Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis

Zhang, Xingtan; Chen, Shuai; Shi, Longqing; Gong, Daping; Zhang, Shengcheng; Zhao, Qian; Zhan, Dongliang; Vasseur, Liette; Wang, Yibin; Yu, Jiaxin; Liao, Zhenyang; Xu, Xindan; Qi, Ruili; Wang, Wenling; Ma, Yunran; Wang, Pengjie; Ye, Naixing; Ma, Dongna; Shi, Yan; Wang, Haifeng; Ma, Xiaokai; Kong, Xiangrui; Lin, Jin-Jia; Wei, Liufeng; Ma, Yaying; Li, Ruoyu; Guiping, Hu; He, Haifang; Zhang, Lin; Ming, Ray; Wang, Gang; Tang, Haibao; You, Minsheng

doi:10.1038/s41588-021-00895-y

Cited by 213 publications

(181 citation statements)

References 69 publications

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“…Only one transcript switched the expressed allele between leaf and stem tissues. This is also similar to the patterns observed in ginger and tea plant [43,44]. We previously reported more genes with ASE for cassava 60444 and TME3 [8] because different RNA isoforms (i.e.…”

Section: Discussionsupporting

confidence: 87%

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

Lim

Patrignani

et al. 2021

Preprint

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BackgroundCassava (Manihot esculenta) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding is limited because cassava has a highly heterozygous, repetitive and difficult to assemble genome.FindingsHere we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present two chromosome scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. Genome comparisons revealed extensive chromosome re-arrangements and abundant intra-genomic and inter-genomic divergent sequences despite high gene synteny, with most large structural variations being LTR-retrotransposon related. Allele-specific expression analysis of different tissues based on the haplotype-resolved transcriptome identified both stable and inconsistent alleles with imbalanced expression patterns, while most alleles expressed coordinately. Among tissue-specific differentially expressed transcripts, coordinately and biasedly regulated transcripts were functionally enriched for different biological processes. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding.ConclusionsThe haplotype-resolved genome allows the first systematic view of the heterozygous diploid genome organization in cassava. The completely phased and annotated chromosome pairs will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy and continuity.

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Section: Discussionsupporting

confidence: 87%

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

Lim

Patrignani

et al. 2021

Preprint

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“…The clean reads were uniquely aligned to the latest reference genome (cv. Tieguanyin) (Zhang et al, 2021) using HISAT2.2.4 (Anders et al, 2015 with the default parameters. The expression abundance and variations were estimated in fragments per kilobase of transcript per million fragments mapped (FPKM).…”

Section: High-throughput Rna-seqmentioning

confidence: 99%

Architecture and Dynamics of the Wounding-Induced Gene Regulatory Network During the Oolong Tea Manufacturing Process (Camellia sinensis)

Yang

et al. 2022

Front. Plant Sci.

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Understanding extensive transcriptional reprogramming events mediated by wounding during the oolong tea manufacturing process is essential for improving oolong tea quality. To improve our comprehension of the architecture of the wounding-induced gene regulatory network, we systematically analyzed the high-resolution transcriptomic and metabolomic data from wounding-treated (after turnover stage) tea leaves at 11 time points over a 220-min period. The results indicated that wounding activates a burst of transcriptional activity within 10 min and that the temporal expression patterns over time could be partitioned into 18 specific clusters with distinct biological processes. The transcription factor (TF) activity linked to the TF binding motif participated in specific biological processes within different clusters. A chronological model of the wounding-induced gene regulatory network provides insight into the dynamic transcriptional regulation event after wounding treatment (the turnover stage). Time series data of wounding-induced volatiles reveal the scientific significance of resting for a while after wounding treatment during the actual manufacturing process of oolong tea. Integrating information-rich expression data with information on volatiles allowed us to identify many high-confidence TFs participating in aroma formation regulation after wounding treatment by using weighted gene co-expression network analysis (WGCNA). Collectively, our research revealed the complexity of the wounding-induced gene regulatory network and described wounding-mediated dynamic transcriptional reprogramming events, serving as a valuable theoretical basis for the quality formation of oolong tea during the post-harvest manufacturing process.

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“…We examined the diversity characteristics in some perennial tree species (Additional file 4: Table S3) and found that unlike common annual crops with dramatic reduction of genetic diversity during crop domestication and improvement, the genetic diversity of domesticated or improved perennial trees is not necessarily lower than their progenitors. For example, in the tea tree population studies [19,20], the nucleotide diversity of cultivated tea plants is higher than their wild ancestors. In European pears, although the θ w of wild population is much higher than domesticated one, the θ π value, on the contrary, is slightly higher in the domesticated population [16] (Additional file 4: Table S3).…”

Section: Genetic Diversity Of Different Walnut Populationsmentioning

confidence: 99%

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

Zhang

et al. 2021

Genome Biol

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Background Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored. Results We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively. Conclusions The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.

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Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis

Cited by 213 publications

References 69 publications

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

Architecture and Dynamics of the Wounding-Induced Gene Regulatory Network During the Oolong Tea Manufacturing Process (Camellia sinensis)

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

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