Comparative Chloroplast Genome Study of Mallus servisii‘Red Delicious’and‘Golden Delicious’

doi:10.16420/j.issn.0513-353x.2021-0378

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (9): 1977-1990.doi: 10.16420/j.issn.0513-353x.2021-0378

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Comparative Chloroplast Genome Study of Mallus servisii‘Red Delicious’and‘Golden Delicious’

DING Zhijie, BAO Jinbo, ROUXIAN Guli, ZHU Tiantian, LI Xueli, MIAO Haoyu, TIAN Xinmin^*()

Xinjiang Key Laboratory of Biological Resources and Genetic Engineering,College of Life Sciences and Technology,Xinjiang University,Urumqi 830046,China

Received:2022-02-17 Revised:2022-05-19 Online:2022-09-25 Published:2022-10-08
Contact: TIAN Xinmin E-mail:tianxm06@lzu.edu.cn

Abstract

Abstract:

The wild apple tree Malus sieversii（Rosaceae）is considered to be the ancestor of modern cultivated apple trees. To effectively conserve apple genetic resources,it would be important to elucidate differences of chloroplast genomes between M. sieversii and cultivated apples,as well as verify whether modern cultivated apples originated from M. sieversii. In this study,we used the next-generation sequencing technology to complete the whole-genome sequencing,assembly,and annotation of M. sieversii as well as two domesticated apple trees‘Red Delicious’and‘Golden Delicious’. We successfully mapped the chloroplast genomes of M. sieversii and the two domesticated apple trees,and subsequently constructed the Malus phylogenetic tree at the level of the chloroplast genome. Through a series of comparative analyses,We obtained the following main results：the chloroplast genome of M. sieversii exhibites a typical quadripartite structure,and the complete genomes ranged between 160 068 and 160 288 bp in length. A total of 131 genes were annotated in M. sieversii and the two domesticated apple trees,including 86 protein-coding,37 tRNA,and eight rRNA genes. The base composition of the chloroplast genomes of M. sieversii and the two domesticated apples varieties were similar. A total of 43,49,and 43 repetitive sequence and 64,61 and 57 simple sequence repeat sites were identified in M. sieversii,‘Red Delicious’and‘Golden Delicious’,respectively. For the simple sequence repeats,the main repeat types were single A or T base repeats. Finally,phylogeny study showed that all the Malus species formed a single monophyletic group（BP = 100）. M. sieversii and the two cultivated varieties were grouped in a subclade with strong support（BP = 100）,supporting the hypothesis that M. sieversii is the putative ancestor of domesticated apples.

Key words: Malus sieversii, chloroplastgenome, variation analysis, phylogeny

CLC Number:

S661.1

DING Zhijie, BAO Jinbo, ROUXIAN Guli, ZHU Tiantian, LI Xueli, MIAO Haoyu, TIAN Xinmin. Comparative Chloroplast Genome Study of Mallus servisii‘Red Delicious’and‘Golden Delicious’[J]. Acta Horticulturae Sinica, 2022, 49(9): 1977-1990.

Figures/Tables 10

References 43

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基本特征 Basic characteristic	新疆野苹果 M. sieversii	‘元帅’ M.× domastica‘Red Delicious’	‘金冠’ M. × domastica‘Golden Delicious’
基因组Genomes/bp	160 230	160 288	160 068
LSC/bp	88 368	88 472	88 273
SSC/bp	19 196	19 174	19 181
IR/bp	26 333	26 321	26 370
蛋白编码基因Protein-coding genes	86	86	86
转运RNA基因tRNA gene	37	37	37
核糖体RNA基因rRNA gene	8	8	8
GC/%	36.5	36.5	36.6

基本特征 Basic characteristic	新疆野苹果 M. sieversii	‘元帅’ M.× domastica‘Red Delicious’	‘金冠’ M. × domastica‘Golden Delicious’
基因组Genomes/bp	160 230	160 288	160 068
LSC/bp	88 368	88 472	88 273
SSC/bp	19 196	19 174	19 181
IR/bp	26 333	26 321	26 370
蛋白编码基因Protein-coding genes	86	86	86
转运RNA基因tRNA gene	37	37	37
核糖体RNA基因rRNA gene	8	8	8
GC/%	36.5	36.5	36.6

