Abstract
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.
Highlights
Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), sometimes are called orphan genes (Fischer and Eisenberg, 1999; Tautz and DomazetLoso, 2011)
Other 126 plant genome sequences were downloaded from Phytozome V13.1 (Supplementary Table S1),the assembled unique transcripts (PUT) sequences of the plants were downloaded from PlantGDB (Supplementary Table S2), Uniprot-KB were downloaded from Uniprot and NR databases were acquired from NCBI, respectively
We identified 1701 Camellia-specific genes (CSGs) from the Camellia sinensis var. sinensis (CSS) genome, accounting for 3.37% of the genome
Summary
Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), sometimes are called orphan genes (Fischer and Eisenberg, 1999; Tautz and DomazetLoso, 2011). Compared with evolutionary conserved genes (ECs), LSGs have some differences in gene length, number of introns and exons, GC content and chromosome distribution preference, owing to the shorter generation time. The GC content of LSGs in zebrafish is higher than conserved genes, this characteristic is similar to the LSGs in rice (Yang et al, 2013). The distribution characteristics of LSGs on chromosomes are different, like zebrafish have uneven distribution of LSGs on chromosomes, with some chromosomes having a high proportion of gene and others having no LSGs, which may be related to the length of chromosome (Yang et al, 2013). LSGs were more expressed in callus in sweet orange, a stem-cell like tissue (Xu et al, 2015) and most LSGs in wheat were expressed in sexual tissues (Ma et al, 2020)
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