Scientia Agricultura Sinica ›› 2020, Vol. 53 ›› Issue (7): 1491-1500.doi: 10.3864/j.issn.0578-1752.2020.07.017

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

Genome-Wide Identification and Characterization of Transposable Elements in Xichuan Black-Bone Chicken

DongHua LI,YaWei FU,ChenXi ZHANG,YanFang CAO,WenTing LI,ZhuanJian LI,XiangTao KANG(),GuiRong SUN()   

  1. College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046
  • Received:2019-01-22 Accepted:2020-01-13 Online:2020-04-01 Published:2020-04-14
  • Contact: XiangTao KANG,GuiRong SUN E-mail:xtkang2001@263.net;grsun2000@126.com

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Abstract: 【Objective】The aim of the study was to analyze the whole genome re-sequencing data of Xichuan black-bone chicken to obtain the identification, classification, distribution of the transposon of Xichuan black-bone chicken, and to explore the pathways involved in transposon-related genes, which not only had important significance for studying the biological function of the Xichuan black-bone chicken transposon elements (TEs), but also provided important basic data for exploring genome amplification, genome function and evolution research. 【Method】In this study, whole genome resequencing of blood DNA of Xichuan black-bone chicken was performed, and the paired-end mapping methods alignment genome was used. The TEs was identified, constructed, corrected and classified by RepeaterModeler, TEclass, RepeatMasker and other processes. All TEs in the whole genome of Xichuan black-bone chicken were obtained to analyze the characteristics, distribution and relationship of their genes. All genes inserted in the TEs were subjected to GO and KEGG databases enrichment, and the functions were described in combination with GO and KEGG annotation results, respectively. 【Result】 After identification, classification and annotation, 370 252 TEs sequences were identified in Xichuan black-bone chicken, which were divided into 19 superfamilies, mainly CR1, TcMar-Mariner, ERVL, ERV1 and other superfamilies, further indicated that the TEs types of Xichuan black-bone chicken were major TEs. The number of TEs was related to chromosome length, and longer the chromosome was, the more the number of TEs was. Number of TEs was inversely proportional to the density of gene. TEs density was relatively low in gene dense regions. The insertion of TEs in genome was not random, LTR/ERVL, LTR/ERV1, DNA/PIF-Harbinger, DNA/Hat-Charlie, RC/Helitron tend to be inserted outside the gene. GO enrichment analysis indicated some of these genes related to TEs were enriched in the following biological process terms: cell process, single-organism process, metabolic process, biological regulation, response to stimulus. In addition, some of these genes related to TEs were enriched in the following molecular function terms: binding and catalytic activity. Furthermore, some of these genes related to TEs were enriched in the following cell component terms: cell parts, organelles, and membranes. KEGG enrichment analysis indicated that these genes related to TEs mainly focused on Glycerolipid metabolism, PPAR signaling pathway, PI3K-Akt signaling pathway, Insulin resistance, and Jak-STAT signaling pathway. This study mainly focused on the pathways related to the characteristics of Xichuan black-bone chicken, such as tyrosine metabolism related to pigmentation, lipid metabolism related to meat quality, fatty acid synthesis, and PI3K-Akt signaling pathway. 【Conclusion】 There was a positive correlation between TEs content and genome size of Xichuan black-bone chicken. Moreover, the TEs of Xichuan black-bone chicken had a certain preference in the distribution of genome. TEs related genes were enriched in the pigmentation related pathway, which might be related to the germplasm characteristics of Xichuan black-bone chicken. The specific regulatory mechanisms remained to be further studied.

Key words: chicken, whole genome resequencing, transposon elements, characterization analysis

Table 1

Statistical analysis of genome TEs"

分类
Class		 类别
Order		 超家族
Superfamily		 数量
Counts
逆转录转座子
Retrotransposons		 LTR Copia 2 182
Gypsy 424
ERV1 12 026
ERVK 7 502
ERVL 57 233
ERV 5 265
LINE CR1 243 531
I 489
L2 591
RTE-X 259
SINE SINE/MIR 208
DNA转座子
DNA transposons		 DNA CMC-EnSpm 1 808
hAT-Ac 486
hAT-Charlie 9 076
MULE-MuDR 462
P 2 853
PIF-Harbinger 4 148
TcMar-Mariner 18 304
RC/Helitron RC/Helitron 3 405

