Additional file 6 of A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don

Supplementary Material 6: Table 2. Gene evidence table. Gene ID: A unique identifier for each gene within SUGI genome annotation version 1; Standard Gene Set: The boolean attribute indicates whether the gene is a part of the standard gene set; PASA Overlap: Denotes the presence of overlapping transcripts from PASA [47, 49], implying that gene authenticity is supported by RNA-seq evidence; Ortholog: Indicates whether there is homology to proteins in other species (UniprotKB, NCBI RefSeq, and Viridiplantae of OrthoDB v10; Not Entirely Masked Sequence: Reveals if the gene sequence is unambiguously distinct from repeat elements; TEsorter Hit: Suggests whether the gene contains sequences that may be derived from transposable elements, as identified by TEsorter version 1.3 using the following options (with database): -db rexdb-plant -dp2 (Viridiplantae v3.0 of REXdb). TESorter was run with the -dp2 option to identify genes that are highly likely to be retrotransposons.

补充材料6：表2 基因证据表。基因ID（Gene ID）：SUGI基因组注释版本1中每个基因的唯一标识符；标准基因集（Standard Gene Set）：用于标识该基因是否属于标准基因集的布尔属性；PASA重叠比对（PASA Overlap）：表示存在来自PASA[47,49]的重叠转录本，意味着该基因的真实性得到了RNA测序证据的支持；直系同源基因（Ortholog）：用于指示该基因是否与其他物种（UniprotKB、NCBI RefSeq以及OrthoDB v10的绿色植物分支）的蛋白质存在同源性；非完全屏蔽序列（Not Entirely Masked Sequence）：表明该基因序列与重复元件存在明确可辨的差异；TEsorter比对结果（TEsorter Hit）：指该基因是否包含可能源自转座因子的序列，由版本1.3的TEsorter通过以下参数（搭配对应数据库）鉴定得到：-db rexdb-plant -dp2（即REXdb绿色植物v3.0数据库）。本次分析使用-dp2参数运行TEsorter，以筛选出极有可能为逆转录转座子的基因。