Comparative Analysis and Sequencing of Chloroplast Genome of Colocasia esculenta var. Redbud and Colocasia esculenta var. Lipu

doi:10.3969/j.issn.1000-2561.2023.05.002

Abstract

Abstract:

To confirm the characteristics and difference of the chloroplast (cp) genome of Colocasia esculenta var. Redbud and Colocasia esculenta var. Lipu, the two taros were taken as experimental materials in the study, their genomic DNA were first extracted form fresh leaves using an improved CTAB method and the two complete cp genomes were obtained using high-throughput sequencing technology and bioinformatics analysis, simple sequence repeat (SSR) identification, multiple sequence alignment, sliding window analysis on DNA polymorphism and phylogenetic tree analysis were then conducted on two complete cp genomes. The results showed that the length of the complete cp genomes of Redbud and Lipu was 162 478 bp and 162 453 bp, respectively, exhibiting the typical cyclic quadripartite structure. A total of 131 genes were annotated both in the two, including 86 protein-coding genes, 37 tRNA genes and 8 rRNA genes, of which 18 genes had two copies and 23 genes had introns. A total of 130 and 124 SSR sites were identified in Redbud and Lipu respectively, the content of A/T in the SSR repeats was 63.08% and 61.29% respectively. 15 SSR polymorphic primers were identified. A total of 236 cp single nucleotide polymorphism (SNP) sites were detected between Redbud and Lipu, of which 26.7% were in the gene coding region, which leading to 25 missense variant genes, the variation of the genes may promote the difference between the two varieties. Compared with the representative species from 13 genus of Aroideae showed that the structure, types, and numbers of gene were relatively conservative. The trnS-trnG and ndhF-rpl32 were the highest variation sites in SSC and LSC region, respectively. The phylogenetics analysis using maximum likelihood method (ML) showed that the genus Colocasia had the closest relationship with the genus Steudnera, but the farthest relationship with the genus Sauromatum in the Ariodeae. The results would provide a theoretical basis for the germplasm resource exploitation,genetic diversity evaluation and phylogenetic analysis of C. esculenta.

Key words: Colocasia esculenta var. Redbud, Colocasia esculenta var. Lipu, chloroplast genome, SSR, SNP, phylogenetic analysis

CLC Number:

S632.3

JIA Xinbi, PAN Rao, XIAO Yao, LUO Sha, SHAN Nan, SUN Jingyu, WANG Shenglin, ZHOU Qinghong, HUANG Yingjin, ZHU Qianglong. Comparative Analysis and Sequencing of Chloroplast Genome of Colocasia esculenta var. Redbud and Colocasia esculenta var. Lipu[J]. Chinese Journal of Tropical Crops, 2023, 44(5): 880-893.

Figures/Tables 16

References 39

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编号 No.	样品名称 Sample name	采集地 Origin	分类 Species	编号 No.	样品名称 Sample name	采集地 Origin	分类 Species
1	赣芋1号	江西赣州	多子芋	17	炮弹芋	四川乐山	魁芋
2	青岛芋	山东青岛	多子芋	18	黎族多子芋	海南白沙黎族自治县	多子芋
3	江芋3号	江西上饶	多子芋	19	扁母芋	河南商丘	多子芋
4	江芋4号	江西上饶	多子芋	20	多子芋	天津西青	多子芋
5	瑞金芋	江西赣州	多子芋	21	泉州魁芋	福建泉州	魁芋
6	于都芋1号	江西赣州	多子芋	22	水毛芋	重庆	多子芋
7	粉红佳人	江西赣州	多子芋	23	紫红嘴芋	江西新余	多子芋
8	粉红芋2号	江西赣州	多子芋	24	登龙粉芋	江西吉安	多子芋
9	于都大野芋	江西赣州	多子芋	25	野生紫柄小水芋	江西抚州南城县	多子芋
10	紫柄芋	江苏宿迁	多子芋	26	花柄食用芋	云南丽江	多子芋
11	钦州芋	广西钦州	多子芋	27	大麻芋2号	云南西双版纳勐腊河边	多子芋
12	紫芽芋	江西南昌	多子芋	28	大香芋	云南西双版纳勐醒	魁芋
13	狗爪芋	云南曲靖	多子芋	29	常德芋	湖南常德	多子芋
14	白肉毛芋	贵州六盘水	多子芋	30	小香芋	云南西双版纳勐醒	魁芋
15	赣州多子芋	江西赣州	多子芋	31	鹰潭红芽芋	江西鹰潭	多子芋
16	红嘴芋	广西南宁	多子芋	32	荔浦芋	广西桂林	魁芋

