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Genome-Wide Identification and Expression Analysis of the NRAMP Family Genes in Tea Plant (Camellia sinensis).

ABSTRACT: The natural resistant-associated macrophage protein (NRAMP) is a kind of integral membrane transporter which could function on a wide range of divalent metal ions in plants. Little is known about the NRAMP family in Camellia sinensis. In this study, 11 NRAMP genes were identified from the tea plant genome. Phylogenetic analysis showed that the 11 CsNRAMP proteins were split into two groups. The proteins of group 1 contained the conserved motif 6 (GQSSTxTG), while most proteins in group 2 (excepting CsNRAMP7 and CsNRAMP10) contained the conserved residues of motif 6 and motif 2 (GQFIMxGFLxLxxKKW). The number of amino acids in coding regions of 11 CsNRAMP genes ranged from 279-1373, and they contained 3-12 transmembrane domains. Quantitative RT-PCR analysis showed that G1 genes, CsNRAMP3, CsNRAMP4, and CsNRAMP5, were extraordinarily expressed in roots, while G2 genes showed higher expression levels in the stems and leaves. The expression levels of CsNRAMPs in roots and leaves were detected to assess their responses to Pb treatment. The results indicated that CsNRAMPs were differentially regulated, and they might play a role in Pb transportation of tea plant. Subcellular localization assay demonstrated that CsNRAMP2 and CsNRAMP5 fused proteins were localized in the plasma membrane. Overall, this systematic analysis of the CsNRAMP family could provide primary information for further studies on the functional roles of CsNRAMPs in divalent metal transportation in tea plants.

SUBMITTER: Li J

PROVIDER: S-EPMC8228228 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.

Dataset Information

Genome-Wide Identification and Expression Analysis of the NRAMP Family Genes in Tea Plant (Camellia sinensis).

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