中国农业科学 ›› 2022, Vol. 55 ›› Issue (9): 1859-1867.doi: 10.3864/j.issn.0578-1752.2022.09.014
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*(
)
收稿日期:
2020-06-09
修回日期:
2022-03-16
出版日期:
2022-05-01
发布日期:
2022-05-19
通讯作者:
高雪
作者简介:
张瑞,E-mail: 基金资助:
ZHANG Rui(),ZHANG TianLiu,FAN TingTing,ZHU Bo,ZHANG LuPei,XU LingYang,GAO HuiJiang,LI JunYa,CHEN Yan,GAO Xue*(
)
Received:
2020-06-09
Revised:
2022-03-16
Online:
2022-05-01
Published:
2022-05-19
Contact:
Xue GAO
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。
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.
表1
牛亚科基因组重复序列的总体分布"
物种 Species | 重复序列 (%) | 转座子 TEs (%) | 串联重复序列 TRs (%) | |||||||
---|---|---|---|---|---|---|---|---|---|---|
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 |
表2
单位点、多位点串联重复序列在牛亚科6个物种的分布"
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 | ||
---|---|---|---|---|
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 |
表3
转座子来源的串联重复序列分布"
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 | ||||
---|---|---|---|---|---|---|
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% |
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