编号 No.	样品名称 Sample name	采集地 Origin	分类 Species	编号 No.	样品名称 Sample name	采集地 Origin	分类 Species
1	赣芋1号	江西赣州	多子芋	17	炮弹芋	四川乐山	魁芋
2	青岛芋	山东青岛	多子芋	18	黎族多子芋	海南白沙黎族自治县	多子芋
3	江芋3号	江西上饶	多子芋	19	扁母芋	河南商丘	多子芋
4	江芋4号	江西上饶	多子芋	20	多子芋	天津西青	多子芋
5	瑞金芋	江西赣州	多子芋	21	泉州魁芋	福建泉州	魁芋
6	于都芋1号	江西赣州	多子芋	22	水毛芋	重庆	多子芋
7	粉红佳人	江西赣州	多子芋	23	紫红嘴芋	江西新余	多子芋
8	粉红芋2号	江西赣州	多子芋	24	登龙粉芋	江西吉安	多子芋
9	于都大野芋	江西赣州	多子芋	25	野生紫柄小水芋	江西抚州南城县	多子芋
10	紫柄芋	江苏宿迁	多子芋	26	花柄食用芋	云南丽江	多子芋
11	钦州芋	广西钦州	多子芋	27	大麻芋2号	云南西双版纳勐腊河边	多子芋
12	紫芽芋	江西南昌	多子芋	28	大香芋	云南西双版纳勐醒	魁芋
13	狗爪芋	云南曲靖	多子芋	29	常德芋	湖南常德	多子芋
14	白肉毛芋	贵州六盘水	多子芋	30	小香芋	云南西双版纳勐醒	魁芋
15	赣州多子芋	江西赣州	多子芋	31	鹰潭红芽芋	江西鹰潭	多子芋
16	红嘴芋	广西南宁	多子芋	32	荔浦芋	广西桂林	魁芋

功能Function	家族名称Family name	基因代码Gene code	基因Gene
自我复制	核糖体小亚基核糖体大亚基 DNA依赖性RNA聚合酶	rps	rps2，rps3，rps4，rps7^a，rps8，rps11，rps12^a，rps14，rps15，rps16^b，rps18，rps19
		rpl	rpl2^a^b，rpl14，rpl16^b，rpl20，rpl22，rpl23^a，rpl32，rpl33，rpl36
		rpo	rpoA，rpoB，rpoC1^b，rpoC2
	rRNA	rrn	rrn4.5S^a，rrn5S^a，rrn16S^a，rrn23S^a
	tRNA	trn	trnA-UGC^a^b，trnC-GCA，trnD-GUC，trnE-UUC，trnfM-CAU，trnF-GAA，trnG-UCC^b，trnG-GCC，trnH，trnI-CAU^a，trnI-GAU^a^b，trnK-UUU^b，trnL-UAA^b，trnL-CAA^a，trnL-UAG，trnM，trnN-GUU^a，trnP-UGG，trnQ-UUG，trnR-UCU，trnR-ACG^a，trnS-GCU，trnS-UGA，trnS-GGA，trnT-GGU，trnT-UGU，trnV-UAC^b ，trnV-GAC^a，trnW-CCA，trnY-GUA
光合作用	ATP合酶亚基	atp	atpA，atpB，atpE，atpF^b，atpH，atpI
	光系统I的亚基	psa	psaA，psaB，psaC，psaI，psaJ
	光系统II的亚基	psb	psbA，psbB，psbC，psbD，psbE，psbF，psbI， psbJ，psbK，psbL，psbM，psbN，psbT，psbZ，ycf3^c
	NADH-脱氢酶的亚基	ndh	ndhA^b，ndhB^a^b，ndhC，ndhD，ndhE，ndhF，ndhG，ndhH，ndhI，ndhJ，ndhK
	细胞色素b/f复合物的亚基	pet	petA，petB^b，petD^b，petG，petL，petN
	二磷酸核酮糖氧合酶/羧化酶亚基	rbc	rbcL
其他	乙酰-CoA-羧化酶的亚基	acc	accD
	c型细胞色素合成基因	ccs	ccsA
	包膜蛋白基因	cem	cemA
	蛋白酶基因	clp	clpP^c
	成熟酶基因	mat	matK
未知功能	保守开放阅读框	ycf	ycf1，ycf2^a，ycf4，ycf68^a^b

