淅川乌骨鸡全基因组转座子的鉴定与分析

doi:10.3864/j.issn.0578-1752.2020.07.017

摘要/Abstract

摘要： 【目的】 通过分析淅川乌骨鸡全基因组重测序数据,获取淅川乌骨鸡转座子的基本信息和特征分布,探究转座子相关基因参与的通路。不仅对研究淅川乌骨鸡转座子的生物学功能具有重要的意义,而且为探索基因组扩增、基因组功能及进化研究提供重要基础数据。 【方法】 对淅川乌骨鸡血液DNA进行全基因组重测序,采用双末端短序列比对基因组,运用RepeatModeler、TEclass、RepeatMasker等使用流程对转座子进行鉴定、构建、校正、分类和注释,获得淅川乌骨鸡整个基因组所有的转座子,对转座子的特征、分布及和基因的关系等方面进行分析。并对转座子插入的所有基因进行GO和KEGG数据库富集,分别结合GO和KEGG注释结果对功能进行描述。 【结果】 经鉴定、分类和注释,淅川乌骨鸡共鉴定到370 252个转座子序列,分为19个超家族,主要为CR1、TcMar-Mariner、ERVL、ERV1等超家族,进一步说明淅川乌骨鸡转座子类型主要是逆转录转座子;转座子的数目和染色体长度有关,染色体越长,转座子数目越多。在基因组中转座子和基因的密度成反比,基因密集的区域中转座子密度较低;基因组内转座子的插入并非随机的,LTR/ERVL、LTR/ERV1、DNA/PIF-Harbinger、DNA/Hat-Charlie、RC/Helitron等转座子倾向于插入基因外部。GO富集分析表明,在生物过程条目中鉴定出的转座子富集相对较多的是细胞过程、单生物过程、代谢过程、生物调节、刺激反应等;分子功能条目中鉴定出的转座子富集相对较多的是结合、催化活性等;细胞组分条目中鉴定出的转座子富集相对较多的是细胞部分、细胞器、膜等。KEGG富集分析表明,鉴定出的转座子主要在甘油酯代谢、PPAR信号通路、PI3K-Akt信号通路、胰岛素抵抗、Jak-STAT信号通路等通路。着重关注了与淅川乌骨鸡特性相关的通路,如和色素沉积有关的酪氨酸代谢、和肉品质有关的脂代谢、脂肪酸的合成、PI3K-Akt信号通路等。 【结论】 转座子含量与基因组大小,具有一定的正相关性,而且淅川乌骨鸡转座子在基因组的分布存在一定偏好性。转座子相关基因在色素相关通路中富集,其可能与淅川乌骨鸡的种质特性有关,具体的调控机制还有待进一步研究。

关键词: 鸡, 全基因组重测序, 转座子, 特征分析

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

李东华,付亚伟,张晨曦,曹艳芳,李文婷,李转见,康相涛,孙桂荣. 淅川乌骨鸡全基因组转座子的鉴定与分析[J]. 中国农业科学, 2020, 53(7): 1491-1500.

DongHua LI,YaWei FU,ChenXi ZHANG,YanFang CAO,WenTing LI,ZhuanJian LI,XiangTao KANG,GuiRong SUN. Genome-Wide Identification and Characterization of Transposable Elements in Xichuan Black-Bone Chicken[J]. Scientia Agricultura Sinica, 2020, 53(7): 1491-1500.

