大蹄蝠全基因组微卫星分布特征分析

doi:10.16829/j.slxb.150724

摘要/Abstract

摘要：

脊椎动物基因组含有丰富的微卫星信息。本研究对翼手目动物中的大蹄蝠全基因组及其基因的微卫星分布特征进行分析，并对含有微卫星编码序列的基因进行注释分析。结果表明，大蹄蝠全基因组大小为2.24 Gb，共含有497 883个微卫星，其中，数量和比例最多的是单碱基和二碱基重复类型，分别有173 953个 (34.94%) 和222 591个 (44.71%)，相对丰度分别为77.78 loci/Mb和99.52 loci/Mb。微卫星数量从单碱基重复到六碱基重复单元最多的类型分别为 (A)_n、(AC)_n、(TAT)_n、(TTTA)_n、(AACAA)_n和 (TATCTA)_n，比例分别为95.14%、55.25%、38.41%、22.17%、48.68%和20.30%。不同基因区和基因间区的数量及丰度不同，其中基因间区的微卫星数量及其丰度最大，分别为322 666 个和2 541.57 loci/Mb，编码区的微卫星数量及其丰度最小，分别为1 461个和461.98 loci/Mb。基因间区和全基因组的微卫星的分布特征相似。编码区最多的微卫星类型为三碱基重复单元，外显子最多的微卫星类型为单碱基、二碱基和三碱基重复单元。在微卫星丰度分布的位置特征分析中，基因上游500 bp、外显子、内含子和基因下游500 bp各个区域微卫星丰度分别为16 400.94 loci/Mb、972.12 loci/Mb、2 180.66 loci/Mb和3 899.89 loci/Mb。大蹄蝠基因中含有微卫星的编码序列 (Coding sequence, CDS) 1 461条，被注释到的基因有1 226个。GO注释到63个主要功能基因中，并分配到26 439个GO条目。KEGG富集最显著的是信号传导通路，含有146个基因。本研究结果不仅为大蹄蝠高质量微卫星的筛选提供参考，还将进一步为翼手目其他物种的全基因组微卫星分布特征分析及其微卫星在全基因组中的生物学功能研究提供参考。

关键词: 翼手目, 大蹄蝠, 全基因组, 微卫星, GO分析, KEGG富集

Abstract:

The vertebrate genome is rich in microsatellite information. In this study, the distribution of microsatellite (SSRs) in the complete genome and its genes of Hipposideros armiger (Chiroptera) was analyzed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) containing microsatellite coding sequence (CDS) were explored. The results showed that the total genome size of H. armiger was 2.24 Gb and contained 497 883 microsatellites. Mononucleotide (173 953 microsatellites) and dinucleotide repeats (222 591 microsatellites) were the most diverse in the genome of H. armiger accounting for 34.94% and 44.71% of whole genome size, with their relative abundance of 77.78 loci/Mb and 99.52 loci/Mb, respectively. The most microsatellite types from mononucleotide repeat to hexanucleotide repeat were (A)_n, (AC)_n, (TAT)_n, (TTTA)_n, (AACAA)_n and (TATATA)_n, with their frequency of 95.14%, 55.25%, 38.41%, 22.17%, 48.68% and 20.30% respectively. The number and abundance of microsatellites were different in both gene regions and intergenic regions. The diversity of microsatellites was highest in intergenic region with 322 666 microsatellites, and its abundance was 2 541.57 loci/Mb, whereas lowest in coding region with 1 461 microsatellites, and its abundance was 461.98 loci/Mb. The distribution characteristics of microsatellites in intergenic region and total genome were similar. Trinucleotide repeat were the most common types of microsatellites in the coding region, while mono-, di- and tri-nucleotide repeat were the most common types of microsatellites in the exons. The positional specificity of microsatellites abundance distributions in 500 bp upstream, exon, intron and 500 bp downstream were 16 400.94 loci/Mb, 972.12 loci/Mb, 2 180.66 loci/Mb and 3 899.89 loci/Mb, respectively. A total of 1 461 microsatellite coding sequences (CDS) were found in the genome of H. armiger, and 1 226 genes were annotated. GO was mainly annotated into 63 functional genes and assigned to 26 439 GO items. The most significant KEGG enrichment was in the signal transduction pathway, which contained 146 genes. The results of this study not only provide a reference for the screening of high-quality microsatellites in H. armiger, it will also provide a reference for genome-wide analysis of microsatellite distribution in other Chiroptera species and the study of their biological functions in the whole genome.