区域 Regin	碱基 Base	新疆野苹果 M. sieversii	‘元帅’ M.× domastica‘Red Delicious’	‘金冠’ M. × domastica‘Golden Delicious’
大单拷贝区/% LSC	A	32.2	32.3	32.2
	C	17.6	17.6	17.6
	G	16.6	16.6	16.6
	T	33.6	33.6	33.6
	GC	34.1	34.1	34.2
小单拷贝区/% SSC	A	34.8	34.8	34.7
	C	16.0	16.0	15.9
	G	14.5	14.5	14.5
	T	34.8	34.8	34.8
	GC	30.4	30.4	30.4
反向重复区/% IRa	A	28.6	28.6	28.5
	C	22.1	22.1	22.1
	G	20.6	20.6	20.6
	T	28.7	28.8	28.8
	GC	42.7	42.7	42.7
总计/% Total	A	31.4	31.4	31.3
	C	18.6	18.6	18.6
	G	17.9	17.9	17.9
	T	32.1	32.1	32.1
	GC	36.5	36.5	36.6

区域 Regin	碱基 Base	新疆野苹果 M. sieversii	‘元帅’ M.× domastica‘Red Delicious’	‘金冠’ M. × domastica‘Golden Delicious’
大单拷贝区/% LSC	A	32.2	32.3	32.2
	C	17.6	17.6	17.6
	G	16.6	16.6	16.6
	T	33.6	33.6	33.6
	GC	34.1	34.1	34.2
小单拷贝区/% SSC	A	34.8	34.8	34.7
	C	16.0	16.0	15.9
	G	14.5	14.5	14.5
	T	34.8	34.8	34.8
	GC	30.4	30.4	30.4
反向重复区/% IRa	A	28.6	28.6	28.5
	C	22.1	22.1	22.1
	G	20.6	20.6	20.6
	T	28.7	28.8	28.8
	GC	42.7	42.7	42.7
总计/% Total	A	31.4	31.4	31.3
	C	18.6	18.6	18.6
	G	17.9	17.9	17.9
	T	32.1	32.1	32.1
	GC	36.5	36.5	36.6

