林麝及其近缘物种编码区微卫星分布规律及功能分析

doi:10.16829/j.slxb.150645

兽类学报 ›› 2022, Vol. 42 ›› Issue (6): 705-715.DOI: 10.16829/j.slxb.150645

林麝及其近缘物种编码区微卫星分布规律及功能分析

赵琪¹, 张琪¹, 李浩玲¹, 兰月², 鄢行安³, 赵贵军³(), 戚文华¹()

^1.重庆三峡学院生物与食品工程学院，重庆 404100
^2.四川大学生命科学学院，成都 610064
^3.重庆市药物种植研究所，重庆 408435

收稿日期:2021-12-01 接受日期:2022-07-05 出版日期:2022-11-30 发布日期:2022-12-02
通讯作者: 赵贵军,戚文华
作者简介:赵琪 (1996- )，女，硕士研究生，主要从事动植物分子/遗传资源利用研究；
张琪 (1995- )，女，硕士研究生，主要从事动植物分子/遗传资源利用研究.第一联系人：张琪共同第一作者
基金资助:
国家自然科学基金(31702032);重庆市自然科学基金(cstc2019jcyj-msxmX0410);重庆市基本科研项目(cstc2021jxjl-jbky10008)

Distinct patterns of microsatellite and functional analysis of forest musk deer and its closely related species

Qi ZHAO¹, Qi ZHANG¹, Haoling LI¹, Yue LAN², Xingan YAN³, Guijun ZHAO³(), Wenhua QI¹()

^1.College of Life Science and Engineering, Chongqing Three Gorges University, Chongqing 404100, China
^2.College of Life Sciences, Sichuan University, Chengdu 610064, China
^3.Chongqing Institute of Medicinal Plant Cultivation, Chongqing 408435, China

Received:2021-12-01 Accepted:2022-07-05 Online:2022-11-30 Published:2022-12-02
Contact: Guijun ZHAO,Wenhua QI

摘要/Abstract

摘要：

麝科和鹿科动物均属于偶蹄反刍类动物，具有重要的经济价值。通过系统的微卫星序列 (Simple sequences repeats, SSRs) 从基因组水平揭示物种间的系统进化关系，探索微卫星序列的基因功能及其富集的信号通路，目前仍缺乏相关研究。随着林麝 (Moschus berezovskii)、原麝 (Moschus moschiferus)、小麂 (Muntiacus reevesi)、赤麂 (Muntiacus vaginalis) 和马鹿 (Cervus elaphus) 基因组测序的完成，本文利用生物信息学方法提取了这些动物蛋白质编码区 (coding sequences, CDS) 序列，统计和分析了其CDS区微卫星序列分布规律及其生物学功能，探索了含SSR 基因富集的信号通路及其与疾病的关联性。结果表明，林麝、原麝、小麂、赤麂和马鹿蛋白质编码区含SSR序列的基因所占比例分别为6.96% (1 696个)、7.18% (2 359个)、7.29% (3 005个)、7.36% (1 916个) 和7.48% (1 924个)，并且这5种动物CDS区SSRs分布模式具有相似性，均是三倍体核苷酸 (即三核苷酸和六核苷酸) SSRs最多，分别为96.85%、94.87%、65.44%、64.23%和88.04%。GO功能富集表明，林麝与其他4种动物蛋白质编码区SSR序列在分子功能、细胞组成和生物学过程3个方面具有较多共同显著富集的功能，包括DNA结合、染色质和生长发育等。KEGG 通路分析表明，林麝及其他4种动物蛋白质编码区SSR序列具有7个共同显著富集的KEGG通路，包括遗传信息调控蛋白家族、转录因子、染色体及相关蛋白、剪接体、转录机制和Notch信号通路和成体糖尿病。通过对林麝编码区含SSR关键免疫基因及其相关联的KEGG通路进行分析，发现10个含SSR的关键免疫基因对应的KEGG通路与疾病密切相关。

关键词: 林麝, 原麝, 小麂, 赤麂, 马鹿, 编码区, 微卫星序列, 功能注释

Abstract:

