江西铅山红芽芋叶绿体基因组特征及系统发育分析

doi:10.13560/j.cnki.biotech.bull.1985.2022-1369

摘要/Abstract

摘要：

为分析江西铅山红芽芋叶绿体基因组的结构组成情况，判定其在芋属中的进化位置及与同芋属叶绿体基因组的区别，为芋属物种鉴定、遗传多样性分析和资源保护提供相关依据。使用Illumina NovaSeq 6000测序平台对江西铅山红芽芋叶绿体基因组进行测序，通过生物信息学分析方法进行序列组装、注释和特征分析，并利用Geneious、MISA、MAFF、FASTTREE、CUSP、Chips和Codon W等生物信息学软件对其基因组结构和数目、密码子偏好性、序列重复、SSR 位点和系统发育进行分析。结果表明，江西铅山红芽芋叶绿体基因组大小为 16 2544 bp，呈现四分体结构。共包含 130个基因，其中84个编码蛋白质的基因，37个tRNA基因，8个核糖体rRNA基因，1个假基因。通过密码子偏好性分析，平均有效密码子数为45.60，ENC值小于45的基因39个，说明其密码子偏好性强。通过 SSR分析，检测到101个SSR 位点，其中单核苷酸重复最多（约占83.17%），且单核苷酸以A/T型为主。与近缘种比较，发现其叶绿体基因组序列高度保守，尤其蛋白质编码序列相似度极高。此外，系统发育分析发现江西铅山红芽芋与芋属、岩芋属聚为一支。本研究得到了江西铅山红芽芋的叶绿体基因组基本情况与系统发育位置，为江西铅山红芽芋的物种辨别、天然种群遗传多样性与功能基因组学提供前期研究铺垫。

关键词: 江西铅山红芽芋, 叶绿体基因组特征, 系统发育分析, SSR分析, IR边界分析, 密码子偏好性

Abstract:

In order to analyze the structure and composition of the chloroplast genome of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, its evolutionary position in Colocasia genus and its difference from the chloroplast genome of the same genus were determined, which may provide relevant basis for species identification, genetic diversity analysis and resource protection of Colocasia genus. The Illumina NovaSeq 6000 sequencing platform was used to sequence the genome of the chloroplast of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan. Bioinformatics analysis methods were to conduct sequence assembly, annotation and feature analysis, and bioinformatics software such as Geneious, MISA, MAFF, FASTREE, CUSP, Chips and Codon W were used to analyze the genome structure and number, codon preference, sequence duplication, SSR sites and phylogeny. The results showed that the chloroplast genome size of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan was 162 544 bp, showing a tetrad structure. It contained 130 genes, including 84 protein coding genes, 37 tRNA genes, 8 ribosomal rRNA genes and 1 pseudogene. By codon preference analysis, the average number of effective codons was 45.60, and 39 genes with ENC value < 45, indicating strong codon preference. Through SSR analysis, 101 SSR sites were detected, of which single nucleotide repeats were the most（about 83.17%）, and single nucleotide was mainly A/T type. Compared with related species, the chloroplast genome sequence was highly conserved, especially the protein coding sequence was highly similar. In addition, the phylogenetic analysis showed that C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan was clustered into one branch with Colocasia genus and Remusatia genus. This study obtained the basic information of chloroplast genome and phylogenetic location of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, and provided a preliminary study for its species identification, genetic diversity of natural population and functional genomics.

Key words: Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, chloroplast genome characterization, phylogenetic analysis, SSR analysis, IR boundary analysis, codon preference

尹明华, 余锾媛, 肖心怡, 王玉婷. 江西铅山红芽芋叶绿体基因组特征及系统发育分析[J]. 生物技术通报, 2023, 39(6): 233-247.

YIN Ming-hua, YU Huan-yuan, XIAO Xin-yi, WANG Yu-ting. Chloroplast Genomic Characterization and Phylogenetic Analysis of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan[J]. Biotechnology Bulletin, 2023, 39(6): 233-247.

图/表 15

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基因分类 Category	基因分组 Gene group	基因名称 Gene name
光合作用 Photosynthesis	光合系统I基因 Photosystem I	psaA、psaB、psaC、psaI、psaJ
	光合系统II基因 Photosystem II	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbK、psbL、psbM、psbT、psbZ
	细胞色素复合物基因 Cytochrome b/f complex	petA、petB、petD、petG、petL、petN
	ATP合成酶基因 ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI
	NADH脱氢酶基因 NADH dehydrogenase	ndhA、ndhB（2）、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK
	二磷酸核酮糖羧化酶大亚基基因 Rubisco large subunit	rbcL
自我复制Self-replication	RNA聚合酶亚基基因RNA polymeras	rpoA、rpoB、rpoC1、rpoC2
	核糖体小亚基基因 Ribosomal proteins（SSU）	rps11、rps12（2）、rps14、rps15、rps16、rps18、 rps19、rps2、rps3、rps4、rps7（2）、rps8
	核糖体大亚基基因 Ribosomal proteins（LSU）	rpl14、rpl16、rpl2（2）、rpl20、rpl22、rpl23（2）、rpl32、rpl33、rpl36、
	转运RNA基因 Transfer RNAs	trnC-GCA、trnD-GUC、trnF-GAA、trnG-GCC、trnH-GUG、trnI-CAU（2）、trnK-UUU、trnL-CAA（2）、trnL-UAA、trnL-UAG、trnM-CAU、trnN-GUU（2）、trnP-UGG、trnQ-UUG、trnR-ACG（2）、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-UGU、trnV-GAC（2）、trnV-UAC、trnW-CCA、trnY-GUA、trnfM-CAU
	核糖体RNA基因 Ribosomal RNAs	rrn16（2）、rrn23（2）、rrn4.5（2）、rrn5（2）
其他基因 Other genes	成熟酶基因 Maturase	matK
	蛋白酶Protease	clpP1
	乙酰辅酶 A 羧化酶Acetyl-CoA carboxylase	accD
	翻译起始因子 Translation initiation factor	infA
	包膜蛋白基因 Envelope membrane protein	cemA
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
未知功能Unknown function	假定叶绿体阅读框 Hypothetical chloroplast reading frames	ycf1、ycf2（2）

