| Repetitive sequences are an important part of the genome of eukaryotes,which is the nuclear DNA appearing in multiple copies,being of great significance to genetic variation,transcriptional regulation and species evolution.The structural characteristics and evolutionary relationships of repetitive sequences have been reported in species such as model animals,humans,and plants,but there are few studies in bovinae.This study aims to reveal the characteristics of repetitive sequences in bovinae genome,study the evolutionary relationship between transposable elements and tandem repeats,and provide theoretical support for the study of repetitive sequences in bovinae.In this paper,six bovinae species were researched including Bos taurus,Bos indicus,Bos mutus,Bubalus bubalis,Bison bison and Bos frontalis.In the six species of bovinae genome,we study the structural characteristics and distribution of tandem repeats and transposable elements,as well as their evolutionary relationship by comparative genomics,the results are as follows:1.Through the identification of repetitive sequences in six bovinae genomes,the highest content of repetitive sequences is 49.13% in Bos taurus,followed by Bubalus bubalis(46.82%),Bos frontalis(46.66%),Bos indicus(42.70%),Bison bison(42.36%),and Bos mutus(42.34%).The content of transposable elements in the genome is between 40.57%-45.71%,which is higher than tandem repeats(1.50%-3.42%).2.The tandem repeats are identified by TRF and RepeatMasker software in the six species of bovinae genome,its proportion in the genome from high to low are: Bos taurus(3.42%),Bos frontalis(2.10%),Bubalus bubalis(1.96%),Bos mutus(1.77%),Bison bison(1.50%),Bos indicus(1.42%).The total number is 564,611,of which the microsatellites is(483,405/85.64%),higher than minisatellites(43,026/7.62%)and satellites(38,180/6.75%).In addition,phylogenetic trees of 1.715 and 1.723 centromeric satellite indicate that these sequences can exist in six bovinae genomes,but different on species or chromosomes.3.Transposable elements are identified by RepeatMasker software in the six species of bovinae genome,its proportion in the genome from high to low are: Bos taurus(49.13%),Bos frontalis(46.66%),Bubalus bubalis(46.23%),Bos indicus(42.70%),Bos mutus(42.53%),Bison bison(42.36%).The proportion of non-LTR was 37.16%,including LINE(25.88%)and SINE(11.28%),while the proportion of LTR(3.73%)and DNA transposons(2.10%)is less.In addition,only 3.06%-8.54% of transposable elements were located in the coding regions by annotating the position information.4.The sequence similarity was analyzed by the BLAST between transposable elements and tandem repeats,the results showed that the proportion of TE-derived tandem repeats is 43% to 84%,and these transposable elements are mainly from non-LTR(SINE and LINE),among which SINE/core-RTE(mainly BOV-A2)has the highest number(14,423-24,193)and relative number(4.06%~6.77%),which is considered to be the youngest and the most dynamic transposable elements.In addition,the study on transposable elements of tandem repeats' characteristics indicates that BovB and L1_BT contain a large number of tandem repeats,respectively in 0-600 bp,1500-2700 bp,indicating that tandem repeats can be used as internal structure component of transposable elements and they interact with each other in the process of genome evolution. |
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