Muscidae and Cervidae belong to artiodactyl ruminants and have important economic value. There is still a lack of relevant studies on using simple sequence repeats (SSRs) to reveal the phylogenetic relationship among species at the genomic level and to explore the gene functions of SSRs and their enriched signaling pathways. With the completion of the genome sequence of the forest musk deer (Moschus berezovskii), Siberian musk deer (Moschus moschiferus), the red deer (Cervus elaphus), the Reeves’ muntjac (Muntiacus reevesi), and the red muntjac (Muntiacus vaginalis), we extracted the coding sequences (CDS) of these species by bioinformatics method and analyzed the distribution patterns of coding SSR and their biological functions. The containing-SSR genes were enriched in the signal pathways and their association with disease were explored. The results prove that the proportion of their coding SSRs were 6.96% (1 696), 7.18% (2 359), 7.29% (3 005), 7.36% (1 916), and 7.48% (1 924), respectively. In addition, the distribution pattern of coding SSRs of the five species was similar, triplet repeats SSR (Tri- and Hexa-SSRs) of the five species were the most similar, which were 96.85%, 94.87%, 65.44%, 64.23%, and 88.04%, respectively. The GO functional enrichment showed that the SSR sequences in the CDS of the five species had many same enriched functions in three aspects: molecular function, cellular component, and biological process, including DNA binding, chromatin, growth, and development. The result of the KEGG pathway enrichment analysis showed that there are 7 KEGG pathways that were significantly co?enriched in forest musk deer and other species.These include protein families: genetic information processing, transcription factors, chromosome and associated proteins, spliceosome, transcription machinery, Notch signaling pathway, and maturity?onset diabetes of the young. By analyzing the SSR-containing key immune genes and their associated KEGG pathways in the CDS region of forset musk deer, 10 SSR-containing key immune genes corresponding to the KEGG pathway were found to be closely associated with the disease.

Key words: Forest musk deer, Siberian musk deer, Red deer, Small suede, Red muntjac, CDS, SSR, Functional analysis

中图分类号:

Q959.8

赵琪, 张琪, 李浩玲, 兰月, 鄢行安, 赵贵军, 戚文华. 林麝及其近缘物种编码区微卫星分布规律及功能分析[J]. 兽类学报, 2022, 42(6): 705-715.

Qi ZHAO, Qi ZHANG, Haoling LI, Yue LAN, Xingan YAN, Guijun ZHAO, Wenhua QI. Distinct patterns of microsatellite and functional analysis of forest musk deer and its closely related species[J]. ACTA THERIOLOGICA SINICA, 2022, 42(6): 705-715.

图/表 7

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参数 Parameters	林麝 Moschus berezovskii	原麝 Moschus moschiferus	小麂 Muntiacusreeves	赤麂 Muntiacus vaginalis	马鹿 Cervus elaphus
编码区基因数量 Total number of genes of CDS	24 352	29 305	26 044	25 737	28 103
GC含量 GC content （%）	53.79	53.37	53.34	53.41	53.60
SSR序列数量 Number of SSRs	2 542	3 118	2 769	2 726	3 729
SSR序列长度 Total length of SSRs （bp）	49 233	76 969	85 507	708 052	67 743
SSR序列占编码区序列的比例 CDS SSRs content （%）	6.96	7.18	7.36	7.48	7.29
丰度 Relative abundance （No./Mb）	75.28	64.63	65.18	60.86	52.64
密度 Relative density （bp/Mb）	1 432.07	1 194.42	1 169.14	1 084.19	10 248.16

参数 Parameters	林麝 Moschus berezovskii	原麝 Moschus moschiferus	小麂 Muntiacusreeves	赤麂 Muntiacus vaginalis	马鹿 Cervus elaphus
编码区基因数量 Total number of genes of CDS	24 352	29 305	26 044	25 737	28 103
GC含量 GC content （%）	53.79	53.37	53.34	53.41	53.60
SSR序列数量 Number of SSRs	2 542	3 118	2 769	2 726	3 729
SSR序列长度 Total length of SSRs （bp）	49 233	76 969	85 507	708 052	67 743
SSR序列占编码区序列的比例 CDS SSRs content （%）	6.96	7.18	7.36	7.48	7.29
丰度 Relative abundance （No./Mb）	75.28	64.63	65.18	60.86	52.64
密度 Relative density （bp/Mb）	1 432.07	1 194.42	1 169.14	1 084.19	10 248.16

