All the assemblies, annotations, variant VCF files and graph-based genome are also available at the Tea Graph Pangenome Database (https://www.tea-pangenome.cn/). Code availability The PanMarker and SRI approach
Our graphical pangenome improves the efficiency of genome-wide association studies and allows the identification of key genes controlling bud flush timing. We also identified strong correlations between allelic variants and flavour-related chemistries. These findings deepen our understanding of the genetic...
The raw data, genome assemblies and annotation have been submitted to the National Genomics Data Center (https://ngdc.cncb.ac.cn/) under accession numberPRJCA013847for the pangenome samples. All the assemblies, annotations, variant VCF files and graph-based genome are also available at the T...
Finally, optimizing the de Bruijn graph permitted us to build 320573 transcripts with average size of 796 bp and an N50 of 1392 bp (Table 2). All the transcripts were then BLAST searched against Arabidopsis database. For those sequences with no BLAST hits (non-BLASTable transcripts), we ...
Subsequently, the remaining clean reads were subjected to paired-end alignment against the tea plant reference genome [1] using Bowtie v2.3.4.3 [36] with default parameters. The ddRAD sequencing generated raw reads has been deposited in the NCBI Sequence-Read Archive (SRA) database under the ...
transformed relative abundance of each genus in samples by a gradient of color from blue (low abundance) to red (high abundance). The taxonomic assignment of each genus was determined by Ribosomal Database Project classifier and the genus name and sample group name was labeled in the graph.e...
The fluorescence images and relative fluorescence intensity graph (Fig. 3c and d) further demonstrate that the addition of alkyl chains at 4″ position of EGCG did not compromise on the prooxidant activity of EGCG. Instead, these modifications have often substantiated the increased affinity and ...
The characteristic secondary metabolites in tea(theanine,caffeine,and catechins)are important factors contributing to unique tea flavors.However,there has been relatively little research on molecular markers related to these metabolites.Thus,we conducted a genome-wide association analysis of the levels of ...
genome sequence information, target gene prediction was performed using theTargetFinder software (v1.6, -c3) [31]. The functional annotation of the target genes was performed using the National Center for Biotechnology Information (NCBI)non-redundant protein (Nr) database [32], Clusters of ...
Furthermore, ≥77 % mapping of reads with the reference genome of tea suggested quality transcriptome data in this study [28,38]. The higher enrichment of 'signal transduction', 'post-embryonic development' and 'pollen-pistil interactions' putatively suggests successful commencement of fertilization ...