Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species
Abstract Background Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available. Results This study identified 55, 58, 50...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-04-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-023-04235-6 |
| _version_ | 1797841052878503936 |
|---|---|
| author | Zengzhi Si Lianjun Wang Zhixin Ji Yake Qiao Kai Zhang Jinling Han |
| author_facet | Zengzhi Si Lianjun Wang Zhixin Ji Yake Qiao Kai Zhang Jinling Han |
| author_sort | Zengzhi Si |
| collection | DOAJ |
| description | Abstract Background Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available. Results This study identified 55, 58, 50 and 47 VQ genes from sweetpotato (I. batatas), I.triflida, I. triloba and I. nil, respectively. The phylogenetic analysis revealed that the VQ genes formed eight clades (I–VII), and the members in the same group exhibited similar exon–intron structure and conserved motifs distribution. The distribution of the VQ genes among the chromosomes of Ipomoea species was disproportional, with no VQ genes mapped on a few of each species' chromosomes. Duplication analysis suggested that segmental duplication significantly contributes to their expansion in sweetpotato, I.trifida, and I.triloba, while the segmental and tandem duplication contributions were comparable in I.nil. Cis-regulatory elements involved in stress responses, such as W-box, TGACG-motif, CGTCA-motif, ABRE, ARE, MBS, TCA-elements, LTR, and WUN-motif, were detected in the promoter regions of the VQ genes. A total of 30 orthologous groups were detected by syntenic analysis of the VQ genes. Based on the analysis of RNA-seq datasets, it was found that the VQ genes are expressed distinctly among different tissues and hormone or stress treatments. A total of 40 sweetpotato differentially expressed genes (DEGs) refer to biotic (sweetpotato stem nematodes and Ceratocystis fimbriata pathogen infection) or abiotic (cold, salt and drought) stress treatments were detected. Moreover, IbVQ8, IbVQ25 and IbVQ44 responded to the five stress treatments and were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis. Conclusions Our study may provide new insights into the evolution of VQ genes in the four Ipomoea genomes and contribute to the future molecular breeding of sweetpotatoes. |
| first_indexed | 2024-04-09T16:24:45Z |
| format | Article |
| id | doaj.art-07c785da242f4c0c92e8ea5f1a679fff |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-09T16:24:45Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-07c785da242f4c0c92e8ea5f1a679fff2023-04-23T11:13:06ZengBMCBMC Plant Biology1471-22292023-04-0123111810.1186/s12870-023-04235-6Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea speciesZengzhi Si0Lianjun Wang1Zhixin Ji2Yake Qiao3Kai Zhang4Jinling Han5Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and TechnologyInstitute of Food Corps, Hubei Academy of Agricultural SciencesHebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and TechnologyHebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and TechnologyHebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and TechnologyHebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and TechnologyAbstract Background Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available. Results This study identified 55, 58, 50 and 47 VQ genes from sweetpotato (I. batatas), I.triflida, I. triloba and I. nil, respectively. The phylogenetic analysis revealed that the VQ genes formed eight clades (I–VII), and the members in the same group exhibited similar exon–intron structure and conserved motifs distribution. The distribution of the VQ genes among the chromosomes of Ipomoea species was disproportional, with no VQ genes mapped on a few of each species' chromosomes. Duplication analysis suggested that segmental duplication significantly contributes to their expansion in sweetpotato, I.trifida, and I.triloba, while the segmental and tandem duplication contributions were comparable in I.nil. Cis-regulatory elements involved in stress responses, such as W-box, TGACG-motif, CGTCA-motif, ABRE, ARE, MBS, TCA-elements, LTR, and WUN-motif, were detected in the promoter regions of the VQ genes. A total of 30 orthologous groups were detected by syntenic analysis of the VQ genes. Based on the analysis of RNA-seq datasets, it was found that the VQ genes are expressed distinctly among different tissues and hormone or stress treatments. A total of 40 sweetpotato differentially expressed genes (DEGs) refer to biotic (sweetpotato stem nematodes and Ceratocystis fimbriata pathogen infection) or abiotic (cold, salt and drought) stress treatments were detected. Moreover, IbVQ8, IbVQ25 and IbVQ44 responded to the five stress treatments and were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis. Conclusions Our study may provide new insights into the evolution of VQ genes in the four Ipomoea genomes and contribute to the future molecular breeding of sweetpotatoes.https://doi.org/10.1186/s12870-023-04235-6Ipomoea speciesVQ genesPhylogenetic analysisChromosome locationDuplication analysisCis-regulatory elements |
| spellingShingle | Zengzhi Si Lianjun Wang Zhixin Ji Yake Qiao Kai Zhang Jinling Han Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species BMC Plant Biology Ipomoea species VQ genes Phylogenetic analysis Chromosome location Duplication analysis Cis-regulatory elements |
| title | Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species |
| title_full | Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species |
| title_fullStr | Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species |
| title_full_unstemmed | Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species |
| title_short | Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species |
| title_sort | genome wide comparative analysis of the valine glutamine motif containing genes in four ipomoea species |
| topic | Ipomoea species VQ genes Phylogenetic analysis Chromosome location Duplication analysis Cis-regulatory elements |
| url | https://doi.org/10.1186/s12870-023-04235-6 |
| work_keys_str_mv | AT zengzhisi genomewidecomparativeanalysisofthevalineglutaminemotifcontaininggenesinfouripomoeaspecies AT lianjunwang genomewidecomparativeanalysisofthevalineglutaminemotifcontaininggenesinfouripomoeaspecies AT zhixinji genomewidecomparativeanalysisofthevalineglutaminemotifcontaininggenesinfouripomoeaspecies AT yakeqiao genomewidecomparativeanalysisofthevalineglutaminemotifcontaininggenesinfouripomoeaspecies AT kaizhang genomewidecomparativeanalysisofthevalineglutaminemotifcontaininggenesinfouripomoeaspecies AT jinlinghan genomewidecomparativeanalysisofthevalineglutaminemotifcontaininggenesinfouripomoeaspecies |