GO term	林麝 Moschus berezovskii	原麝 Moschus moschiferus	小麂 Muntiacus reeves	赤麂 Muntiacus vaginalis	马鹿 Cervus elaphus
Positive regulation of nitrogen compound metabolic process	+	+	+	+	+
Positive regulation of RNA biosynthetic process	+	+	+	+	+
Negative regulation of RNA biosynthetic process	+	+	+	+	-
Regulation of nucleobase-containing compound metabolic process	+	+	+	+	+
Regulation of nucleic acid-templated transcription	+	+	+	+	+
Transcription， DNA-templated	+	+	+	+	+
Regulation of biosynthetic process	+	+	+	+	+
Negative regulation of metabolic process	+	+	+	+	-
Positive regulation of metabolic process	+	+	+	+	+
Gene expression	+	+	+	+	+
Regulation of macromolecule biosynthetic process	+	+	+	+	+
Negative regulation of macromolecule biosynthetic process	+	+	+	+	-
Positive regulation of macromolecule metabolic process	+	+	+	+	+
Negative regulation of gene expression	+	+	-	+	-
Positive regulation of transcription， DNA-templated	+	+	+	+	+
Negative regulation of nucleobase-containing compound metabolic process	+	+	-	+	-
Negative regulation of cellular metabolic process	+	+	-	+	-
Negative regulation of cellular biosynthetic process	+	+	+	+	-
Nucleic acid-templated transcription	+	+	-	+	+
Negative regulation of biological process	+	+	+	+	-
Stem cell differentiation	+	+	+	+	+
RNA biosynthetic process	+	+	-	+	+
Negative regulation of transcription by RNA polymerase Ⅱ	+	+	-	+	-
Regulation of nitrogen compound metabolic process	+	+	-	+	+
Regulation of RNA metabolic process	+	+	-	+	+
Central nervous system neuron differentiation	+	+	+	+	+
Negative regulation of RNA metabolic process	+	+	+	+	-
Regulation of RNA biosynthetic process	+	+	-	+	+
Negative regulation of transcription， DNA-templated	+	+	+	+	-
Positive regulation of cellular metabolic process	+	+	+	+	+

GO term	林麝 Moschus berezovskii	原麝 Moschus moschiferus	小麂 Muntiacus reeves	赤麂 Muntiacus vaginalis	马鹿 Cervus elaphus
Positive regulation of nitrogen compound metabolic process	+	+	+	+	+
Positive regulation of RNA biosynthetic process	+	+	+	+	+
Negative regulation of RNA biosynthetic process	+	+	+	+	-
Regulation of nucleobase-containing compound metabolic process	+	+	+	+	+
Regulation of nucleic acid-templated transcription	+	+	+	+	+
Transcription， DNA-templated	+	+	+	+	+
Regulation of biosynthetic process	+	+	+	+	+
Negative regulation of metabolic process	+	+	+	+	-
Positive regulation of metabolic process	+	+	+	+	+
Gene expression	+	+	+	+	+
Regulation of macromolecule biosynthetic process	+	+	+	+	+
Negative regulation of macromolecule biosynthetic process	+	+	+	+	-
Positive regulation of macromolecule metabolic process	+	+	+	+	+
Negative regulation of gene expression	+	+	-	+	-
Positive regulation of transcription， DNA-templated	+	+	+	+	+
Negative regulation of nucleobase-containing compound metabolic process	+	+	-	+	-
Negative regulation of cellular metabolic process	+	+	-	+	-
Negative regulation of cellular biosynthetic process	+	+	+	+	-
Nucleic acid-templated transcription	+	+	-	+	+
Negative regulation of biological process	+	+	+	+	-
Stem cell differentiation	+	+	+	+	+
RNA biosynthetic process	+	+	-	+	+
Negative regulation of transcription by RNA polymerase Ⅱ	+	+	-	+	-
Regulation of nitrogen compound metabolic process	+	+	-	+	+
Regulation of RNA metabolic process	+	+	-	+	+
Central nervous system neuron differentiation	+	+	+	+	+
Negative regulation of RNA metabolic process	+	+	+	+	-
Regulation of RNA biosynthetic process	+	+	-	+	+
Negative regulation of transcription， DNA-templated	+	+	+	+	-
Positive regulation of cellular metabolic process	+	+	+	+	+

