Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis)

Song, Xiaoming; Liu, Tongkun; Duan, Weike; Ma, Qinghua; Ren, Jun; Wang, Zhen; Li, Ying; Hou, Xilin

doi:10.1016/j.ygeno.2013.12.004

Cited by 122 publications

(144 citation statements)

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“…rapa genes belonging to different gene families or having important biological functions have been systematically analyzed. Based on the genome sequencing and comparative genomic study of B. rapa, the evolution of many gene families or categories such as circadian clock genes, 41 resistance genes, 42 stress response genes, [43][44][45] glucosinolate genes, 38 anthocyanin biosynthesis genes, 46 phytohormone-related genes, 47 certain transcript factor families 48 and other genes, [49][50][51][52][53][54] were accurately determined individually and studied in detail. Moreover, some functionally important genes related to self-incompatibility, 55,56 male sterility, 57 flowering regulation, 58-60 leaf heading 61 or color 62 have been identified or cloned, and functional studies have been conducted for some of these genes.…”

Section: Two-step Theory To Illustrate the Wgt Process Inmentioning

confidence: 99%

Genome Triplication Drove the Diversification of Brassica Plants

Cheng¹,

Wu²,

Liang³

et al. 2015

Compendium of Plant Genomes

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The genus Brassica belongs to the plant family Brassicaceae, which includes many important crop species that are used as oilseed, condiments, or vegetables throughout the world. Brassica plants comprise many diverse species, and each species contains rich morphotypes showing extreme traits. Brassica species experienced an extra whole genome triplication (WGT) event compared with the model plant Arabidopsis thaliana. Whole genome sequencing of the Brassica species Brassica rapa, Brassica oleracea and others demonstrated that WGT plays an important role in the speciation and morphotype diversification of Brassica plants. Comparative genomic analysis based on the genome sequences of B. rapa and A. thaliana clearly identified the WGT event and further demonstrated that the translocated Proto-Calepine Karyotype (tPCK, n57) was the diploid ancestor of the three subgenomes in B. rapa. Following WGT, subsequent extensive genome fractionation, block reshuffling and chromosome reduction accompanied by paleocentromere descent from the three tPCK subgenomes during the rediploidization process produced stable diploid species. Genomic rearrangement of the diploid species and their hybridization then contributed to Brassica speciation. The subgenome dominance effect and biased gene retention, such as the over-retention of auxin-related genes after WGT, promoted functional gene evolution and thus propelled the expansion of rich morphotypes in the Brassica species. In conclusion, the WGT event initiated subsequent genomic and gene-level evolution, which further drove Brassica speciation and created rich morphotypes in each species. GENUS BRASSICA IN BRASSICACEAE Plants of the genus Brassica are grouped into the tribe Brassiceae, which belongs to the plant family Brassicaceae. Brassicaceae comprises a large family of plants that exhibit common and distinct features in their flowers. The flowers have cruciform petals and six stamens, two of which are short outer stamens. In total, Brassicaceae is composed of 3709 species and 338 genera, 1 with 308 of the 338 genera further assigned to 44 tribes.2 Among the abundant Brassicaceae species, the genus Brassica is important because it contains many economically valuable crops that are used as oilseeds, condiments, and culinary vegetables. Brassica species share an additional common feature in that they all experienced an extra whole genome triplication (WGT) event, which occurred approximately 9-15 million years ago 3,4 or even approximately 28 million years ago. 5-7THE U'S TRIANGLE MODEL DESCRIBES THE RELATIONSHIP AMONG BRASSICA CROPS Six species of the genus Brassica are used widely throughout the world as oilseed, condiments, fodder or vegetable crops. Three of these species are diploid (Brassica rapa, n510; B. nigra, n58; and B. oleracea, n59), whereas the other three are allotetraploids (B. juncea, n518; B. napus, n519; B. carinata, n517) derived from each pair of the three diploid species. The genetic relationships of these species were identified and confirmed by extensive experi...

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Section: Two-step Theory To Illustrate the Wgt Process Inmentioning

confidence: 99%

Genome Triplication Drove the Diversification of Brassica Plants

Cheng¹,

Wu²,

Liang³

et al. 2015

Compendium of Plant Genomes

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“…Recently, increasing number of studies on the GRAS gene family in plants has been published. For example, the GRAS gene family has been reported in Arabidopsis, rice (Tian et al, 2004), grape (Sun et al, 2011), cabbage (Song et al, 2014), physic nut (Jatropha curcas L.) (Wu et al, 2015), and tobacco ; however, there have been no reports on the GRAS gene family in B. kirghisorum. Therefore, this study investigated 19 BkGRAS genes obtained through transcriptome sequencing.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic analyses of GRAS genes in Betula kirghisorum based on transcriptome data

Yang

Cui

2016

Genet. Mol. Res.

