薄壳山核桃（Carya illinoinensis）叶绿体基因组及其特征分析

doi:10.16420/j.issn.0513-353x.2021-0389

摘要/Abstract

摘要：

利用Illumina平台对薄壳山核桃（Carya illinoinensis）品种‘金华’‘波尼’和1株实生古树单株的叶绿体全基因组进行测序,并对其特征进行分析。3个薄壳山核桃叶绿体基因组均呈典型的四分体结构,大小分别为160 819、162 611和160 762 bp,基因序列高度保守。三者均注释得到124个基因,包括79种蛋白编码基因、38个tRNA和7个rRNA基因;三者有相似的重复序列类型,在其叶绿体基因组序列中分别检测出74、74和73个SSR位点;系统发育分析表明,三者均与喙核桃（Annamocarya sinensis）亲缘关系最为密切。

关键词: 山核桃, 叶绿体基因组, 简单重复序列, 系统发育关系

Abstract:

The whole chloroplast genome resequencing of Carya illinoinensis cultivars‘Jinhua’‘Pawnee’and an old seedling individual were sequenced using Illumina sequencing platform,and their chloroplast genome characteristics were analyzed. The results showed that the three pecan chloroplast genomes were a typical tetrad structures with 160 819,162 611 and 160 762 bp in size,respectively. The gene sequences were highly conserved. A total of 124 genes,including 79 protein-coding genes,38 tRNA genes,and seven rRNA genes were identified from each of three pecan chloroplast genomes;repeat sequences detected were similar in categories,and 74,74 and 73 SSR loci were identified in their chloroplast genome sequence,respectively;phylogenetic analysis showed that they were most closely related to Annamocarya sinensis.

Key words: Carya cathayensis, chloroplast genome, simple sequence repeat, phylogeny relationship

中图分类号:

S664.1

蒋思思, 袁军, 周文君, 钮根花, 周俊琴. 薄壳山核桃（Carya illinoinensis）叶绿体基因组及其特征分析[J]. 园艺学报, 2022, 49(8): 1772-1784.

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.

图/表 8

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品种 Cultivar	LSC			SSC			IR			Genome
品种 Cultivar	长度/bp Length	G + C/%	长度/% Length	长度/bp Length	G + C/%	长度/% Length	长度/bp Length	G + C/%	长度/% Length	长度/bp Length
金华 Jinhua	90 022	33.74	55.98	18 791	29.89	11.68	26 003	42.58	16.17	160 819
波尼 Pawnee	90 022	33.74	55.36	16 999	29.93	10.45	27 795	41.74	17.09	162 611
实生单株 Seedling individual	89 964	33.75	55.96	18 792	29.88	11.69	26 003	42.58	16.17	160 762

品种 Cultivar	LSC			SSC			IR			Genome
品种 Cultivar	长度/bp Length	G + C/%	长度/% Length	长度/bp Length	G + C/%	长度/% Length	长度/bp Length	G + C/%	长度/% Length	长度/bp Length
金华 Jinhua	90 022	33.74	55.98	18 791	29.89	11.68	26 003	42.58	16.17	160 819
波尼 Pawnee	90 022	33.74	55.36	16 999	29.93	10.45	27 795	41.74	17.09	162 611
实生单株 Seedling individual	89 964	33.75	55.96	18 792	29.88	11.69	26 003	42.58	16.17	160 762

基因分类 Category for gene	基因分组 Group of gene	基因名称 Name of gene
自我复制 Self replication	rRNA	rrn16S,rrn23,rrn23S,rrn4.5,rrn4.5S,rrn5,rrn5S
	tRNA	trnA-UGC^,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC^,trnG-UCC,trnH-GUG,trnI-CAU,trnI-GAU^,trnK-UUU^,trnL-CAA,trnL-UAA^,trnL-UAG,trnM-CAU,trnN-GUU,trnP-GGG,trnP-UGG,trnQ-UUG,trnR-ACG,trnR-UCU,trnS-CGA,trnS-GCU,trnS-GGA,trnStop-UUA,trnS-UGA,trnT-AAG,trnT-AGU,trnT-CAG,trnT-GGU,trnT-UAG,trnT-UGU,trnV-AAC,trnV-GAC,trnV-UAC^,trnW-CCA,trnY-GUA
	RNA聚合酶亚基 RNA polymerase	rpoA,rpoB,rpoC1^,rpoC2*
	核糖体小亚基 Ribosomal protein（SSU）	rps2,rps3,rps4,rps7,rps8,rps11,rps12^T,,rps14,rps15,rps16^,rps18,rps19
	核糖体大亚基 Ribosomal protein（LSU）	rpl2^,rpl14,rpl16^,rpl20,rpl22,rpl23,rpl32,rpl33,rpl36
光合作用相关 Genes for photo- synthesis	ATP 合酶 ATP synthase	atpA,atpB,atpE,atpF^,atpH,atpI*
	光和系统Ⅰ Photosystem Ⅰ	psaA,psaB,psaC,psaI,psaJ
	光和系统Ⅱ Photosystem Ⅱ	psbA,psbB,psbC,psbD,psbE,psbF,psbI,psbJ,psbK,psbH,psbL,psbM,psbN,psbT,psbZ,ycf3^**
	二磷酸核酮糖羧化酶亚基 Subunit of rubisco	rbcL
	细胞色素复合物 Cytochrome b/f complex	petA,petB^,petD^,petG,petL,petN
	NADH脱氢酶 NADH-dehydrogenase	ndhA^,ndhB^,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
其他与未知功能 Other and unknown function		accD,ccsA,cemA,clpP^,matK,ycf1,ycf2,ycf4,ycf15^a