Pathway Class	Pathway name	林麝 Moschus berezovskii	原麝 Moschus moschiferus	小麂 Muntiacus reeves	赤麂 Muntiacus muntjak	马鹿 Cervus elaphus
遗传信息调控 Genetic information processing	Protein families： genetic information processing	1.83E-08	8.79E-14	1.55E-13	0	0
	Transcription factors	9.35E-07	1.10E-13	1.33E-13	0	1.15E-11
	Chromosome and associated proteins	1.24E-05	1.76E-13	9.18E-04	6.37E-05	5.97E-09
	Spliceosome	4.03E-03	3.56E-06	1.15E-04	1.22E-05	1.26E-12
	Transcription machinery	2.36E-02	9.71E-04	1.32E-2	5.29E-3	1.64E-07
	Ion channels	—	5.50E-3	4.93E-3	5.93E-3	8.34E-07
	Transcription	—	1.82E-2	4.68E-2	4.46E-2	6.83E-3
	Ribosome biogenesis	—	—	4.10E-3	4.55E-3	3.73E-2
新陈代谢 Metabolism	GnRH secretion	3.78E-03	1.09E-05	1.80E-2	—	9.93E-3
	Lysine degradation	8.37E-03	2.12E-07	—	4.53E-2	1.99E-3
	Parathyroid hormone synthesis， secretion and action	—	2.00E-2	3.08E-2	—	—
	Renin secretion	—	2.98E-2	—	—	—
	Cortisol synthesis and secretion	—	—	3.52E-2	—	3.59E-2
	Insulin secretion	—	—	3.83E-2	—	2.27E-2
机体系统 Organismal systems	Dorso-ventral axis formation	—	1.70E-03	—	—	—
	Endocrine system	—	5.84E-3	—	—	—
	Vascular smooth muscle contraction	—	2.27E-2	—	—	—
	Cell adherens junction	—	2.19E-2	—	—	1.24E-2
环境信息调控 Environmental information processing	Notch signaling pathway	6.88E-03	9.53E-04	4.33E-3	6.37E-3	7.64E-05
	Signal transduction	2.18E-02	1.25E-03	—	—	7.89E-3
	cAMP signaling pathway	4.33E-02	—	—	—	—
	MAPK signaling pathway	—	4.32E-03	—	—	2.08E-2
	cGMP-PKG signaling pathway	—	2.91E-2	4.01E-2	—	5.93E-3
	Wnt signaling pathway	—	—	2.85E-2	—	—
疾病 Diseases	Maturity onset diabetes of the young	1.63E-02	5.50E-03	3.63E-2	1.07E-2	2.21E-2
	Type Ⅱ diabetes mellitus	—	1.78E-3	—	1.03E-2	1.02E-04
	Bladder cancer	—	2.04E-2	—	—	4.37E-2
	Spinocerebellar ataxia	—	2.05E-2	—	—	—
	Breast cancer	—	4.98E-2	2.28E-2	—	—
	Cushing syndrome	—	—	3.60E-3	5.97E-3	4.72E-2

林麝及其近缘物种编码区微卫星分布规律及功能分析

Distinct patterns of microsatellite and functional analysis of forest musk deer and its closely related species

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基因名称	微卫星类型	Map ID	KEGG pathway
CEBPB	（GCC）₅ （GCC）₈	Map04657 Map05152 Map05202	IL-17 signaling pathway Tuberculosis Transcriptional misregulation in cancer
ZEB1	（GAG）₅	Map05206 Map05202 Map05215	MicroRNAs in cancer Transcriptional misregulation in cancer Prostate cancer
THY1	（GCT）₆	Map04670	Leukocyte transendothelial migration
Bcl2	（CCG）₆	Map05200 Map05206 Map05022 Map05202 Map04115 Map05210 Map05212 Map05220 Map05222 Map05215 Map05226 Map04932 Map05012 Map05221 Map05225	Pathways in cancer MicroRNAs in cancer Pathways of neurodegeneration-multiple diseases Transcriptional misregulation in cancer p53 signaling pathway Colorectal cancer Pancreatic cancer Chronic myeloid leukemia Small cell lung cancer Prostate cancer Gastric cancer Non-alcoholic fatty liver disease Parkinson disease Acute myeloid leukemia Hepatocellular carcinoma
PDCD1	（CTG）₆	Map04660 Map05235	T cell receptor signaling pathway PD-L1 expression and PD-1 checkpoint pathway in cancer
WAS	（ATG）₆	Map04933 Map04936 Map05231	AGE-RAGE signaling pathway in diabetic complications Alcoholic liver disease Choline metabolism in cancer
HDAC5	（AGC）₅ （GAC）₅ （GGA）₅	Map05203 Map05206	Viral carcinogenesis MicroRNAs in cancer
MYH9	（GGA）₅	Map05130	Pathogenic Escherichia coli infection
JAG2	（GCT）₅	Map05200 Map05224	Pathways in cancer Breast cancer
NOTCH4	（GCT）₅	Map05206 Map05224 Map05200	MicroRNAs in cancer Breast cancer Pathways in cancer

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