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Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.

ABSTRACT: 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.

SUBMITTER: Alam I

PROVIDER: S-EPMC6814106 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.

Alam Intikhab I Liu Cui-Cui CC Ge Hong-Liu HL Batool Khadija K Yang Yan-Qing YQ Lu Yun-Hai YH

BMC genomics 20191024 1

<h4>Background</h4>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 ...[more]

PMID: 31651238

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Project description:C2H2 zinc finger protein (ZFP) genes have been extensively studied in many organisms and can function as transcription factors and be involved in many biological processes including plant growth and development and stress responses. In the current study, a comprehensive genomics analysis of the C2H2-ZFP genes in B. rapa was performed. A total of 301 B. rapa putative C2H2-ZFP (BrC2H2-ZFP) genes were identified from the available Brassica genome databases, and further characterized through analysis of conserved amino acid residues in C2H2-ZF domains and their organization, subcellular localization, phylogeny, additional domain, chromosomal location, synteny relationship, Ka/Ks ratio, and expression pattern. We also analyzed the expression patterns of eight B. rapa C2H2-ZFP genes under salt and drought stress conditions by using qRT-PCR technique. Our results showed that about one-third of these B. rapa C2H2-ZFP genes were originated from segmental duplication caused by the WGT around 13 to 17 MYA, one-third of them were highly and consecutively expressed in all tested tissues, and 92% of them were located in nucleus by prediction supporting then their functional roles as transcription factors, of which some may play important roles in plant growth and development. The Ka/Ks ratios of 264 orthologous C2H2-ZFP gene pairs between A. thaliana and B. rapa were all, except two, inferior to 1 (varied from 0.0116 to 1.4919, with an average value of 0.3082), implying that these genes had mainly experienced purifying selection during species evolution. The estimated divergence times of the same set of gene pairs ranged from 6.23 to 38.60 MY, with an average value of 18.29 MY, indicating that these gene members have undergone different selective pressures resulting in different evolutionary rates during species evolution. In addition, a few of these B. rapa C2H2-ZFPs were shown to be involved in stress responses in a similar way as their orthologs in A. thaliana. Comparison between A. thaliana and B. rapa orthologous C2H2-ZFP genes showed that the majority of these C2H2-ZFP gene members encodes proteins with conserved subcellular localization and functional domains between the two species but differed in their expression patterns in five tissues or organs. Thus, our study provides valuable information for further functional determination of each C2H2-ZFP gene across the Brassica species, and may help to select the appropriate gene targets for further in-depth studies, and genetic engineering and improvement of Brassica crops.

Project description:The crop species Brassica rapa L. has significant economic importance around the world. However, the global distribution and complex evolutionary history of the species has made investigating its genetic population structure difficult. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption, and fodder for livestock. These subspecies include the oilseed morphotypes. oleifera (turnip rape), ssp. dichotoma (brown sarson/toria), ssp. trilocularis (yellow sarson); ssp. rapa (turnip); and Asian leafy vegetables ssp. pekinensis (Chinese cabbage), ssp. chinensis (bok choy), ssp. nipposinica (mizuna/mibuna), ssp. rapifera (rapini/broccoli rabe), ssp. narinosa (tatsoi), ssp parachinensis (choy sum), and ssp. perviridis (komatsuna). To date, studies have had insufficient sampling to determine the relationship of all morphotypes, especially oilseed morphotypes, and questions remain over the contribution of morphotype and geographic origin to population structure. We used genotyping-by-sequencing to score 18,272 single nucleotide polymorphism markers in a globally diverse panel of 333 B. rapa National Plant Germplasm System accessions that included 10 recognized subspecies. Our population genetic and phylogenetic analyses were broadly congruent and revealed five subpopulations that were largely reflective of morphotype and geography. These subpopulations were 1. European turnips/oilseed, 2. Asian turnips/oilseed, 3. yellow/brown sarson (ssp. trilocularis and ssp. dichotoma), 4. Chinese cabbage (ssp. pekinensis), and 5. bok choy, choy sum, and tatsoi (ssp. chinensis, ssp. parachinensis, ssp. narinosa). Additionally, we found evidence of polyphyly and/or paraphyly, particularly for oilseed morphotypes (ssp. oleifera and ssp. dichotoma) and turnips. The results of this study have provided improved resolution to the genetic and phylogenetic relationships of subspecies within the species B. rapa. Understanding of these relationships is key to the future genetic study and improvement of this globally important crop species.

Dataset Information

Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.

Publications

Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.

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