Genome-wide analysis of the expansin gene superfamily reveals Brassica rapa-specific evolutionary dynamics upon whole genome triplication

Krishnamurthy, Panneerselvam; Hong, Joon Ki; Kim, Jin A; Jeong, Mi‐Jeong; Lee, Yeon-Hee; Lee, Soo In

doi:10.1007/s00438-014-0935-0

Cited by 36 publications

(32 citation statements)

References 28 publications

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“…About 500 RING finger genes were identified in the Arabidopsis genome (Table S4); therefore, up to 1500 RING finger genes could be produced by the WGT event in the B. rapa genome. However, only 715 RING finger genes were identified in the B. rapa genome (Table S1), suggesting that more than 50% of duplicated RING finger genes were either lost or fixed by nonfunctionalization (silencing) after WGT565758. Similar results were also observed for other gene families in Brassica species5859.…”

Section: Discussionsupporting

confidence: 70%

“…However, only 715 RING finger genes were identified in the B. rapa genome (Table S1), suggesting that more than 50% of duplicated RING finger genes were either lost or fixed by nonfunctionalization (silencing) after WGT565758. Similar results were also observed for other gene families in Brassica species5859. In fact, our analysis of syntenic relationships between RING finger genes of B. rapa and A. thaliana showed that, only in 50 cases, the triplicated copies were well retained on all the three subgenomes (LF, MF1 and MF2) of B. rapa , while in 146 cases, only two of the three triplicated copies were retained, and in 294 cases, only one of the three triplicated copies was retained in B. rapa genome.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa

Álam

Yang

Wang

et al. 2017

Sci Rep

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More and more RING finger genes were found to be implicated in various important biological processes. In the present study, a total of 731 RING domains in 715 predicted proteins were identified in Brassica rapa genome (AA, 2n = 20), which were further divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1). The 715 RING finger proteins were further classified into 51 groups according to the presence of additional domains. 700 RING finger protein genes were mapped to the 10 chromosomes of B. rapa with a range of 47 to 111 genes for each chromosome. 667 RING finger protein genes were expressed in at least one of the six tissues examined, indicating their involvement in various physiological and developmental processes in B. rapa. Hierarchical clustering analysis of RNA-seq data divided them into seven major groups, one of which includes 231 members preferentially expressed in leaf, and constitutes then a panel of gene candidates for studying the genetic and molecular mechanisms of leafy head traits in Brassica crops. Our results lay the foundation for further studies on the classification, evolution and putative functions of RING finger protein genes in Brassica species.

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Section: Discussionsupporting

confidence: 70%

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa

Álam

Yang

Wang

et al. 2017

Sci Rep

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“…The majority of the EXPA members (82%) had three exons, while EXLB genes presented the largest number of exons, ranging from four to six, similar to Malus x Domestica and G. max (Zhang et al 2014b; Zhu et al 2014). The EXLA members had the same gene structure (4-exon/3-intron) in both Arachis species which differs from the usual 5-exon/4-intron EXLA structure of other plants (Ding et al 2016; Krishnamurthy et al 2014; Sampedro et al 2005). …”

Section: Resultsmentioning

confidence: 92%

Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene

et al. 2017

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Expansins are plant cell wall-loosening proteins involved in adaptive responses to environmental stimuli and various developmental processes. The first genome-wide analysis of the expansin superfamily in the Arachis genus identified 40 members in A. duranensis and 44 in A. ipaënsis, the wild progenitors of cultivated peanut (A. hypogaea). These expansins were further characterized regarding their subfamily classification, distribution along the genomes, duplication events, molecular structure, and phylogeny. A RNA-seq expression analysis in different Arachis species showed that the majority of these expansins are modulated in response to diverse stresses such as water deficit, root-knot nematode (RKN) infection, and UV exposure, with an expansin-like B gene (AraEXLB8) displaying a highly distinct stress-responsive expression profile. Further analysis of the AraEXLB8 coding sequences showed high conservation across the Arachis genotypes, with eight haplotypes identified. The modulation of AraEXLB8 expression in response to the aforementioned stresses was confirmed by qRT-PCR analysis in distinct Arachis genotypes, whilst in situ hybridization revealed transcripts in different root tissues according to the stress imposed. The overexpression of AraEXLB8 in soybean (Glycine max) composite plants remarkably decreased the number of galls in transformed hairy roots inoculated with RKN. This study improves the current understanding of the molecular evolution, divergence, and gene expression of expansins in Arachis, and provides molecular and functional insights into the role of expansin-like B, the less-studied plant expansin subfamily.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-017-0594-8) contains supplementary material, which is available to authorized users.

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“…Although we did not detect orthologs for some genes involved in flavonoid biosynthesis (e.g., TT4, TT6 , and AHA10 ), in accordance with the fact that the excessive gene loss is typical after polyploidy formation in eukaryotes (Sankoff et al, 2010; Wang et al, 2011), we identified orthologs of many of these genes by querying the Brassica genome databases with the sequences of A. thaliana genes involved in flavonoid biosynthesis. In addition, it has been widely suggested that the genome structures are highly conserved among Brassica species (Krishnamurthy et al, 2014; Thamilarasan et al, 2014; Dong et al, 2016). Each of the gene copies was found to be distributed in orthologous blocks by collinearity analysis between the A and C subgenomes (Figure 2).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Survey of Flavonoid Biosynthesis Genes and Gene Expression Analysis between Black- and Yellow-Seeded Brassica napus

Zhao

et al. 2016

Front. Plant Sci.

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Flavonoids, the compounds that impart color to fruits, flowers, and seeds, are the most widespread secondary metabolites in plants. However, a systematic analysis of these loci has not been performed in Brassicaceae. In this study, we isolated 649 nucleotide sequences related to flavonoid biosynthesis, i.e., the Transparent Testa (TT) genes, and their associated amino acid sequences in 17 Brassicaceae species, grouped into Arabidopsis or Brassicaceae subgroups. Moreover, 36 copies of 21 genes of the flavonoid biosynthesis pathway were identified in Arabidopsis thaliana, 53 were identified in Brassica rapa, 50 in Brassica oleracea, and 95 in B. napus, followed the genomic distribution, collinearity analysis and genes triplication of them among Brassicaceae species. The results showed that the extensive gene loss, whole genome triplication, and diploidization that occurred after divergence from the common ancestor. Using qRT-PCR methods, we analyzed the expression of 18 flavonoid biosynthesis genes in 6 yellow- and black-seeded B. napus inbred lines with different genetic background, found that 12 of which were preferentially expressed during seed development, whereas the remaining genes were expressed in all B. napus tissues examined. Moreover, 14 of these genes showed significant differences in expression level during seed development, and all but four of these (i.e., BnTT5, BnTT7, BnTT10, and BnTTG1) had similar expression patterns among the yellow- and black-seeded B. napus. Results showed that the structural genes (BnTT3, BnTT18, and BnBAN), regulatory genes (BnTTG2 and BnTT16) and three encoding transfer proteins (BnTT12, BnTT19, and BnAHA10) might play an crucial roles in the formation of different seed coat colors in B. napus. These data will be helpful for illustrating the molecular mechanisms of flavonoid biosynthesis in Brassicaceae species.

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Genome-wide analysis of the expansin gene superfamily reveals Brassica rapa-specific evolutionary dynamics upon whole genome triplication

Cited by 36 publications

References 28 publications

Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa

Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa

Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene

Genome-Wide Survey of Flavonoid Biosynthesis Genes and Gene Expression Analysis between Black- and Yellow-Seeded Brassica napus

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