基因组成 Group of genes	基因名称Gene name
基因组成 Group of genes	新疆野苹果M. sieversii	‘元帅’ M. × domastica‘Red Delicious’	‘金冠’ M. × domastica‘Golden Delicious’
核糖体RNA基因Ribosomal RNA genes	rrn16,rrn23,rrn4.5,rrn5	rrn23,rrn16,rrn4.5,rrn5	rrn23,rrn16,rrn4.5,rrn5
转运RNA基因 Transefer RNA genes	trnH-GUG,trnK-UUU,trnQ-UUG,trnS-GGU,trnG-UCC,trnR-UCU,trnC-GCA,trnD-GUC,trnY-GUA,trnT-GGU,trnS-UGA,trnG-GCC,trnfM-CAC,trnS-GGA,trnT-UGU,trnT-UAA,trnF-GAA,trnV-UAC,trnM-CAU,trnW-CCA,trnP-UGG,trnL-CAU,trnL-CAA,trnL-GAU,trnA-UGC,trnR-ACG,trnN-GUU,trnA-UGC,trnV-GAC,trnL-CAA	trnH-GUG,trnK-UUU,trnQ-UUG,trnS-GCU,trnG-UCC,trnR-UCU,trnC-GCA,trnD-GUC,trnE-UUC,trnT-GGU,trnS-UGA,trnfM-CAU,trnS-GGA,trnT-UGC,trnL-UAA,trnV-UAC,trnM-CAU,trnW-CCA,trnP-UGG,trnL-CAU,trnV-GAC,trnL-GAU,trnA-UGC,trnR-ACG,trnN-GUU,trnL-UAG,trnR-ACG,trnL-CAA,trnL-CAU	trnH-GUG,trnK-UUU,trnQ-UUG,trnS-GCU,trnG-UCC,trnR-UCU,trnC-GCA,trnD-GUC,trnY-GUA,trnE-UUC,trnT-GGU,trnS-UGA,trnfM-CAU,trnS-GGA,trnT-UGC,trnF-UGC,trnL-UAA,trnV-UAC,trnM-CAU,trnW-CCA,trnP-UGG,trnL-CAU,trnL-GAU,trnA-UGC,trnR-ACG,trnN-GUU,trnL-UAG,trnR-ACG,trnN-ACG,trnL-GAU,trnV-GAU,trnL-CAA,trnL-CAU
核糖体小亚基Small subunit of ribosom	rps16,rps2,rps14,rps4,rps8,rps7,rps19	rps16,rps19,rps2,rps14,rps4,rps12,rps11,rps8,rps7,rps15	rps16,rps14,rps4,rps18,rps8,rps12,rps3,rps7,rps15,rps19
核糖体大亚基 Large subunit of ribosom	rpl33,rpl20,rpl14,rpl16,rpl22,rpl12,rpl32,rpl23	rpL33,rpL20,rpL36,rpL14,rpL16,rpL22,rpL12,rpL23	rpL33,rpL20,rpL36,rpL14,rpL16,rpL23,rpL22,rpL38,rpL23,rpL2
DNA依赖型RNA聚合酶 DNA dependent RNA polymerase	rpoC1,rpoC2,rpoA	rpoC1,rpoC2,rpoB	rpoC1,rpoC2,rpoB
光合系统Ⅰ Subunit of photosestenⅠ	psa1,psa7,psaB	psaB,psaA,psaL,psaJ,psaC	psaA,psaB,psaL,psaJ,psaC
光合系统Ⅱ Subunit of photosestenⅡ	psbA,psbK,psbL,psbM,psbD,psbZ,psbJ,psbB,psbT,psbE,psbN	psbA,psbK,psbL,psbD,psbC,psbZ,psbJ,psbF,psbE,psbT,psbN,psbH,psbM	PsbB,psbK,psbL,psbM,psbD,psbC,psbZ,psbJ,psbL,psbF,psbE,psbT,psbH,psbN
细胞色素亚基Subunit of Cytochrome	petN,petA,petB,petD	petN,petA,petL,petG,petD,petB	petN,petA,petL,petG,petB,petD
ATP合成酶亚基Subunit of ATP synthase	atpE,atpA,atpH,atp1	atpA,atpF,atpL,atpE,atpB	atpA,atpF,atpH,atpL,atpB,atpE
ATP依赖型蛋白酶ATP dependent protease	clpP	clpP	clpP
Rubisco大亚基Large subunit of Rubisco	rbcL	rbcL	rbcL
NADH亚基 Subunit of NADH	ndhB,ndhF,ndhI,ndhJ,ndhC,ndhG,ndhE,ndhD,ndhH,ndhA,ndhK	ndhJ,ndhK,ndhC,ndhA,ndhG,ndhE,ndhD,ndhB,ndhF,ndhH,ndhI	ndhJ,ndhK,ndhC,ndhB,ndhF,ndhD,ndhA,ndhE,ndhG,ndhH,ndhI
成熟酶 Maturase	matK	matK	matK
外膜蛋白基因Envelop membrane protein	cemA	cemA	cemA
乙酰-CoA-羧基酶亚基 Subunit of Acetyl-CoA- Carboxyase	accD	accD	accD
C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA	ccsA	ccsA
保守的开放阅读框Conserved open reading frames	ycf3,ycf1,ycf4,ycf2	ycf3,ycf1,ycf4,ycf2	ycf3,ycf2,ycf1

Comparative Chloroplast Genome Study of Mallus servisii‘Red Delicious’and‘Golden Delicious’

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类型和区域 Type and region	名称 Name	新疆野苹果 M. sieversii	‘元帅’ M. × domestica‘Red Delicious’	‘金冠’ M. × domestica‘Golden Delicious’
类型 Type	单核苷酸重复 Single nucleotide repeats	51	50	48
	二核苷酸重复 Dinucleotide repeats	3	3	2
	多核苷酸重复 Poly nucleotide repeats	10	8	7
区域Region	大单拷贝区 LSC	46	48	46
	小单拷贝区 SSC	9	9	7
	反向重复区 IR	9	4	4
合计Total		64	61	57