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ABSTRACT. The transcriptomes of salt-stressed and unstressed Betula kirghisorum plants were analyzed using high throughput sequencing technology. A total of 52,239,804 and 51,772,998 clean reads were obtained from the two libraries, respectively, and de novo assembled into 60,545 all-unigenes. A total of 39,997 unigenes were annotated using public databases. Overall, 7206 genes were differentially expressed in unigenes and were involved in 127 pathways. Thirteen transcription factor families were identified in B. kirghisorum, including GRAS proteins, which are plant-specific transcription factors. By using bioinformatic methods to predict and analyze physicochemical properties, structural data were obtained on the 19 potential GRAS proteins. The results revealed that these proteins are hydrophilic, with significant differences in their length and molecular weight. The main secondary structures were alpha helices and random coils. BkGRAS proteins possess typical GRAS domains: LHR I; VHIID motif; LHR II; PFYRE motif; and SAW motif. In the majority of BkGRAS proteins, AGG, AGA, UCU, GCU, GGG, CCA, GUU, GUG, AUU, GAU, and AAG codons were used preferentially. Aside from the BkGRAS17 gene (relative synonymous codon usage (RSCU) = 1.20), usage of the UUA codon by other BkGRAS genes was low (RSCU < 1.0). The effective number of codons showed that BkGRAS genes have low codon bias. Subcellular localization analysis that predicted these proteins are found in the nucleus, cytoplasm, or chloroplast. BkGRAS proteins were divided into six subfamilies: SCR, LISCL, SCL3, DELLA, HAM, and PAT1. These results provide important information for the further functional study of GRAS genes in B. kirghisorum.

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“…Proteins with high sequence identity generally have similar functions across different species (Song et al, 2014). Thus, the phylogenetic analysis of GRAS proteins from different plants will provide a solid foundation for functional studies of NtGRASLs in future.…”

Section: Phylogenetic Analysis Of the Gras Gene Family And Calculatiomentioning

confidence: 99%

“…To date, at least 33, 60, and 48 GRAS genes have been identified, respectively, in the whole genome of Arabidopsis, rice, and Chinese cabbage, many of which have been functionally characterized (Tian et al, 2004;Itoh et al, 2005;Lee et al, 2008;Tong et al, 2009;Song et al, 2014). Furthermore, two GRAS proteins have already been described in the model legumes Medicago truncatula and Lotus japonicus (Kalo et al, 2005;Smit et al, 2005;Heckmann et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Homology-based analysis of the GRAS gene family in tobacco

Chen¹,

Tai²,

Wang³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Members of the GRAS gene family are important transcriptional regulators. In this study, 21 GRAS genes were identified from tobacco, and were classified into eight subgroups according to the classification of Arabidopsis thaliana. Here, we provide a preliminary overview of this gene family in tobacco, describing the gene structure, gene expression, protein motif organization, phylogenetic analysis, and comparative analysis in tobacco, Arabidopsis, and rice. Using the sequences of 21 GRAS genes in Arabidopsis to search against the American tobacco genome database, 21 homologous GRAS genes in tobacco were identified. Sequence analysis indicates that these GRAS proteins have five conserved domains, which is consistent with their counterparts in other plants. Phylogenetic analyses divided the GRAS gene family into eight subgroups, each of which has distinct conserved domains and biological functions. Furthermore, the expression pattern of these 21 GRAS genes reveals that most are expressed in all six 15189Cloning and expression analysis of GRAS genes in tobacco ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 15188-15200 (2015) tissues studied; however, some have tissue specificity. Taken together, this comprehensive analysis will provide a rich resource to assist in the study of GRAS protein functions in tobacco.

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Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis)

Cited by 122 publications

References 49 publications

Genome Triplication Drove the Diversification of Brassica Plants

Genome Triplication Drove the Diversification of Brassica Plants

Bioinformatic analyses of GRAS genes in Betula kirghisorum based on transcriptome data

Homology-based analysis of the GRAS gene family in tobacco

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