The Genome Assembly Of 'longjing43' And Tea Plants Population Analysis

Tea is an important economic crop characterized by a large genome size,high heterozygosity and species diversity.Shuchazao and Yunkang 10 were not characterized at the chromosome scale,and the associated scaffold N50 values were less than 1.4 Mb,thereby precluding an evaluation of the phenotypic variation and genome evolution in important intergenic regions.Moreover,annotation of the core genes(Benchmarking Universal Single-Copy Orthologs)of the Shuchazao and Yunkang10 genomes was respectively only 80.58% and 68.58% complete,and this has tended to hamper further population selection,functional genomics analysis,and molecule breeding research.Tea plant taxonomy generally lacks comprehensive genomic evidence,further analyses using population resequencing are required to optimize taxonomic assignments at the whole-genome level.Herein,we describe the sequencing,assembly,and analysis of a high quality of chromosome-level genome using the cultivar Camellia sinensis var.sinensis cv.Longjing 43.Population resequencing of 139 tea samples from the world showed that the domestication of cultivation tea,revealed the phylogenetic relationship of tea population.The main results were shown: 1.High quality of tea genome assemblyTo enhance genome assembly,196 Gb SMRT long reads were initially assembled using WTDBG(Version 1.2.8),which resulted in a 3.26-Gb assembled genome,To further improve the integrity of the assembled genome,contigs were scaffolded based on chromosome conformation capture sequencing(HiC)and the final assembly of 3.26 Gb was generated with a scaffold N50 value of 144 Mb.Longjing43 had the most complete gene set in tea genomes with 33556 genes.2.The most comprehensive tea tree resequencingPopulation resequencing of 139 tea samples from the world showed that the domestication of cultivation tea,revealed the phylogenetic relationship of tea population.This project supplies new resource for tea genomic research and maker-assistant breeding,and brings more opportunities for future genetic and evolution research.3.The origin of teaOur data also indicated that the CSR population is the ancestral to the CSS and CSA,though this was a critical step toward the detail scenarios of the origin and domestication of CSS and CSA,it remain necessary to identify the closest ancestor of tea and to examine a larger number of CSR accessions in the future.4.The domestication of tea plantIt indicates that the selection for INA bacterial resistance and flavor during domestication has been stronger in CSS than in CSA.Population genetics and transcriptomics revealed that the selection on disease resistance and flavor in Camellia sinensis var.sinensis population were stronger than Camellia sinensis var.assamica population during domestication.