Key words: Chiroptera, Hipposideros armiger, Genome, Microsatellite, GO analysis, KEGG enrichment

中图分类号:

Q754

邵伟伟, 乔芬, 蔡玮, 林植华, 韦力. 大蹄蝠全基因组微卫星分布特征分析[J]. 兽类学报, 2023, 43(2): 182-192.

Weiwei SHAO, Fen QIAO, Wei CAI, Zhihua LIN, Li WEI. Characteristics of microsatellite distributions in genomes of Hipposideros armiger (Chiroptera)[J]. ACTA THERIOLOGICA SINICA, 2023, 43(2): 182-192.

图/表 8

表1 大蹄蝠微卫星在全基因组中的分布情况

Table 1 Distribution of microsatellites in the genomes of Hipposideros armiger

微卫星类型 Type of SSR	微卫星数量 Number of SSRs	长度 Length （bp）	丰度Abundance （loci/Mb）	比例 Percentage （%）
单碱基 Mononucleotide	173 953	2 451 423	77.78	34.94
二碱基 Dinucleotide	222 591	6 114 126	99.52	44.71
三碱基 Trinucleotide	37 566	800 058	16.8	7.55
四碱基 Tetranucleotide	47 250	1 517 188	21.13	9.49
五碱基 Pentanucleotide	13 134	310 285	5.87	2.64
六碱基 Hexanucleotide	3 389	98 148	1.52	0.68
SSR总数 Total of SSRs	497 883	11 291 228	222.61	100
总基因组大小 Whole genome length （bp）	2 236 581 172
微卫星含量 SSR content of genome （%）	0.50

图1 大蹄蝠各重复单元微卫星重复次数分布比较

Fig. 1 Repeat distribution of each microsatellite type in Hipposideros armiger

表2 大蹄蝠最多微卫星重复单元的比较

Table 2 The most frequent microsatellite motifs found in genomes of Hipposideros armiger

模体单元 Motif length	重复单元 Repeat unit	微卫星数量 Microsatellites	比例 Percentage （%）
单碱基重复 Mononucleotide repeat	A	165 494	95.14
单碱基重复 Mononucleotide repeat	G	8 459	4.86
二碱基重复 Dinucleotide repeat	AC	122 977	55.25
	CT	42 659	19.16
	GC	1 460	0.66
	TA	55 495	24.93
三碱基重复 Trinucleotide repeat	TAT	14 429	38.41
	CAA	7 164	19.07
	ACC	3 653	9.72
	CAT	3 408	9.07
四碱基重复 Tetranucleotide repeat	TTTA	10 475	22.17
	AAAC	8 049	17.03
	ATAG	7 078	14.98
	CATT	4 959	10.50
五碱基重复 Pentanucleotide repeat	AACAA	6 393	48.68
	TTATT	2 544	19.37
	TTTCT	795	6.05
	TATTA	354	2.70
六碱基重复 Hexanucleotide repeat	TATCTA	688	20.30
	AAACAA	510	15.05
	GAGAGG	284	8.38
	AATAAA	133	3.92

表3 大蹄蝠微卫星在不同基因区和基因间区的数量及丰度比较

Table 3 The number and abundance of microsatellites in different genomic regions of Hipposideros armiger

指标

Index

基因区Genetic region

基因间区

Intergenic region

编码区

CDS

非翻译区

Untranslated

外显子

Exon

内含子

Intron

数量

Number

丰度

Abundance(loci/Mb)

图2 大蹄蝠不同基因组区微卫星类型的分布比较. A：全基因组；B：编码区；C：外显子；D：基因间区. 1 ~ 6分别表示单碱基，二碱基，三碱基，四碱基，五碱基，六碱基

Fig. 2 The distribution of microsatellite types in different genomic regions.Genome (A), CDS (B), Exon (C) and Intergenetic (D) of Hipposideros armiger. 1 - 6 indicated mono-, di-, tri-, tetra-, penta-, hexa-nucleotide respectively

图3 大蹄蝠基因区及其上、下游微卫星丰度的比较.代码1 ~ 13分别表示基因上游500 bp、第一外显子、第一内含子、第二外显子、第二内含子、中间左外显子、中间内含子、中间右外显子、倒数第二内含子、倒数第二外显子、倒数第一内含子、倒数第一外显子、基因下游500 bp

