, NL, CN, N, TNL, TN, and RNL. Phylogenetic analysis showed that the I. trifida NBS genes clustered into three independent clades: RNL, TNL, and CNL. Chromosome location analysis revealed that the distribution of ItfNBS genes in chromosomes was uneven, with a number ranging from 3 to 45. Multiple stress-related regulatory elements were detected in the promoters of the NBS-encoding genes, and their expression profiles were obtained. The qRT-PCR analysis revealed that IbNBS10, IbNBS20, IbNBS258, and IbNBS88 responded to stem nematode infection. These results provide critical proof for further characterization and analysis of NBS-encoding genes with important functions.https://doi.org/10.1515/biol-2022-0052sweet potatonbs-encoding genesphylogenetic analysischromosomes locationexpression profiles |
| spellingShingle | Si Zengzhi Qiao Yake Zhang Kai Ji Zhixin Han Jinling Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) Open Life Sciences sweet potato nbs-encoding genes phylogenetic analysis chromosomes location expression profiles |
| title | Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) |
| title_full | Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) |
| title_fullStr | Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) |
| title_full_unstemmed | Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) |
| title_short | Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) |
| title_sort | genome wide identification and characterization of nbs encoding genes in the sweet potato wild ancestor ipomoea trifida h b k |
| topic | sweet potato nbs-encoding genes phylogenetic analysis chromosomes location expression profiles |
| url | https://doi.org/10.1515/biol-2022-0052 |
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