Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Alam I

PROVIDER: S-EPMC5240574 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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

Alam Intikhab I Yang Yan-Qing YQ Wang Yong Y Zhu Mei-Lan ML Wang Heng-Bo HB Chalhoub Boulos B Lu Yun-Hai YH

Scientific reports 20170117

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 additiona ...[more]

PMID: 28094809

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Project description:BACKGROUND:Members of the MtN3/saliva/SWEET gene family are present in various organisms and are highly conserved. Their precise biochemical functions remain unclear, especially in Chinese cabbage. Based on the whole genome sequence, this study aims to identify the MtN3/saliva/SWEETs family members in Chinese cabbage and to analyze their classification, gene structure, chromosome distribution, phylogenetic relationship, expression pattern, and biological functions. RESULTS:We identified 34 SWEET genes in Chinese cabbage and analyzed their localization on chromosomes and transmembrane regions of their corresponding proteins. Analysis of a phylogenetic tree indicated that there were at least 17 supposed ancestor genes before the separation in Brassica rapa and Arabidopsis. The expression patterns of these genes in different tissues and flower developmental stages of Chinese cabbage showed that they are mainly involved in reproductive development. The Ka/Ks ratio between paralogous SWEET gene pairs of B. rapa were far less than 1. In our previous study, At2g39060 homologous gene Bra000116 (BraSWEET9, also named BcNS, Brassica Nectary and Stamen) played an important role during flower development in Chinese cabbage. Instantaneous expression experiments in onion epidermal cells showed that the gene encoding this protein is localized to the plasma membrane. A basal nectary split is the phenotype of transgenic plants transformed with the antisense expression vector. CONCLUSION:This study is the first to perform a sequence analysis, structures analysis, physiological and biochemical characteristics analysis of the MtN3/saliva/SWEETs gene in Chinese cabbage and to verify the function of BcNS. A total of 34 SWEET genes were identified and they are distributed among ten chromosomes and one scaffold. The Ka/Ks ratio implies that the duplication genes suffered strong purifying selection for retention. These genes were differentially expressed in different floral organs. The phenotypes of the transgenic plants indicated that BcNs participates in the development of the floral nectary. This study provides a basis for further functional analysis of the MtN3/saliva/SWEETs gene family.

Project description:BACKGROUND:Plant homeodomain (PHD) finger proteins are widely present in all eukaryotes and play important roles in chromatin remodeling and transcriptional regulation. The PHD finger can specifically bind a number of histone modifications as an "epigenome reader", and mediate the activation or repression of underlying genes. Many PHD finger genes have been characterized in animals, but only few studies were conducted on plant PHD finger genes to this day. Brassica rapa (AA, 2n = 20) is an economically important vegetal, oilseed and fodder crop, and also a good model crop for functional and evolutionary studies of important gene families among Brassica species due to its close relationship to Arabidopsis thaliana. RESULTS:We identified a total of 145 putative PHD finger proteins containing 233 PHD domains from the current version of B. rapa genome database. Gene ontology analysis showed that 67.7% of them were predicted to be located in nucleus, and 91.3% were predicted to be involved in protein binding activity. Phylogenetic, gene structure, and additional domain analyses clustered them into different groups and subgroups, reflecting their diverse functional roles during plant growth and development. Chromosomal location analysis showed that they were unevenly distributed on the 10 B. rapa chromosomes. Expression analysis from RNA-Seq data showed that 55.7% of them were constitutively expressed in all the tested tissues or organs with relatively higher expression levels reflecting their important housekeeping roles in plant growth and development, while several other members were identified as preferentially expressed in specific tissues or organs. Expression analysis of a subset of 18 B. rapa PHD finger genes under drought and salt stresses showed that all these tested members were responsive to the two abiotic stress treatments. CONCLUSIONS:Our results reveal that the PHD finger genes play diverse roles in plant growth and development, and can serve as a source of candidate genes for genetic engineering and improvement of Brassica crops against abiotic stresses. This study provides valuable information and lays the foundation for further functional determination of PHD finger genes across the Brassica species.

Dataset Information

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

Publications

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

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