Fig. 3 The microsatellite abundance in gene regions and their upstream and downstream regions of Hipposideros armiger. Number 1 - 13 indicated upstream 500 bp, exon 1, intron1, exon 2, intron 2, mid left exon, mid intron, mid right exon,intron reverse 2, exon reverse 2, intron reverse 1, exon reverse 1, downstream 500 bp, respectively

图 4 大蹄蝠微卫星分布于外显子的基因GO功能分类. 1：生殖；2：生殖细胞杀伤；3：免疫系统过程；4：行为；5：代谢；6：细胞增殖；7：碳水化合物利用；8：细胞过程；9：氮的利用；10：生殖过程；11：生物粘附；12：信号；13：多细胞生物突；14：发育过程；15：生长；16：运动；17：色素沉着；18：生物相；19：节律过程；20：生物过程的正向调节；21：生物过程负调节；22：生物过程调节；23：对刺激的反应；24：定位；25：多生物过程；26：生物调节；27：细胞组成或生物发生；28：细胞聚集；29：解毒；30：与化学突触传递有关的突触前过程；31：细胞外区；32：细胞；33：类核；34：膜；35：病毒粒子；36：细胞连接；37：膜封闭腔；38：含蛋白复合物；39：细胞器；40：其他生物；41：其他有机体部分；42：胞外区部分；43：细胞器部分；44：病毒粒子部分；45：薄膜部分；46：突触部分；47：细胞部分；48：突触；49：共质体；50：超分子络合物；51：催化活性；52：信号传感器活动；53：结构分子活性；54：转运活动；55：连接；56：抗氧化活性；57：货物受体活性；58：转换调节器活性；59：毒素活性；60：分子功能调节剂；61：被劫持的分子功能；62：分子载体活性；63：转录调节因子活性.黑色、条纹和白色区域分别代表生物过程、细胞组分和分子功能

Fig. 4 GO classifications of coding sequencings with microsatellites in the genomes of Hipposideros armiger. 1: Reproduction; 2: Cell killing; 3: Immune system process; 4: Behavior; 5: Metabolic process; 6: Cell proliferation; 7: Carbohydrate utilization; 8: Cellular process; 9: Nitrogen utilization; 10: Reproductive process; 11: Biological adhesion; 12: Signaling; 13: Multicellular organismal process; 14: Developmental process; 15: Growth; 16: Locomotion; 17: Pigmentation; 18: Biological phase; 19: Rhythmic process; 20: Positive regulation of biological process; 21: Negative regulation of biological process; 22: Regulation of biological process; 23: Response to stimulus; 24: Localization; 25: Multi-organism process; 26: Biological regulation; 27: Cellular component organization or biogenesis; 28: Cell aggregation; 29: Detoxification; 30: Presynaptic process involved in chemical synaptic transmission; 31: Extracellular region; 32: Cell; 33: Nucleoid; 34: Membrane; 35: Virion; 36: Cell junction; 37: Membrane-enclosed lumen; 38: Protein-containing complex; 39: Organelle; 40: Other organism; 41: Other organism part; 42: Extracellular region part; 43: Organelle part; 44: Virion part; 45: Membrane part; 46: Synapse part; 47: Cell part; 48: Synapse; 49: Symplast; 50: Supramolecular complex; 51: Catalytic activity; 52: Signal transducer activity; 53: Structural molecule activity; 54: Transporter activity; 55: Binding; 56: Antioxidant activity; 57: Cargo receptor activity; 58: Translation regulator activity; 59: Toxin activity; 60: Molecular function regulator; 61: Hijacked molecular function; 62: Molecular carrier activity; 63: Transcription regulator activity. The black, stripe and white area indicated biological process, cellular component and molecular function, respectively

图5 大蹄蝠微卫星分布于外显子的基因KEGG富集. A：代谢；B：环境信息处理；C：遗传信息处理；D：细胞过程；E：生物体系统；F：人类疾病与药物开发

Fig. 5 The KEGG enrichment of exon microsatellites in Hipposideros armiger. A: Metabolism; B: Environmental information processing; C: Genetic information processing; D: Cell process; E: Organismal systems; F: Human diseases and drug development

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