草蛙（欧洲林蛙）大串联重复序列的电子克隆和原位分析

Large tandem repeats of grass frog (Rana temporaria) in silico and in situ.

作者信息

Popova Marina A, Komissarov Aleksey S, Ostromyshenskii Dmitrii I, Podgornaya Olga I, Travina Aleksandra O

机构信息

Institute of Cytology RAS, Saint-Petersburg, 194064, Russia.

Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.

出版信息

BMC Genomics. 2025 May 6;26(1):445. doi: 10.1186/s12864-025-11643-5.

DOI:10.1186/s12864-025-11643-5

PMID:40329174

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12054243/

Abstract

BACKGROUND

Genomes of higher eukaryotes contain a large fraction of non-coding repetitive DNA, including tandem repeats (TRs) and transposable elements (TEs). The impact of TRs on genome structure and function and the importance of TR transcripts have been described for several model species. Amphibians have one of the most diverse genome sizes among vertebrates, attributed to the abundance of repetitive non-coding DNA. Consequently, amphibians are good models for the analysis of repetitive sequences, including TRs. However, few studies have focused on amphibian genomes.

RESULTS

Bioinformatic analyses were performed to characterise the content and localisation of TRs in the sequenced grass frog Rana temporaria genome. By applying different bioinformatic approaches, 76 TR families and 314 single TR arrays (not grouped into families) were identified. Each TR was characterised on the basis of chromosomal position, monomer length and variability and GC content. Bioinformatic analysis revealed a great diversity of TRs, with a clear predominance of TRs with short monomers (< 100 bp), although TRs with long monomers (> 1000 bp) also exist. The six most abundant TRs were successfully mapped by fluorescence in situ hybridization (FISH), which highlighted the presence of specific TR sequences in strategic chromosomal regions, i.e., the pericentromeric regions. A comparison of the results of in situ and in silico TR mapping revealed some inaccuracies in the assembly of heterochromatic regions. A putative new non-autonomous TE called "FEDoR" (Frog Element Dispersed organised Repeat) is also described. FEDoR is ∼ 3.5 kb in length, has no significant similarity to any known TE family, contains multiple internal TR motifs, and is flanked on both sides by pairs of inverted repeat sequences (IRSs) and target site duplications (TSDs).

CONCLUSION

Characterisation of TRs in this frog species has provided some insights regarding TR biology in Anuran amphibians.

摘要

背景

高等真核生物的基因组包含很大一部分非编码重复DNA，包括串联重复序列（TRs）和转座元件（TEs）。对于几种模式生物，已经描述了TRs对基因组结构和功能的影响以及TR转录本的重要性。两栖动物是脊椎动物中基因组大小最多样化的类群之一，这归因于丰富的重复非编码DNA。因此，两栖动物是分析包括TRs在内的重复序列的良好模型。然而，很少有研究关注两栖动物基因组。

结果

进行了生物信息学分析，以表征已测序的林蛙基因组中TRs的含量和定位。通过应用不同的生物信息学方法，鉴定出76个TR家族和314个单个TR阵列（未归类为家族）。每个TR根据染色体位置、单体长度、变异性和GC含量进行表征。生物信息学分析揭示了TRs的巨大多样性，短单体（<100 bp）的TRs明显占优势，尽管也存在长单体（>1000 bp）的TRs。通过荧光原位杂交（FISH）成功绘制了六种最丰富的TRs图谱，这突出了特定TR序列在关键染色体区域即着丝粒周围区域的存在。原位和电子TR图谱结果的比较揭示了异染色质区域组装中的一些不准确之处。还描述了一种推定的新的非自主TE，称为“FEDoR”（蛙类分散组织重复元件）。FEDoR长度约为3.5 kb，与任何已知的TE家族没有显著相似性，包含多个内部TR基序，两侧由成对的反向重复序列（IRSs）和靶位点重复序列（TSDs）侧翼。