Genome-Wide Identification, Phylogeny, Duplication, and Expression Analyses of Two-Component System Genes in Chinese Cabbage (Brassica rapa ssp. pekinensis)

Liu, Zhenning; Zhang, Mei; Kong, Linggang; Lv, Yanxia; Zou, Minghua; Lü, Gang; Cao, Jiashu; Yu, Xiaolin

doi:10.1093/dnares/dsu004

Cited by 54 publications

(104 citation statements)

References 112 publications

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“…The HK(L) proteins in these nine species were divided into seven distinct clades, the cytokinin receptor, ethylene receptor, PHY-like, CKI1-like, CKI2/AHK5-like, AHK1-like, and PDK-like subfamilies; this finding is similar to that reported in previous studies [5,10]. Tomato HL(L)s usually have much closer relationships to that of soybean and Lotus japonicas than that of other species, which both are leguminous crops.…”

Section: Resultssupporting

confidence: 88%

“…In this study, 31 tomato TCS genes were detected, and most genes appear to be regulated by drought- and salt-stresses (Figure 12). Most of tomato TCS genes negatively respond to salt stress, and similar results were found in soybean and Chinese cabbage [10,23]. However, 18 out of 31 genes are obviously induced by drought treatment, which differ from that in Arabidopsis , soybean and Chinese cabbage [10,17,18,19,23].…”

Section: Discussionmentioning

confidence: 76%

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Genome-Wide Identification and Expression Analysis of Two-Component System Genes in Tomato

et al. 2016

IJMS

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The two-component system (TCS), which comprises histidine kinases (HKs), phosphotransfers (HPs), and response regulator proteins (RRs), plays pivotal roles in regulating plant growth, development, and responses to biotic and abiotic stresses. TCS genes have been comprehensively identified and investigated in various crops but poorly characterized in tomato. In this work, a total of 65 TCS genes consisting of 20 HK(L)s, six HPs, and 39 RRs were identified from tomato genome. The classification, gene structures, conserved domains, chromosome distribution, phylogenetic relationship, gene duplication events, and subcellular localization of the TCS gene family were predicted and analyzed in detail. The amino acid sequences of tomato TCS family members, except those of type-B RRs, are highly conserved. The gene duplication events of the TCS family mainly occurred in the RR family. Furthermore, the expansion of RRs was attributed to both segment and tandem duplication. The subcellular localizations of the selected green fluorescent protein (GFP) fusion proteins exhibited a diverse subcellular targeting, thereby confirming their predicted divergent functionality. The majority of TCS family members showed distinct organ- or development-specific expression patterns. In addition, most of TCS genes were induced by abiotic stresses and exogenous phytohormones. The full elucidation of TCS elements will be helpful for comprehensive analysis of the molecular biology and physiological role of the TCS superfamily.

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Section: Resultssupporting

confidence: 88%

Section: Discussionmentioning

confidence: 76%

Genome-Wide Identification and Expression Analysis of Two-Component System Genes in Tomato

et al. 2016

IJMS

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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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“…For phytohormone treatments, one of the following solutions of 100 μM GA, 100 μM MeJA, and 100 μM ABA was sprayed on all leaves (Liu et al, 2014; Duan et al, 2015). Control plants were sprayed with distilled water.…”

Section: Methodsmentioning

confidence: 99%

Genomic, Molecular Evolution, and Expression Analysis of Genes Encoding Putative Classical AGPs, Lysine-Rich AGPs, and AG Peptides in Brassica rapa

Han¹,

Dong²,

Cui³

et al. 2017

Front. Plant Sci.

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Arabinogalactan proteins (AGPs) belong to a class of Pro/Hyp-rich glycoproteins and are some of the most complex types of macromolecules found in plants. In the economically important plant species, Brassica rapa, only chimeric AGPs have been identified to date. This has significantly limited our understanding of the functional roles of AGPs in this plant. In this study, 64 AGPs were identified in the genome of B. rapa, including 33 classical AGPs, 28 AG peptides and three lys-rich AGPs. Syntenic gene analysis between B. rapa and A. thaliana suggested that the whole genome triplication event dominated the expansion of the AGP gene family in B. rapa. This resulted in a high retained proportion of the AGP family in the B. rapa genome, especially in the least fractionated subgenome. Phylogenetic and motif analysis classified the classical AGPs into six clades and three orphan genes, and the AG peptides into three clades and five orphan genes. Classical AGPs has a faster rate of molecular evolution than AG peptides revealed by estimation of molecular evolution rates. However, no significant differences were observed between classical AGPs and lys-rich AGPs. Under control conditions and in response to phytohormones treatment, a complete expression profiling experiment has identified five anther-specific AGPs and quite a number of AGPs responding to abscisic acid, methyl jasmonate and/or gibberellin. In this study, we presented a bioinformatics approach to identify important types of AGPs. Moreover, the association between their function and their protein structure, as well as the evolution and the expression of AGP genes were investigated, which might provide fundamental information for revealing the roles of AGPs in B. rapa.

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Genome-Wide Identification, Phylogeny, Duplication, and Expression Analyses of Two-Component System Genes in Chinese Cabbage (Brassica rapa ssp. pekinensis)

Cited by 54 publications

References 112 publications

Genome-Wide Identification and Expression Analysis of Two-Component System Genes in Tomato

Genome-Wide Identification and Expression Analysis of Two-Component System Genes in Tomato

Genome Triplication Drove the Diversification of Brassica Plants

Genomic, Molecular Evolution, and Expression Analysis of Genes Encoding Putative Classical AGPs, Lysine-Rich AGPs, and AG Peptides in Brassica rapa

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