The landscape of transposable element distribution in the genome of Neotropical fish Apareiodon sp. (Characiformes: Parodontidae).

IF 2.4 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Fernanda Souza de Oliveira, Toby Brann, Ivan Rodrigo Wolf, Viviane Nogaroto, Cesar Martins, Anna Victoria Protasio, Marcelo Ricardo Vicari
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Abstract

Transposable elements (TEs) are widely present in eukaryotic genomes, where they can contribute to genome size and functional modifications. As new genomes are sequenced and annotated, more studies can be conducted regarding TE content, distribution, and genome evolution. TEs are extensively diversified in fish genomes resulting in an important role in genome and chromosome evolution. However, curated TE libraries are still scarce in non-model organisms, making it difficult to evaluate TE's impact on genomic modifications thoroughly. Here, we aimed to obtain a curated TE library from the neotropical fish Apareiodon sp. genome. The prospection and curation of the TE library resulted in 244 families from 18 superfamilies of DNA transposons and retrotransposons, which comprise about 10% of the genome, with most insertions fitting in one or a few families. A greater diversity of retrotransposon families is present, especially for Ty3 superfamily. Despite the greater number of retrotransposon families, DNA transposons are the most abundant in the genome, with 37% of all TE insertions belonging to the Tc1-Mariner superfamily. Complete TE copies were observed for almost all superfamilies, with most of the sequences on the Tc1-Mariner group. DNA transposons and SINEs presented older insertions in the genome, followed by LINEs and LTR retrotransposons. TE genome density is highest in the cs25 scaffold, and enriched for Helitron elements. With these data, allied to previous studies on chromosome evolution, we suggest that cs25 bears the W chromosome specific region of the Apareiodon sp. genome, with the presence of significant amount of Helitron insertions.

新热带鱼parareiodon sp.基因组转座因子分布景观(特征:parareiodon科)。
转座因子(te)广泛存在于真核生物基因组中,它们可以影响基因组的大小和功能修饰。随着新基因组的测序和注释,可以对TE的含量、分布和基因组进化进行更多的研究。te在鱼类基因组中广泛分布,在基因组和染色体进化中起着重要作用。然而,在非模式生物中,精心策划的TE文库仍然很少,这使得很难彻底评估TE对基因组修饰的影响。在这里,我们的目标是从新热带鱼Apareiodon sp.基因组中获得一个精心策划的TE文库。通过对DNA转座子和反转录转座子库的筛选和整理,发现了来自18个DNA转座子和反转录转座子超家族的244个家族,约占基因组的10%,大多数插入适合于一个或几个家族。逆转录转座子家族存在更大的多样性,特别是Ty3超家族。尽管逆转录转座子家族数量较多,但DNA转座子在基因组中最为丰富,所有TE插入中有37%属于Tc1-Mariner超家族。在几乎所有超家族中都观察到完整的TE拷贝,其中大部分序列位于Tc1-Mariner群上。DNA转座子和SINEs在基因组中的插入时间较早,其次是LINEs和LTR反转录转座子。TE基因组密度在cs25支架中最高,并且富含Helitron元素。根据这些数据,结合先前的染色体进化研究,我们认为cs25携带Apareiodon sp.基因组的W染色体特异区域,存在大量的Helitron插入。
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来源期刊
Chromosome Research
Chromosome Research 生物-生化与分子生物学
CiteScore
4.70
自引率
3.80%
发文量
31
审稿时长
1 months
期刊介绍: Chromosome Research publishes manuscripts from work based on all organisms and encourages submissions in the following areas including, but not limited, to: · Chromosomes and their linkage to diseases; · Chromosome organization within the nucleus; · Chromatin biology (transcription, non-coding RNA, etc); · Chromosome structure, function and mechanics; · Chromosome and DNA repair; · Epigenetic chromosomal functions (centromeres, telomeres, replication, imprinting, dosage compensation, sex determination, chromosome remodeling); · Architectural/epigenomic organization of the genome; · Functional annotation of the genome; · Functional and comparative genomics in plants and animals; · Karyology studies that help resolve difficult taxonomic problems or that provide clues to fundamental mechanisms of genome and karyotype evolution in plants and animals; · Mitosis and Meiosis; · Cancer cytogenomics.
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