基因分类 Category	基因分组 Gene group	基因名称 Gene name
光合作用 Photosynthesis	光合系统I基因 Photosystem I	psaA、psaB、psaC、psaI、psaJ
	光合系统II基因 Photosystem II	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbK、psbL、psbM、psbT、psbZ
	细胞色素复合物基因 Cytochrome b/f complex	petA、petB、petD、petG、petL、petN
	ATP合成酶基因 ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI
	NADH脱氢酶基因 NADH dehydrogenase	ndhA、ndhB（2）、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK
	二磷酸核酮糖羧化酶大亚基基因 Rubisco large subunit	rbcL
自我复制Self-replication	RNA聚合酶亚基基因RNA polymeras	rpoA、rpoB、rpoC1、rpoC2
	核糖体小亚基基因 Ribosomal proteins（SSU）	rps11、rps12（2）、rps14、rps15、rps16、rps18、 rps19、rps2、rps3、rps4、rps7（2）、rps8
	核糖体大亚基基因 Ribosomal proteins（LSU）	rpl14、rpl16、rpl2（2）、rpl20、rpl22、rpl23（2）、rpl32、rpl33、rpl36、
	转运RNA基因 Transfer RNAs	trnC-GCA、trnD-GUC、trnF-GAA、trnG-GCC、trnH-GUG、trnI-CAU（2）、trnK-UUU、trnL-CAA（2）、trnL-UAA、trnL-UAG、trnM-CAU、trnN-GUU（2）、trnP-UGG、trnQ-UUG、trnR-ACG（2）、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-UGU、trnV-GAC（2）、trnV-UAC、trnW-CCA、trnY-GUA、trnfM-CAU
	核糖体RNA基因 Ribosomal RNAs	rrn16（2）、rrn23（2）、rrn4.5（2）、rrn5（2）
其他基因 Other genes	成熟酶基因 Maturase	matK
	蛋白酶Protease	clpP1
	乙酰辅酶 A 羧化酶Acetyl-CoA carboxylase	accD
	翻译起始因子 Translation initiation factor	infA
	包膜蛋白基因 Envelope membrane protein	cemA
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
未知功能Unknown function	假定叶绿体阅读框 Hypothetical chloroplast reading frames	ycf1、ycf2（2）

区域Area	碱基长度 Base length/ bp	T/%	C/%	A/%	G/%	GC/%	AT偏斜值AT skew	GC 偏斜值GC skew
大单拷贝区LSC	89 814	33.58	17.59	32.04	16.79	34.38	-0.023 5	-0.023 3
小单拷贝区SSC	22 074	36.02	15.12	34.97	13.89	29.01	-0.014 8	-0.042 4
反向重复序列a（IRa）	25 328	29.01	21.95	28.59	20.44	42.40	-0.007 3	-0.035 6
反向重复序列b（IRb）	25 328	28.59	20.44	29.01	21.95	42.40	0.007 3	0.035 6
总基因组	162 544	32.42	18.38	31.43	17.77	36.15	-0.015 5	-0.016 9

区域Area	碱基长度 Base length/ bp	T/%	C/%	A/%	G/%	GC/%	AT偏斜值AT skew	GC 偏斜值GC skew
大单拷贝区LSC	89 814	33.58	17.59	32.04	16.79	34.38	-0.023 5	-0.023 3
小单拷贝区SSC	22 074	36.02	15.12	34.97	13.89	29.01	-0.014 8	-0.042 4
反向重复序列a（IRa）	25 328	29.01	21.95	28.59	20.44	42.40	-0.007 3	-0.035 6
反向重复序列b（IRb）	25 328	28.59	20.44	29.01	21.95	42.40	0.007 3	0.035 6
总基因组	162 544	32.42	18.38	31.43	17.77	36.15	-0.015 5	-0.016 9

核苷酸类型 Nucleotide type	简单重复序列 Simple sequence repeat	重复序列个数 Number of SSR
单核苷酸 Mononucleotide	A	45
	C	2
	G	1
	T	36
二核苷酸 Dinucleotide	AT	5
二核苷酸 Dinucleotide	TA	10
三核苷酸 Trinucleotide	TTA	1
四核苷酸 Tetranucleotide	TATG	1