牛亚科物种转座子与串联重复序列之间的进化关系

doi:10.3864/j.issn.0578-1752.2022.09.014

摘要/Abstract

摘要：

【目的】重复序列是真核生物基因组中重要组成部分,对物种进化、基因遗传变异、转录调控等具有重要作用。研究旨在揭示牛亚科物种重复序列特征,研究转座子和串联重复序列间的进化关系,为牛亚科物种重复序列的研究提供理论支撑。【方法】以普通牛、瘤牛、牦牛、水牛、野牛以及大额牛6个牛亚科物种的基因组序列为研究对象,利用TRF和RepeatMasker软件对6个牛亚科物种基因组中的串联重复序列（tandem repeats sequence,TRs）和转座子（transposable elements,TEs）进行鉴定,并通过本地BLAST比对,分析两类重复序列间的相似性,单位点（single-locus TRs, slTRs）和多位点串联重复序列（mutiple-locus TRs, mlTRs）以及转座子内部的串联重复特征。【结果】（1）6个牛亚科物种中,重复序列在普通牛中的比例最高,为49.13%,其次为水牛46.82%、大额牛46.66%、瘤牛42.70%、野牛42.36%、牦牛42.34%;其中转座子在基因组中的比例为40.57%—45.71%,高于串联重复序列的比例（1.50%—3.42%）。（2）串联重复序列中,mlTRs的比例（76%—99%）显著高于slTRs（1%—24%）,表明mlTRs为6个牛亚科物种中串联重复序列的主要组成。（3）TE-derieved的串联重复序列分析表明,TRs中43%—84%的序列来源于转座子,其中多位点串联重复序列可高达94%。（4）TRs-related 转座子及其活性分析表明,与TRs具有相似性的转座子主要来自非长末端重复序列（non-Long Terminal Repeats, non-LTR）,包括SINE（Short Interspersed Nuclear Element, SINE）和长末端重复序列（Long Interspersed Nuclear Element, LINE）,其中SINE/Core-RTE（主要为BOV-A2）的数量（14 423—24 193）和相对丰度（4.06%—6.77%）最高,被认为是牛亚科物种中最年轻且最具活力的转座子。（5）转座子的串联重复特征分析表明,BovB在0—600 bp,L1_BT在1 500—2 700 bp的序列分别发生了大量的串联重复,与consensus序列的一致性分别达93%和87%以上,且两段区域均为非编码区。【结论】重复序列在牛亚科物种中具有相似的分布特征, non-LTR是牛亚科物种TRs-related TEs的重要来源,且SINE/Core-RTE（主要为BOV-A2）为牛亚科物种最年轻且最具活力的转座子;同时串联重复序列又可作为转座子内部结构的组成部分,表明串联重复序列与转座子在基因组的进化过程相互影响、相互作用。

关键词: 牛亚科, 转座子, 串联重复序列, 进化

Abstract:

【Objective】The repetitive sequence is an important part of eukaryotic genomes and plays an important role in species evolution, gene genetic variation, and transcriptional regulation. The purpose of this study was to reveal the characteristics of tandem repeats in bovinae by investigating the evolutionary relationship between transposons and tandem repeats, so as to provide the theoretical support for the study of tandem repeats in bovinae. 【Method】 In this paper, the six genomes were selected as research object, including Bos taurus, Bos indicus, Bos mutus, Bubalus bubalis, Bison bison and Bos frontalis. The transposable elements and tandem repeats in six genomes was identified through TRF and RepeatMasker software. Meanwhile, the sequence similarity between the two types of tandem repeats was analyzed by BLAST, and single-locus tandem repeats (single-locus TRs, mlTRs), multiple-locus tandem repeats (multiple-locus TRs, mlTRs) and the characteristics of tandem repeat for the transposable elements were investigated too. 【Result】 (1) In the six bovinae genomes, the percent of tandem repeats in Bos taurus was the highest (49.13%), followed by Bos frontalis (46.82%), Bubalus bubalis (46.23%), Bos indicus (42.70%), Bos mutus (42.53%), and Bison bison (42.36%), in which the content of transposable elements in the genome ranged from 40.57%-45.71%, and was higher than that of tandem repeats (1.50%-3.42%). (2) In the tandem repeats, the proportion of mlTRs (76%-99%) was significantly higher than that of slTRs(1%-24%), indicating that the mlTRs was the main component of tandem repeats in six bovinae species. (3) The proportion of TE-derived tandem repeats was 43% to 84%, among them mutiple-locus tandem repeats could reach up to 94%. (4) The analysis of TRs-related transposable elements and their activity showed that these transposable elements were mainly from non-Long Terminal Repeats (non-LTR, including SINE and LINE) and long interspersed nuclear element (LINE), among which SINE/core-RTE (mainly BOV-A2) had the highest number (14 423-24 193) and relative number (4.06%-6.77%), which was considered to be the youngest and the most dynamic transposable elements. (5) The study on transposable elements of tandem repeats’ characteristics indicated that BovB and L1_BT contained a large number of tandem repeats in 0-600 bp and 1 500 bp-2 700 bp, respectively, which were more than 93% and 87% consistent with the consensus sequence, respectively, and the sequences were located in the non-coding region. 【Conclusion】 The repetitive sequence had similar distribution characteristics, non-LTR was an important source of TRs-related TEs, and SINE/Core-RTE(mainly BOV-A2) was the youngest and most dynamic transposable elements. At the same time, the tandem repeats could be used as internal structure component of transposable elements, indicating that tandem repeats and transposable elements interacted with each other in the process of genome evolution.