功能Function	家族名称Family name	基因代码Gene code	基因Gene
自我复制	核糖体小亚基核糖体大亚基 DNA依赖性RNA聚合酶	rps	rps2，rps3，rps4，rps7^a，rps8，rps11，rps12^a，rps14，rps15，rps16^b，rps18，rps19
		rpl	rpl2^a^b，rpl14，rpl16^b，rpl20，rpl22，rpl23^a，rpl32，rpl33，rpl36
		rpo	rpoA，rpoB，rpoC1^b，rpoC2
	rRNA	rrn	rrn4.5S^a，rrn5S^a，rrn16S^a，rrn23S^a
	tRNA	trn	trnA-UGC^a^b，trnC-GCA，trnD-GUC，trnE-UUC，trnfM-CAU，trnF-GAA，trnG-UCC^b，trnG-GCC，trnH，trnI-CAU^a，trnI-GAU^a^b，trnK-UUU^b，trnL-UAA^b，trnL-CAA^a，trnL-UAG，trnM，trnN-GUU^a，trnP-UGG，trnQ-UUG，trnR-UCU，trnR-ACG^a，trnS-GCU，trnS-UGA，trnS-GGA，trnT-GGU，trnT-UGU，trnV-UAC^b ，trnV-GAC^a，trnW-CCA，trnY-GUA
光合作用	ATP合酶亚基	atp	atpA，atpB，atpE，atpF^b，atpH，atpI
	光系统I的亚基	psa	psaA，psaB，psaC，psaI，psaJ
	光系统II的亚基	psb	psbA，psbB，psbC，psbD，psbE，psbF，psbI， psbJ，psbK，psbL，psbM，psbN，psbT，psbZ，ycf3^c
	NADH-脱氢酶的亚基	ndh	ndhA^b，ndhB^a^b，ndhC，ndhD，ndhE，ndhF，ndhG，ndhH，ndhI，ndhJ，ndhK
	细胞色素b/f复合物的亚基	pet	petA，petB^b，petD^b，petG，petL，petN
	二磷酸核酮糖氧合酶/羧化酶亚基	rbc	rbcL
其他	乙酰-CoA-羧化酶的亚基	acc	accD
	c型细胞色素合成基因	ccs	ccsA
	包膜蛋白基因	cem	cemA
	蛋白酶基因	clp	clpP^c
	成熟酶基因	mat	matK
未知功能	保守开放阅读框	ycf	ycf1，ycf2^a，ycf4，ycf68^a^b

基因Gene	外显子I Exon I/bp	内含子I Intron I/bp	外显子Ⅱ Exon Ⅱ/bp	内含子Ⅱ Intron Ⅱ/bp	内含子Ⅲ Exon Ⅲ/bp
trnA-UGC	38	799	35
trnA-UGC	38	799	35
trnG-UCC	24	725	48
trnK-UUU	37	2541	42
trnL-UAA	37	515	50
trnI-GAU	42	942	35
trnI-GAU	42	942	35
trnV-UAC	38	590	37
rps16	40	988	197
atpF	145	813	401
rpoC1	453	750	1620
ycf3	124	738	230	794	153
ycf68	24	31	321
ycf68	24	31	321
clpP	71	801	294	640	244
petB	6	57	642
petD	8	735	475
rpl2	388	663	431
rpl2	388	663	431
rpl16	9	1082	399
ndhA	553	1094	539
ndhB	775	677	758
ndhB	775	677	758