[1]	JIANG Sisi, YUAN Jun, ZHOU Wenjun, NIU Genhua, ZHOU Junqin. Complete Chloroplast Genome Sequence and Characteristics Analysis of Carya illinoinensis [J]. Acta Horticulturae Sinica, 2022, 49(8): 1772-1784.
[2]	MEI Chuang, ZHANG Xiaoyan, YAN Peng, Aisajan Mamat, FENG Beibei, MA Kai, HAN Liqun, DONG Lianxin, WANG Jixun. Identification of TIFY Family in Apple and Their Expression Analysis Under Insect Stress [J]. Acta Horticulturae Sinica, 2021, 48(2): 233-242.
[3]	GUO Xiangyang1，GAO Jie1，SONG Xiqiang1，LING Peng1，ZHOU Yang1，HAO Daicheng2，LI Weishi2，and DING Qiong1,*. A Preliminary Study on Identity and Pathogenicity of Common Fungi Associated with Diseased Leaves of Oncidium sp. in Hainan Island [J]. ACTA HORTICULTURAE SINICA, 2020, 47(7): 1369-1382.
[4]	LI Qian1，GUO Qiqiang2，GAO Chao2，and LI Huie1,*. Characterization of Complete Chloroplast Genome of Camellia weiningensis in Weining，Guizhou Province [J]. ACTA HORTICULTURAE SINICA, 2020, 47(4): 779-787.
[5]	WANG Hongfei and SHANG Qingmao*. Genome-wide Identification and Expression Analysis of the SAUR Gene Family in Cucumis sativus [J]. ACTA HORTICULTURAE SINICA, 2019, 46(6): 1093-1111.
[6]	ZHANG Huanxin，LI Guoquan，YANG Huidong，CAO Na，and ZHU Fanghong*. Genome-wide Identification and Expression of Dof Family in Melon（Cucumis melo） [J]. ACTA HORTICULTURAE SINICA, 2019, 46(11): 2176-2187.
[7]	WEI Ruimin，ZHENG Jingyuan，LIU Feng，MA Yanqing，LI Xuefeng，YANG Bozhi，ZOU Xuexiao，XIE Lingling，and DAI Xiongze. Genome Wide Identification and Expression Analysis of the bZIP Gene Family in Pepper [J]. ACTA HORTICULTURAE SINICA, 2018, 45(8): 1535-1550.
[8]	LIN Li1,2，LIN Lejing2，ZHU Zhiyong2，DING Yulong1，and KUAI Benke1,*. Studies on the Taxonomy and Molecular Phylogeny of Acer in China [J]. ACTA HORTICULTURAE SINICA, 2017, 44(8): 1535-1547.
[9]	ZHANG Huanxin，DONG Chunjuan，and SHANG Qingmao*. Genome-wide Identification and Expression Analysis of GRAS Gene Family in Pepper [J]. ACTA HORTICULTURAE SINICA, 2017, 44(12): 2305-2317.
[10]	ZHENG Zhong-fan1，ZHANG Ya-li3，HU Can2，DAI Xiong-ze2，LIU Feng2,，and YUAN Zu-hua1,2,. Genome-wide Identification and Expressing Analysis of LBD Transcription Factors in Pepper [J]. ACTA HORTICULTURAE SINICA, 2016, 43(4): 683-694.
[11]	YANG Yong1,2，WANG Shun-li1,，XUE Jing-qi1，REN Xiu-xia1，LI Dan-dan1，YANG Ruo-wen1，ZENG Xiu-li3,，and ZHANG Xiu-xin1,*. Cloning of Five House-keeping Genes and Their Application in Phylogenetic Analysis of Tree Peony [J]. ACTA HORTICULTURAE SINICA, 2016, 43(2): 307-319.
[12]	LIU Lei1,2，YAO Xiao-hong1，and HUANG Hong-wen3,. Development of EPIC Markers in Actinidia* and Their Application for Phylogenetic Analysis of Genus Actinidia [J]. ACTA HORTICULTURAE SINICA, 2013, 40(6): 1162-.
[13]	WANG Guo-xun;and ZHANG Ming-li;. A Molecular Phylogeny of Sorbus（Rosaceae）Based on ITS Sequence [J]. ACTA HORTICULTURAE SINICA, 2011, 38(12): 2387-2394.
[14]	WANG Hua-kun;TAO Jian-min;QU Shen-chun;FANG Jing-gui;MA Rui-juan;ZHANG Zhen;and LOU Xiao-ming;. Molecular Evolution and Phylogeny of Stone Fruit Trees Based onSequences of the Internal Transcribed Spacers（ITS）of Nuclear RibosomalDNA [J]. ACTA HORTICULTURAE SINICA, 2010, 37(3): 363-374.
[15]	ZHENG Xiao-yan;CAO J ia-Shu;TENG Yuan-wen. Research Progress of Plant Molecular Phylogenetic Analyses Based on DNA Sequence Data—A Case Review in Rosaceae [J]. ACTA HORTICULTURAE SINICA, 2009, 36(12): 1827-1836.