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参考文献 47

[1]	OKADA N . Transfer RNA-like structure of the human Alu family: implications of its generation mechanism and possible functions. Journal of Molecular Evolution, 1990,31(6):500-510.
[2]	FINNEGAN D J . Eukaryotic transposable elements and genome evolution. Trends in Genetics, 1989,5(4):103-107.
[3]	LISCH D . How important are transposons for plant evolution? Nature Reviews Genetics, 2013,14(1):49.
[4]	MCCLINTOCK B . The origin and behavior of mutable loci in maize. Proceedings of the National Academy of Sciences of the United States of America, 1950,36(6):344.
[5]	DOOLITTLE W F, SAPIENZA C . Selfish genes, the phenotype paradigm and genome evolution. Nature, 1980,284(5757):601-603.
[6]	HOSKINS R A, CARLSON J W, KENNEDY C, ACEVEDO D, EVANSHOLM M, FRISE E, WAN K H, PARK S, MENDEZLAGO M, ROSSI F . Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science, 2007,316(5831):1625-1628.
[7]	NENE V, WORTMAN J R, LAWSON D, HAAS B, KODIRA C, TU Z J, LOFTUS B, XI Z, MEGY K, GRABHERR M . Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 2007,316(5832):1718-1723.
[8]	GALLAGHER L A, SHENDURE J, MANOIL C . Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq. mBio, 2011,2(1):00315-00310.
[9]	REARDEN A, MAGNET A, KUDO S, FUKUDA M . Glycophorin B and glycophorin E genes arose from the glycophorin A ancestral gene via two duplications during primate evolution. Journal of Biological Chemistry. 1993,268(3):2260-2267.
[10]	MANDAOKAR A, KUMAR V D, AMWAY M, BROWSE J . Microarray and differential display identify genes involved in jasmonate-dependent anther development. Plant Molecular Biology, 2003,52(4):775.
[11]	MACIA A, BLANCO-JIMENEZ E, GARC A-P REZ J L. Retrotransposons in pluripotent cells: Impact and new roles in cellular plasticity. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2015,1849(4):417-426.
[12]	SLOTKIN R K, MARTIENSSEN R . Transposable elements and the epigenetic regulation of the genome. Nature Reviews Genetics, 2007,8(4):272-285.
[13]	TIAN Z, ZHAO M, SHE M, DU J, CANNON S B, LIU X, XU X, QI X, LI M W, LAM H M . Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell, 2012,24(11):4422-4436.
[14]	CLARK L A, WAHL J M, REES C A, MURPHY K E . Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog. Proceedings of the National Academy of Sciences of the United States of America, 2006; 103(5):1376-1381.
[15]	STEFANIA DO, EMILIO S, LUCA F, MARCO T . Analysis of the 227 bp short interspersed nuclear element (SINE) insertion of the promoter of the myostatin (MSTN) gene in different horse breeds. Veterinaria Italiana, 2014; 50(3):193-197.
[16]	MIKAWA S, SATO S, NII M, MOROZUMI T, GOU Y, IMAEDA N, YAMAGUCHI T, HAYASHI T, AWATA T . Identification of a second gene associated with variation in vertebral number in domestic pigs. BMC Genetics,12,1(2011-01-14). 2011,12(1):5-5.
[17]	IVICS Z, GARRELS W, MÁTÉS L, YAU T Y, BASHIR S, ZIDEK V, LANDA V, GEURTS A, PRAVENEC M, RÜLICKE T, KUES W A, IZSVÁK Z. Germline transgenesis in pigs by cytoplasmic microinjection of Sleeping Beauty transposons. Nature Protocols, 2014, 9(4):810-827.
[18]	BAILLIE J K, BARNETT M W, UPTON K R, GERHARDT D J, RICHMOND T A, DE S F, BRENNAN P M, RIZZU P, SMITH S, FELL M . Somatic retrotransposition alters the genetic landscape of the human brain. Nature, 2011, 479(7374):534-537.
[19]	GOODIER J L . Retrotransposition in tumors and brains. Mobile DNA, 2014,5(1):11-17.
[20]	WICKER T, SABOT F, HUAVAN A, BENNETZEN J L, CAPY P, CHALHOUB B, FLAVELL A, LEROY P, MORGANTE M, PANAUD O . A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 2007(8):973-982.
[21]	CONESA A, GTZ S, GARC A G, MEZ J M, TEROL J, TAL N M, ROBLES M . Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005,21(18):3674-3676.
[22]	ASAF L, SCHRAGA S, GIL A . Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements. Nucleic Acids Research, 2009,38(5):1515-1530.
[23]	LINHEIRO R S, BERGMAN C M . Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS ONE, 2012,7(2):e30008.
[24]	INITIATIVE AG . Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 2000,408(6814):796-815.
[25]	SCHNABLE P S, WARE D, FULTON R S, STEIN J C, WEI F, PASTERNAK S, LIANG C, ZHANG J, FULTON L, GRAVES T A . The B73 maize genome: complexity, diversity, and dynamics. Science, 2009,326(5956):1112-1115.
[26]	MA B, XIN Y, KUANG L, HOU F, HE N . Identification and characterization of reverse transcriptase fragments of long interspersed nuclear elements (LINEs) in the Morus notabilis genome. American Journal of Molecular Biology, 2017, 7(3):138-152.
