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 <i>Capra hircus</i> (goat), the genomic features of TEs are not well annotated. To benefit TEs research in <i>Capra hircus</i>, we generated detailed annotation files for goat TEs at both subfamily and location levels. The Ensembl curated<i> Capra hircus</i> 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<i> Capra hircus</i> genome were annotated using the <i>RepeatMasker</i> (version 4.1.6) software, with default mode run using <i>rmblastn </i>(version 2.14.0+) and <i>FamDB</i> (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）是一类由重复序列组成的可移动遗传元件，约占哺乳动物基因组的一半。由于其重复序列的固有特性，转座因子在常规基因组与转录组分析中常被忽视——这是因为比对模糊的短读长测序片段，会使得将其精准归因至特定转座因子的过程变得复杂且充满不确定性。对于山羊（*Capra hircus*）这类研究较少的物种，其转座因子的基因组特征尚未得到充分注释。为推动山羊转座因子的相关研究，我们分别在亚家族与基因组位置两个层面，生成了山羊转座因子的详细注释文件。本研究采用Ensembl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）开展基因组比对与注释工作。随后使用RepeatMasker（版本4.1.6）软件对山羊基因组的转座因子进行注释，该软件以默认模式运行，搭配rmblastn（版本2.14.0+）与FamDB（RBRM 3.8）工具。我们对RepeatMasker生成的注释表格进行过滤，剔除了rRNA、scRNA、snRNA、srpRNA及tRNA等非目标重复序列类型。使用makeTEgtf.pl脚本（下载链接：http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz）将过滤后的注释表格重新格式化为可用于后续分析的GTF文件。相关文件的生成与使用代码已附于Code_for_goat_TE.txt文件中。

搜集汇总

背景与挑战

背景概述

该数据集提供山羊（Capra hircus）基因组中可转座元件（TEs）的详细注释GTF文件，基于Ensembl的ARS1基因组组装，使用RepeatMasker软件生成，并过滤了非TEs重复序列。数据集包含亚家族和位置级别的注释，旨在支持山羊TEs研究，适用于基因组学、转录组学等相关分析。