Key words: bovinae, transposable elements, tandem repeats, evolution

张瑞,张天留,范婷婷,朱波,张路培,徐凌洋,高会江,李俊雅,陈燕,高雪. 牛亚科物种转座子与串联重复序列之间的进化关系[J]. 中国农业科学, 2022, 55(9): 1859-1867.

ZHANG Rui,ZHANG TianLiu,FAN TingTing,ZHU Bo,ZHANG LuPei,XU LingYang,GAO HuiJiang,LI JunYa,CHEN Yan,GAO Xue. Evolutionary Relationship Between Transposable Elements and Tandem Repeats in Bovinae Species[J]. Scientia Agricultura Sinica, 2022, 55(9): 1859-1867.

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物种 Species	重复序列 (%)	转座子 TEs (%)					串联重复序列 TRs (%)
物种 Species	重复序列 (%)	SINE	LINE	LTR	DNA	Total	Micro-satellite	Mini-satellite	Satellite	Total
大额牛 Bos frontalis	46.66	11.44	27.38	3.63	2.11	44.56	0.74	0.45	0.90	2.10
普通牛 Bos taurus	49.13	11.52	27.32	4.75	2.12	45.71	0.85	1.98	0.59	3.42
瘤牛 Bos indicus	42.70	10.82	25.07	3.38	2.01	41.28	0.67	0.26	0.48	1.42
牦牛 Bos mutus	42.34	11.51	23.4	3.49	2.17	40.57	0.75	0.33	0.70	1.77
水牛 Bubalus bubalis	46.82	11.58	27.48	3.65	2.15	44.86	0.82	0.51	0.63	1.96
野牛 Bison bison	42.36	10.78	24.61	3.46	2.01	40.86	0.7	0.38	0.42	1.50
平均值 Mean	45.00	11.28	25.88	3.73	2.10	42.97	0.76	0.65	0.62	2.03

物种 Species	单位点串联重复序列 Single-locus TRs		多位点串联重复序列 Muti-locus TRs
物种 Species	数量 Number	比例 Percent (%)	数量 Number	比例 Percent (%)
大额牛 Bos frontalis	10141	18	46203	82
普通牛 Bos taurus	7471	17	37474	83
瘤牛 Bos indicus	257	1	37152	99
牦牛 Bos mutus	11156	24	34847	76
水牛 Bubalus bubalis	6920	15	38586	85
野牛 Bison bison	6315	16	34166	84
平均值 Mean	7043	15	38071	85

物种 Species	串联重复序列 Total TRs	转座子来源的串联重复序列 TE-derieved TRs
物种 Species	数量 Number	数量 Number	比例 Percent (%)	单位点串联重复序列 slTRs (%)	多位点串联重复序列 mlTRs (%)
大额牛 Bos frontalis	56344	31959	57%	10%	90%
普通牛 Bos taurus	44945	36696	82%	5%	95%
瘤牛 Bos indicus	37409	31381	84%	0%	100%
牦牛 Bos mutus	46003	27442	60%	13%	87%
水牛 Bubalus bubalis	45506	19711	43%	5%	95%
野牛 Bison bison	40481	30525	75%	5%	95%
平均值 Mean	45115	29619	67%	6%	94%