[27]	MILLS R E, BENNETT E A, ISKOW R C, DEVINE S E . Which transposable elements are active in the human genome? Trends in Genetics, 2007, 23(4):183-191.
[28]	SMIT A F . Interspersed repeats and other mementos of transposable elements in mammalian genomes. Current Opinion in Genetics & Development, 1999,9(6):657-663.
[29]	高波, 王伟, 钱跃, 陈才, 钟继汉, 沈丹, 陈伟, 宋成义 . 斑马鱼转座子时空表达特性. 生物信息学, 2017,15(4):201-206.
	GAO B, WANG W, QIAN Y, CHEN C, ZHONG J H, SHEN D, CHEN W, SONG C Y . Temporal and spatial expression characteristics of transposons in zebrafish. Chinese Journal of Bioinformatics, 2017, 15(4):201-206. (in Chinese)
[30]	HAWKINS J S, GROVER C E, WENDEL J F . Repeated big bangs and the expanding universe: Directionality in plant genome size evolution. Plant Science, 2008,174(6):557-562.
[31]	SANMIGUEL P, BENNETZEN J L . Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annals of Botany, 1998, 82(suppl_1):37-44.
[32]	PEREIRA V . Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biology, 2004,5(10):R79.
[33]	WRIGHT S I, AGRAWAL N, BUREAU T E . Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Research ,2003, 13(8):1897.
[34]	LOWE C B, BEJERANO G, HAUSSLER D . Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proceedings of the National Academy of Sciences of the United States of America, 2007,104(19):8005-8010.
[35]	IZSV K Z, IVICS Z, PLASTERK R H . Sleeping Beauty, a wide host-range transposon vector for genetic transformation in vertebrates. Journal of Molecular Biology, 2000,302(1):93-102.
[36]	HORIE K, KUROIWA A, IKAWA M, OKABE M, KONDOH G, MATSUDA Y, TAKEDA J . Efficient chromosomal transposition of a Tc1/mariner-like transposon Sleeping Beauty in mice. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98(16):9191-9196.
[37]	CARLSON C M, DUPUY A J, FRITZ S, ROBERGPEREZ K J, FLETCHER C F, LARGAESPADA D A . Transposon mutagenesis of the mouse germline. Genetics, 2003, 165(1):243.
[38]	MISKEY C, IZSV K Z, PLASTERK R H, IVICS Z . The Frog Prince: A reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells. Nucleic Acids Research, 2003, 31(23):6873-6881.
[39]	MISKEY C, PAPP B, MÁTÉS L, SINZELLE L, KELLER H, IZSV K Z, IVICS Z. The ancient mariner sails again: Transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. Molecular & Cellular Biology, 2007,27(12):4589-4600.
[40]	TAKEUCHI M, MATSUDA K, YAMAGUCHI S, ASAKAWA K, MIYASAKA N, LAL P, YOSHIHARA Y, KOGA A, KAWAKAMI K, SHIMIZU T . Establishment of Gal4 transgenic zebrafish lines for analysis of development of cerebellar neural circuitry. Developmental Biology, 2015,397(1):1-17.
[41]	ASAKAWA K, SUSTER M L, MIZUSAWA K, NAGAYOSHI S, KOTANI T, URASAKI A, KISHIMOTO Y, HIBI M, KAWAKAMI K . Genetic dissection of neural circuits by Tol2 transposon-mediated Gal4 gene and enhancer trapping in zebrafish. Proceedings of the National Academy of Sciences of the United States of America, 2008,105(4):1255.
[42]	ZHONGJIE Y, QIPENG L, SHAN C, XIAOYU L . The function of LINE-1-encoded reverse transcriptase in tumorigenesis. Hereditas, 2017,39(5):368-376.
[43]	QIAN L, JINHUI W, XIAOYU L, SHAN C . The connection between LINE-1 retrotransposition and human tumorigenesis. Hereditas, 2016: 93-102.
[44]	BOULLIOU A, LE P J, HUBERT G, DONAL R, SMILEY M . The endogenous retroviral ev21 locus in commercial chicken lines and its relationship with the slow-feathering phenotype (K). Poultry Science, 1992,71(1):38.
[45]	LU X Q, HAN J R, LIU X F, LIN T H, LI Y L . The LTR of endogenous retrovirus ev21 retains promoter activity and exhibits tissue specific transcription in chicken. Chinese Science Bulletin, 2009,54(24):4664-4670.
[46]	GAVORA J S, KUHNLEIN U, CRITTENDEN L B, SPENCER J L, SABOUR M P . Endogenous viral genes: Association with reduced egg production rate and egg size in White Leghorns. Poult Sciences, 1991,70(3):618-623.
[47]	WANG Z, QU L, YAO J, YANG X, LI G, ZHANG Y, LI J, WANG X, BAI J, XU G . An EAV-HP Insertion in 5′ flanking region of SLCO1B3 causes Blue Eggshell in the chicken. Plos Genetics, 2013,9(1):e1003183.

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

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
DNA转座子 DNA transposons	DNA	hAT-Charlie	8963	1578789	0.13
未分类 Unclassified			60019	25121370	2.04
总计 Total			635295	224900544	18.29

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

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