PDF(Pubmed)
Abstract：
Transposable elements (TEs) are DNA sequences that can move or replicate within a genome, and their study has become increasingly important in understanding genome evolution and function. The Tridactylidae family, including Xya riparia (pygmy mole cricket), harbors a variety of transposable elements (TEs) that have been insufficiently investigated. Further research is required to fully understand their diversity and evolutionary characteristics. Hence, we conducted a comprehensive repeatome analysis of X. riparia species using the chromosome-level assembled genome. The study aimed to comprehensively analyze the abundance, distribution, and age of transposable elements (TEs) in the genome. The results indicated that the genome was 1.67 Gb, with 731.63 Mb of repetitive sequences, comprising 27% of Class II (443.25 Mb), 16% of Class I (268.45 Mb), and 1% of unknown TEs (19.92 Mb). The study found that DNA transposons dominate the genome, accounting for approximately 60% of the total repeat size, with retrotransposons and unknown elements accounting for 37% and 3% of the genome, respectively. The members of the Gypsy superfamily were the most abundant amongst retrotransposons, accounting for 63% of them. The transposable superfamilies (LTR/Gypsy, DNA/nMITE, DNA/hAT, and DNA/Helitron) collectively constituted almost 70% of the total repeat size of all six chromosomes. The study further unveiled a significant linear correlation (Pearson correlation: r = 0.99, p-value = 0.00003) between the size of the chromosomes and the repetitive sequences. The average age of DNA transposon and retrotransposon insertions ranges from 25 My (million years) to 5 My. The satellitome analysis discovered 13 satellite DNA families that comprise about 0.15% of the entire genome. In addition, the transcriptional analysis of TEs found that DNA transposons were more transcriptionally active than retrotransposons. Overall, the study suggests that the genome of X. riparia is complex, characterized by a substantial portion of repetitive elements. These findings not only enhance our understanding of TE evolution within the Tridactylidae family but also provide a foundation for future investigations into the genomic intricacies of related species.
摘要：
转座因子（TE）是可以在基因组中移动或复制的DNA序列，他们的研究在理解基因组进化和功能方面变得越来越重要。Tridactylidae家族，包括Xyariparia（侏儒痣板球），藏有各种未得到充分研究的转座因子（TE）。需要进一步研究以充分了解它们的多样性和进化特征。因此，我们使用染色体水平的组装基因组对X.riparia物种进行了全面的重复性分析.这项研究旨在全面分析丰度，分布，和基因组中转座因子（TE）的年龄。结果表明，基因组为1.67Gb，具有731.63Mb的重复序列，占II类(443.25Mb)的27%，I类的16%（268.45Mb），和1%的未知TEs(19.92Mb)。研究发现DNA转座子在基因组中占主导地位,约占总重复大小的60%，逆转录转座子和未知元素占基因组的37%和3%，分别。吉普赛超家族的成员是反转录转座子中最丰富的，占其中的63%。转座超家族（LTR/吉普赛，DNA/nMITE,DNA/hAT,和DNA/Helitron）共同构成了所有六个染色体总重复大小的近70％。该研究进一步揭示了染色体大小与重复序列之间的显着线性相关（皮尔逊相关：r=0.99，p值=0.00003）。DNA转座子和反转录转座子插入的平均年龄从25My(百万年)到5My。卫星组分析发现了13个卫星DNA家族，约占整个基因组的0.15％。此外,TEs的转录分析发现，DNA转座子比逆转录转座子更具转录活性。总的来说,这项研究表明，里帕里亚的基因组很复杂，以相当大一部分的重复元素为特征。这些发现不仅增强了我们对Tridactylidae家族中TE进化的理解，而且为未来对相关物种基因组复杂性的研究奠定了基础。
