Genome-wide investigation of the MADS gene family and dehulling genes in tartary buckwheat (Fagopyrum tataricum)

Liu, Moyang; Fu, Qiankun; Ma, Zhaotang; Sun, Wenjun; Huang, Li; Wu, Qi; Tang, Zizhong; Bu, Tongliang; Li, Chenglei; Chen, Hui

doi:10.1007/s00425-019-03089-3

Cited by 41 publications

(22 citation statements)

References 51 publications

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“…We downloaded the whole genome in the gff, cds, pep and FASTA file format from the EnsemblPlants- Cucumber genome database (ASM407v2) ( ) ( Li et al, 2019b ). The TPS (Glyco-transf-20, PF00982) and TPP (Trehalose_PPase, PF02358) domains’ hidden Markov Models (HMM) were downloaded from the Pfam database ( ) ( Liu et al, 2019a ). HMMsearch software and the TPS and TPP’s HMMs were used to search all possible TPS candidate sequences containing typical TPS and TPP domains under a Linux system ( Chen et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

Dan

Niu

Wang

et al. 2021

PeerJ

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Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber TPS family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, cis-acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven CsTPS genes in the cucumber genome and named CsTPS1–CsTPS7 according to their locations in the chromosomes. Seven CsTPS genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from Arabidopsis, rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from Arabidopsis and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16–17 introns, while Class II genes (except CsTPS7) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, CsTPS genes possessed numerous cis-acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of CsTPS genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of CsTPSs under different treatments showed that CsTPS genes may participate in the response to abiotic stress, plant hormones and sugar treatments.

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Section: Methodsmentioning

confidence: 99%

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

Dan

Niu

Wang

et al. 2021

PeerJ

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“…The recent completion of Tartary buckwheat genome sequencing allowed us to study the NAC gene family of Tartary buckwheat at the genome level [52]. To date, only the ARF and MADS gene families have been systematically analyzed in Tartary buckwheat [53, 54]. In this article, we report the gene structure, chromosomal location, duplication, global expression and potential developmental roles of Tartary buckwheat NAC genes.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)

et al. 2019

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BackgroundThe NAC (NAM, ATAF1/2, and CUC2) transcription factor family represents a group of large plant-specific transcriptional regulators, participating in plant development and response to external stress. However, there is no comprehensive study on the NAC genes of Tartary buckwheat (Fagopyrum tataricum), a large group of extensively cultivated medicinal and edible plants. The recently published Tartary buckwheat genome permits us to explore all the FtNAC genes on a genome-wide basis.ResultsIn the present study, 80 NAC (FtNAC) genes of Tartary buckwheat were obtained and named uniformly according to their distribution on chromosomes. Phylogenetic analysis of NAC proteins in both Tartary buckwheat and Arabidopsis showed that the FtNAC proteins are widely distributed in 15 subgroups with one subgroup unclassified. Gene structure analysis found that multitudinous FtNAC genes contained three exons, indicating that the structural diversity in Tartary buckwheat NAC genes is relatively low. Some duplication genes of FtNAC have a conserved structure that was different from others, indicating that these genes may have a variety of functions. By observing gene expression, we found that FtNAC genes showed abundant differences in expression levels in various tissues and at different stages of fruit development.ConclusionsIn this research, 80 NAC genes were identified in Tartary buckwheat, and their phylogenetic relationships, gene structures, duplication, global expression and potential roles in Tartary buckwheat development were studied. Comprehensive analysis will be useful for a follow-up study of functional characteristics of FtNAC genes and for the development of high-quality Tartary buckwheat varieties.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5500-0) contains supplementary material, which is available to authorized users.

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“…The auxin response factor gene family has been identified from tartary buckwheat, and the potential role of Fagopyrum tataricum ARF2 ( FtARF2 ) in tartary Buckwheat fruit size has been deeply studied [27, 28]. Meanwhile, the MADS gene family has also been identified from tartary buckwheat [29]. With the increasing demand for tartary buckwheat, understanding the potential regulatory mechanism of growth and development has been a key problem.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum)

Liu

Sun

et al. 2019

BMC Plant Biol

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Background AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis thaliana ( A. thaliana ) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of tartary buckwheat ( Fagopyum tataricum ), which is an important edible and medicinal crop. The recently published whole genome sequence of tartary buckwheat allowed us to study the tissue and expression profiles of AP2/ERF genes in tartary buckwheat on a genome-wide basis. Results In this study, 134 AP2/ERF genes of tartary buckwheat ( FtAP2/ERF ) were identified and renamed according to the chromosomal distribution of the FtAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic tree analysis, namely, AP2 (15 members), ERF (116 members) and RAV (3 members). A total of 10 motifs were detected in tartary buckwheat AP2/ERF genes, and some of the unique motifs were found to be important for the function of AP2/ERF genes. Conclusion A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and fruit development stages by quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of tartary buckwheat, and genes that might regulate flower and fruit development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of FtAP2/ERF genes and improvement of tartary buckwheat crops. Electronic supplementary material The online version of this article (10.1186/s12870-019-1681-6) contains supplementary material, which is available to authorized users.

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Genome-wide investigation of the MADS gene family and dehulling genes in tartary buckwheat (Fagopyrum tataricum)

Cited by 41 publications

References 51 publications

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)

Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum)

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