Scientia Agricultura Sinica ›› 2022, Vol. 55 ›› Issue (9): 1859-1867.doi: 10.3864/j.issn.0578-1752.2022.09.014

• ANIMAL SCIENCE·VETERINARY SCIENCE·RESOURCE INSECT • Previous Articles     Next Articles

Evolutionary Relationship Between Transposable Elements and Tandem Repeats in Bovinae Species

ZHANG Rui(),ZHANG TianLiu,FAN TingTing,ZHU Bo,ZHANG LuPei,XU LingYang,GAO HuiJiang,LI JunYa,CHEN Yan,GAO Xue*()   

  1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193
  • Received:2020-06-09 Revised:2022-03-16 Online:2022-05-01 Published:2022-05-19
  • Contact: Xue GAO E-mail:1245103873@qq.com;gaoxue76@126.com

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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

Table 1

The distribution of repeats in the bovinae genomes"

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

Table 2

The distribution of slTRs and mlTRs in six species of bovinae"

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

Table 3

The distribution of TE-derieved TRs"

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%

Fig. 1

Relative number and actual number of TRs- related TEs The ordinate represents the transposable, the abscissa represents the relative number (%). The number on the right side of each column: the percentage number represents the relative number and the actual number of corresponding transposons in parentheses"

Fig. 2

Self-alignment dotplot of BovB (A) and L1_BT (B) A：BovB;B：L1_BT。Each short line indicates that the sequence can be matched with a window size of 50 and a threshold of 50"

Fig. 3

Internal TRs sequence alignment of BovB (a) and L1_BT (b)"

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