Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics

Yan, Chao; Lin, Peng-Cheng; Lyu, Tao; Hu, Zhikang; Fan, Zhengqi; Li, Xinlei; Yao, Xiaohua; Li, Jiyuan; Yin, Hengfu

doi:10.3390/genes9100488

Cited by 12 publications

(6 citation statements)

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“…An appropriate statistical model can reduce spurious genotype–phenotype associations and increase statistical power [ 63 ]. In this study, four analysis models were used to test the statistical association between genetic variants (SNPs and InDels) and eight oil traits in TASSEL (v5.2.24) [ 64 ], and the optimal model mixed linear model (MLM) was confirmed for each trait by comparing the expected and observed P values in QQ plot (Additional File 2 : Fig.…”

Section: Methodsmentioning

confidence: 99%

The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication

Lin

Wang

et al. 2022

Genome Biol

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Background As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. Camellia oleifera Abel. is a sister species to the tea plant, which is extensively cultivated for edible oil production. However, the molecular mechanism of the domestication of oil-Camellia is still limited due to the lack of sufficient genomic information. Results To elucidate the genetic and genomic basis of evolution and domestication, here we report a chromosome-scale reference genome of wild oil-Camellia (2.95 Gb), together with transcriptome sequencing data of 221 cultivars. The oil-Camellia genome, assembled by an integrative approach of multiple sequencing technologies, consists of a large proportion of repetitive elements (76.1%) and high heterozygosity (2.52%). We construct a genetic map of high-density corrected markers by sequencing the controlled-pollination hybrids. Genome-wide association studies reveal a subset of artificially selected genes that are involved in the oil biosynthesis and phytohormone pathways. Particularly, we identify the elite alleles of genes encoding sugar-dependent triacylglycerol lipase 1, β-ketoacyl-acyl carrier protein synthase III, and stearoyl-acyl carrier protein desaturases; these alleles play important roles in enhancing the yield and quality of seed oil during oil-Camellia domestication. Conclusions We generate a chromosome-scale reference genome for oil-Camellia plants and demonstrate that the artificial selection of elite alleles of genes involved in oil biosynthesis contributes to oil-Camellia domestication.

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Section: Methodsmentioning

confidence: 99%

The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication

Lin

Wang

et al. 2022

Genome Biol

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“…Nowadays, a multitude of RNA-seq projects have been carried out in diverse Camellia species, which greatly facilitates the identification and characterization of genes implicated in various fundamental biological processes. 39 For instance, in a comparative transcriptome study, genes encoding late embryogenesis abundant (LEA) protein were found to extraordinary amplify in C. taliensis, which might confer this wild relative of cultivated tea plant with a wide range stress tolerance. 43 Two yellow-flowering Camellia plants (C. chuongtsoensis and C. nitidissima) showed a remarkable expansion in the group C clade of UDP-glycosyltransferases, which could contribute to the pigmentation diversification of the genus Camellia.…”

Section: ■ Discussionmentioning

confidence: 99%

“…Currently, a large number of phytochemicals, transcriptomics, and functional genomics studies have been carried out in tea plants, which provided a great starting point to understand the complex molecular mechanisms of tea plant development and metabolism. , However, the core mechanism underlying the dynamic regulation of tea plant development and secondary metabolism remains to be unearthed. In addition, most of these studies lack the power to resolve the complex gene interactions among pathways due to the limited sample sizes and lack of appropriate system biology approaches for data integration.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Identifying Conserved Functional Gene Modules Underlying the Dynamic Regulation of Tea Plant Development and Secondary Metabolism

Zheng

et al. 2020

J. Agric. Food Chem.

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Tea plants adjust development and metabolism by integrating environmental and endogenous signals in complex but poorly defined gene networks. Here, we present an integrative analysis framework for the identification of conserved modules controlling important agronomic traits using a comprehensive collection of RNA-seq datasets in Camellia plants including 189 samples. In total, 212 secondary metabolism-, 182 stress response-, and 182 tissue development-related coexpressed modules were revealed. Functional modules (e.g., drought response, theobromine biosynthesis, and new shoot development-related modules) and potential regulators that were highly conserved across diverse genetic backgrounds and/or environmental conditions were then identified by cross-experiment comparisons and consensus clustering. Moreover, we investigate the preservation of gene networks between Camellia sinensis and other Camellia species. This revealed that the coexpression patterns of several recently evolved modules related to secondary metabolism and environmental adaptation were rewired and showed higher connectivity in tea plants. These conserved modules are excellent candidates for modeling the core mechanism of tea plant development and secondary metabolism and should serve as a great resource for hypothesis generation and tea quality improvement.

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“…Advances in next-generation sequencing (NGS) approaches have dramatically changed access to genome data, not only with respect to reference sequencing for many species, but increasingly for population studies of genomic variation (e.g., [1–3]. Applications of NGS include the creation of detailed maps of genetic variation [4–6], DNA methylation [7, 8], and transcription factor binding sites [9, 10].…”

Section: Introductionmentioning

confidence: 99%

SRAssembler: Selective Recursive local Assembly of homologous genomic regions

2019

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Background The falling cost of next-generation sequencing technology has allowed deep sequencing across related species and of individuals within species. Whole genome assemblies from these data remain high time- and resource-consuming computational tasks, particularly if best solutions are sought using different assembly strategies and parameter sets. However, in many cases, the underlying research questions are not genome-wide but rather target specific genes or sets of genes. We describe a novel assembly tool, SRAssembler, that efficiently assembles only contigs containing potential homologs of a gene or protein query, thus enabling gene-specific genome studies over large numbers of short read samples. Results We demonstrate the functionality of SRAssembler with examples largely drawn from plant genomics. The workflow implements a recursive strategy by which relevant reads are successively pulled from the input sets based on overlapping significant matches, resulting in virtual chromosome walking. The typical workflow behavior is illustrated with assembly of simulated reads. Applications to real data show that SRAssembler produces homologous contigs of equivalent quality to whole genome assemblies. Settings can be chosen to not only assemble presumed orthologs but also paralogous gene loci in distinct contigs. A key application is assembly of the same locus in many individuals from population genome data, which provides assessment of structural variation beyond what can be inferred from read mapping to a reference genome alone. SRAssembler can be used on modest computing resources or used in parallel on high performance computing clusters (most easily by invoking a dedicated Singularity image). Conclusions SRAssembler offers an efficient tool to complement whole genome assembly software. It can be used to solve gene-specific research questions based on large genomic read samples from multiple sources and would be an expedient choice when whole genome assembly from the reads is either not feasible, too costly, or unnecessary. The program can also aid decision making on the depth of sequencing in an ongoing novel genome sequencing project or with respect to ultimate whole genome assembly strategies. Electronic supplementary material The online version of this article (10.1186/s12859-019-2949-4) contains supplementary material, which is available to authorized users.

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Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics

Cited by 12 publications

References 116 publications

The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication

The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication

Identifying Conserved Functional Gene Modules Underlying the Dynamic Regulation of Tea Plant Development and Secondary Metabolism

SRAssembler: Selective Recursive local Assembly of homologous genomic regions

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