该文章对‘碧云’茶树品种进行基因组测序，结合SMRT和Hi-C将基因组挂载到了15条假染色体上，最终获得了2.92Gb大小的茶树基因组，预测到40812个蛋白编码基因。并基于长末端重复序列（LTR）逆转座子分析表明非自主型LTR逆转座子的近期爆发可能是驱动茶树基因组扩张的主要动力。

In conclusion, we have first generated a highly contiguous and accurate tea tree genome assemblyof C. sinensis var. sinensis cv. Biyun using SMRT technology, which is muchmore improved. This effort has added one more successful example that sequencingthe highly repetitive and heterozygous and relatively large tea tree genome maybe achieved using high-depth long SMRT reads to resolve ambiguous genomicregions harboring predominantly repetitive sequences. The exceptionallycontiguous and precise genome assembly of the tea tree is powerful to fullyidentify all types of long LTR retrotransposons and almost entirelycharacterize the abundance of retrotransposon diversity to resolve the natureof repetitive landscape of such a large genome. The evolutionary history ofvery recently augmented LTR retrotransposon families, which have not been doneever before, could now be tracked genome-wide by dating bursts ofnon-autonomous LTR retrotransposons and undertaking their interaction withautonomous LTR retrotransposons, afterwards driving the genome size evolution.Such a high-quality reference genome of the tea tree is timely and willtherefore be welcome to the broad tea research community, which is essential toenable researchers to accurately obtain functionally significant gene familiesthat not only involve in the biosynthesis of numerous metabolites but alsodetermine agronomically important traits relevant to the improvement of teaquality and production.

该文章基于前期组装的‘舒茶早’茶树基因组草图，进一步结合SMRT和Hi-C将其基因组挂载到了15条假染色体上，最终获得了2.94Gb大小的'舒茶早‘茶树基因组，其中2.55Gb为重复序列，预测到50525个蛋白编码基因。本研究对茶树基因组杂合性分析发现’舒茶早‘基因组杂合区域占整个基因组的18.81%，包含3440个蛋白编码基因；本研究同样发现茶树基因组中存在大量的LTR逆转座子，而LTR逆转座子的插入是驱动茶树基因组扩张的主要动力，并且还发现香气相关基因在茶树基因组中存在明显扩张。

此外，本研究还对81个来源广泛的茶树材料进行了重测序，系统进化将其分为野生型、阿萨姆型和中国种3类，其中地方资源与优良品种的亲缘关系比与野生型的更近，而与野生型和地方资源相比，现有品种的遗传多样性有所降低，研究结果还支持茶树起源于中国的西南，随后传播到西亚的路径；另外，研究发现598个基因从野生型到地方资源得到了选择，而977个基因从地方资源到现有品种得到了选择，这些基因主要涉及环境适应和代谢，其中从野生型选择到地方资源的基因主要集中在抗逆性，而从地方资源到现有品种的基因主要与次生代谢相关。

Abstract

Tea plant is animportant economic crop, which produces the world’s oldest and widely consumedtea beverages. We here present a high-quality reference genome of the tea plant(Camellia sinensis var. sinensis) consisting of 15 pseudo-chromosomes, 70.38%of which are LTR retrotransposons. We show the evidence that LTR-RTs playcritical roles in the genome size expansion and transcriptional diversificationof tea plant genes through preferential gene insertions in promoter regions andintrons. Genes, particularly those for terpene biosynthesis, associated withtea aroma and stress resistance are significantly amplified forming geneclusters through recent tandem duplications in the tea plant genome.Phylogenetic analyses of the sequences of 81 tea plant accessions of diverseorigins revealed three well-differentiated tea plant populations, supportingthe proposition for the southwest origin of the cultivated tea plants in Chinaand its later spreading to western Asian through introduction. Domesticationand modern breeding left significant signatures on hundreds of genes in the teaplant genome, particularly those associated with tea quality and stressresistance. The genomic sequences of the reported reference and resequenced teaplant accessions provided valuable resources for future functional genomic andbreeding research of tea plants and understanding the genome evolution offlowering plants.