GTF files for annotating transposable elements in <i>Capra hircus</i> (goat) genome

Transposable elements (TEs, also called transposons) are mobile genetic elements consist of repetitive sequences, accounting for about half of a mammal genome. TEs are somewhat overlooked in typical genomic and transcriptomic analyses due to its repetitive nature, rendering complexities and uncertainty in attributing ambiguously aligned short reads to the exact elements. In less studied species like Capra hircus (goat), the genomic features of TEs are not well annotated. To benefit TEs research in Capra hircus, we generated detailed annotation files for goat TEs at both subfamily and location levels. The Ensembl curated Capra hircus genome assembly ARS1 (GCA_001704415.1, accessed at https://ftp.ensembl.org/pub/release-112/fasta/capra_hircus/dna/Capra_hircus.ARS1.dna.toplevel.fa.gz,) was used for genome mapping and annotation. The TEs of the Capra hircus genome were annotated using the RepeatMasker (version 4.1.6) software, with default mode run using rmblastn (version 2.14.0+) and FamDB (RBRM 3.8). The RepeatMasker annotation tables were parsed to filter out repeats like rRNA, scRNA, snRNA, srpRNA, and tRNA. The makeTEgtf.pl script (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) was used to reformat RepeatMasker table into GTF file for further use. Detailed codes for making and using these files were attached in the Code_for_goat_TE.txt file.转座因子（Transposable elements，TEs，又称转座子）是一类携带重复序列的可移动遗传因子，约占哺乳动物基因组的一半。由于其重复序列的固有特性，TEs在常规基因组与转录组分析中常被忽视，这使得将比对模糊的短读段精准归属到特定TE元件的过程变得复杂且充满不确定性。在山羊（Capra hircus）这类研究较少的物种中，TEs的基因组特征尚未得到充分注释。为推动山羊TEs的相关研究，我们分别在亚家族与基因组位置层面，为山羊TEs构建了精细化注释文件。本研究采用经Ensembl人工注释的山羊基因组组装版本ARS1（登录号GCA_001704415.1，下载链接：https://ftp.ensembl.org/pub/release-112/fasta/capra_hircus/dna/Capra_hircus.ARS1.dna.toplevel.fa.gz）进行基因组比对与注释工作。我们使用RepeatMasker（版本4.1.6）软件对山羊基因组的TEs进行注释，采用默认运行模式，搭配rmblastn（版本2.14.0+）与FamDB（RBRM 3.8）作为比对工具与数据库。随后对RepeatMasker生成的注释表格进行解析，过滤掉rRNA、scRNA、snRNA、srpRNA及tRNA等非TE重复序列。使用makeTEgtf.pl脚本（下载链接：http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz）将RepeatMasker注释表格重新格式化为GTF文件，以供后续分析使用。上述注释文件的构建与使用代码已附于Code_for_goat_TE.txt文件中。