Table 2

Annotation of TEs superfamilies in whole-genome resequencing assembly"

分类
Class		 类别
Order		 超家族
Superfamily		 数量
Counts		 比对序列
Masked (bp)		 Masked序列所占比
Percentage of Masked (%）
逆转录转座子Retrotransposons
 LTR LTR 77112 34594642 2.81
ERVL 45563 18364082 1.49
ERV_classI 11039 5027391 0.41
ERV_classII 3659 2027848 0.16
SINE SINE 208 16102 0.01
LINE LINE 234961 79044697 6.43
LINE2 589 336996 0.03
L3/CR1 233726 78474296 6.38
DNA转座子
DNA transposons		 DNA DNA 36568 14908973 1.21
hAT-Charlie 8963 1578789 0.13
未分类 Unclassified 60019 25121370 2.04
总计 Total 635295 224900544 18.29

Table 3

Distribution of transposons on chromosomes"

染色体
Chromosome		 TEs数量
TEs Counts		 所占比例
Proportion (%)		 染色体
Chromosome		 TEs数量
TEs Counts		 所占比例
Proportion (%)
Chr1 71257 26.74 Chr15 1767 0.66
Chr2 47150 17.69 Chr17 1584 0.59
Chr3 29426 11.04 Chr18 1732 0.65
Chr4 20621 7.74 Chr19 1511 0.57
Chr5 11618 4.36 Chr20 2043 0.77
Chr6 5725 2.15 Chr21 434 0.16
Chr7 6196 2.32 Chr22 863 0.32
Chr8 5233 1.96 Chr23 901 0.34
Chr9 3829 1.44 Chr24 626 0.23
Chr10 2981 1.12 Chr26 534 0.20
Chr11 2963 1.11 Chr27 1503 0.56
Chr12 2911 1.09 Chr28 753 0.28
Chr13 2670 1.00 ChrZ 33206 12.46
Chr14 1656 0.62 ChrW 4822 0.01

Fig. 2

Distribution of TEs and genes A: Chromosome 1；B: Chromosome 2; C: Chromosome 4; D:Chromosome Z. Green line: TEs number; Blue line: Genes number"

Fig. 2

Preferential distribution of TEs in genes in genome"

Fig. 3

GO categories enrichment analysis of genes related to TEs"

Table 4

Top 20 metabolic pathways involving genes related to TEs"

代谢通路 KEGG ID KEGG通路名称 Name of KEGG 数量 Numbers
ko00561 甘油酯代谢 Glycerolipid metabolism 392
ko03320 PPAR信号通路 PPAR signaling pathway 391
ko04151 PI3K-Akt信号通路 PI3K-Akt signaling pathway 211
ko04931 胰岛素抵抗 Insulin resistance 173
ko04630 Jak-STAT信号通路 Jak-STAT signaling pathway 169
ko04810 肌动蛋白细胞骨架调节 Regulation of actin cytoskeleton 143
ko04120 泛素介导的蛋白水解 Ubiquitin mediated proteolysis 139
ko00240 嘧啶代谢 Pyrimidine metabolism 137
ko04020 钙信号途径 Calcium signaling pathway 136
ko05205 癌症中的蛋白多糖 Proteoglycans in cancer 129
ko04080 神经活性配体-受体相互作用 Neuroactive ligand-receptor interaction 123
ko04510 粘附斑激酶 Focal adhesion 121
ko04014 Ras信号通路 Ras signaling pathway 116
ko04724 谷氨酸突触 Glutamatergic synapse 115
ko04010 MAPK信号通路 MAPK signaling pathway 109
ko05166 HTLV-I感染 HTLV-I infection 106
ko04024 cAMP信号通路 cAMP signaling pathway 98
ko04072 磷脂酶D信号通路 Phospholipase D signaling pathway 98
ko01521 表皮生长因子受体酪氨酸激酶抑制剂耐药性 EGFR tyrosine kinase inhibitor resistance 92
ko04144 胞吞 Endocytosis 92

Fig. 4

Pathway enrichment analysis of TEs related genes"

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