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锥头蝗科和蝗科(直翅目:蝗亚目)的重复基因组比较分析揭示了重复DNA在基因组巨大化中的作用。

Comparative repeatome analysis of Pyrgomorphidae and Acrididae (Orthoptera: Caelifera) revealed the contribution of repetitive DNA in genome gigantism.

作者信息

Salman Muhammad, Liu Xuanzeng, Liu Nian, Huang Yuan

机构信息

College of Life Sciences, Shaanxi Normal University, Xi'an, China.

出版信息

PLoS One. 2025 Jun 2;20(6):e0325165. doi: 10.1371/journal.pone.0325165. eCollection 2025.

Abstract

Eukaryotic genomes are often rich in DNA repetitive elements, involving both transposable elements (TE) and tandemly repeated satellite DNA. Grasshopper species, known for their large genome sizes, comprising relatively a high proportion of genomic repeats. This study aimed to identify and perform a comparative analysis of DNA repetitive content in eight grasshopper species from the Pyrgomorphidae and Acrididae families. We utilized unassembled low-coverage Illumina paired-end short reads in the RepeatExplorer2 pipeline to identify genomic repeats, and RepeatMasker to estimate their abundance and divergence activity. Flow cytometry estimated genome sizes, ranging from 1C = 7.670 pg to 18.612 pg, with Aularches miliaris (18.612 pg) being the second largest insect genome reported to date. The repeat content ranged from 51% to 74%, with a mean value of 64.26% of the total genome. The major identified repeat elements included LINE, Ty3_Gypsy, Penelope, Ty1-copia, Helitron, Maverick, and satellite repeats, with LINE elements being the most abundant, constituting 24% to 54% of the total repetitive content in Apalacris varicornis and A. miliaris, respectively. The positive correlation of repetitive content and TEs with genome size suggests that their expansion has contributed to the large genome sizes observed. Satellite DNA analysis identified 65 satDNA families across the eight species. Additionally, phylogenetic analysis of TE protein domains revealed that consensus sequences from the same domain cluster together, suggesting domain-specific evolutionary pathways for TEs in the genome. This study reveals new dynamics into the role of repetitive DNA in genome gigantism as well as other evolutionary mechanisms in the Pyrgomorphidae and Acrididae families of Orthoptera.

摘要

真核生物基因组通常富含DNA重复元件,包括转座元件(TE)和串联重复卫星DNA。蚱蜢物种以其大基因组大小而闻名,基因组重复序列占比较高。本研究旨在鉴定并比较蝗科和锥头蝗科八个蚱蜢物种的DNA重复序列含量。我们在RepeatExplorer2流程中使用未组装的低覆盖度Illumina双端短读长序列来鉴定基因组重复序列,并使用RepeatMasker来估计其丰度和分歧活性。流式细胞术估计基因组大小范围为1C = 7.670 pg至18.612 pg,其中长戟大兜虫(18.612 pg)是迄今为止报道的第二大昆虫基因组。重复序列含量范围为51%至74%,平均占基因组总量的64.26%。鉴定出的主要重复元件包括LINE、Ty3_Gypsy、Penelope、Ty1-copia、Helitron、Maverick和卫星重复序列,其中LINE元件最为丰富,分别占变色无翅蝗和长戟大兜虫总重复序列含量的24%至54%。重复序列含量和转座元件与基因组大小的正相关表明它们的扩增导致了所观察到的大基因组大小。卫星DNA分析在这八个物种中鉴定出65个卫星DNA家族。此外,转座元件蛋白结构域的系统发育分析表明,来自同一结构域的共有序列聚集在一起,这表明基因组中转座元件存在结构域特异性的进化途径。本研究揭示了重复DNA在基因组巨大化中的作用以及直翅目蝗科和锥头蝗科其他进化机制的新动态。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2035/12129174/e7f4829a3d90/pone.0325165.g001.jpg

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