基因分类 Category for gene	基因分组 Group of gene	基因名称 Name of gene
自我复制 Self replication	rRNA	rrn16S,rrn23,rrn23S,rrn4.5,rrn4.5S,rrn5,rrn5S
	tRNA	trnA-UGC^,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC^,trnG-UCC,trnH-GUG,trnI-CAU,trnI-GAU^,trnK-UUU^,trnL-CAA,trnL-UAA^,trnL-UAG,trnM-CAU,trnN-GUU,trnP-GGG,trnP-UGG,trnQ-UUG,trnR-ACG,trnR-UCU,trnS-CGA,trnS-GCU,trnS-GGA,trnStop-UUA,trnS-UGA,trnT-AAG,trnT-AGU,trnT-CAG,trnT-GGU,trnT-UAG,trnT-UGU,trnV-AAC,trnV-GAC,trnV-UAC^,trnW-CCA,trnY-GUA
	RNA聚合酶亚基 RNA polymerase	rpoA,rpoB,rpoC1^,rpoC2*
	核糖体小亚基 Ribosomal protein（SSU）	rps2,rps3,rps4,rps7,rps8,rps11,rps12^T,,rps14,rps15,rps16^,rps18,rps19
	核糖体大亚基 Ribosomal protein（LSU）	rpl2^,rpl14,rpl16^,rpl20,rpl22,rpl23,rpl32,rpl33,rpl36
光合作用相关 Genes for photo- synthesis	ATP 合酶 ATP synthase	atpA,atpB,atpE,atpF^,atpH,atpI*
	光和系统Ⅰ Photosystem Ⅰ	psaA,psaB,psaC,psaI,psaJ
	光和系统Ⅱ Photosystem Ⅱ	psbA,psbB,psbC,psbD,psbE,psbF,psbI,psbJ,psbK,psbH,psbL,psbM,psbN,psbT,psbZ,ycf3^**
	二磷酸核酮糖羧化酶亚基 Subunit of rubisco	rbcL
	细胞色素复合物 Cytochrome b/f complex	petA,petB^,petD^,petG,petL,petN
	NADH脱氢酶 NADH-dehydrogenase	ndhA^,ndhB^,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
其他与未知功能 Other and unknown function		accD,ccsA,cemA,clpP^,matK,ycf1,ycf2,ycf4,ycf15^a

基因 Gene	正负链 Strand	起始 Start			终止 End			外显子 Ⅰ/bp ExonⅠ	内含子 Ⅰ/bp IntronⅠ	外显子 Ⅱ/bp ExonⅡ	内含子 Ⅱ/bp Intron Ⅱ	外显子 Ⅲ/bp Exon Ⅲ
基因 Gene	正负链 Strand	金华 Jinhua	波尼 Pawnee	实生单株 Seedling individual	金华 Jinhua	波尼 Pawnee	实生单株 Seedling individual	外显子 Ⅰ/bp ExonⅠ	内含子 Ⅰ/bp IntronⅠ	外显子 Ⅱ/bp ExonⅡ	内含子 Ⅱ/bp Intron Ⅱ	外显子 Ⅲ/bp Exon Ⅲ
trnK-UUU	-	1 607	1 607	1 607	4 237	4 237	4 237	37	2 559	35
rps16	-	5 086	5 086	5 086	6 257	6 257	6 257	39	905	228
trnG-GCC	+	10 135	10 135	10 134	10 919	10 919	10 918	23	715	47
atpF	-	13 185	13 185	13 184	14 490	14 490	14 489	145	751	410
rpoC1	-	22 810	22 810	22 811	25 681	25 681	25 683	432	814	1 626
ycf3	-	47 097	47 097	47 034	49 116	49 116	49 053	124	720	230	793	153
trnL-UAA	+	52 205	52 205	52 142	52 815	52 815	52 752	37	524	50
trnV-UAC	-	56 413	56 413	56 350	57 102	57 102	57 039	38	615	37
clpP	-	75 722	75 722	75 665	77 773	77 773	77 715	71	847	294	614	226
petB	+	80 745	80 745	80 687	82 207	82 207	82 149	6	815	642
petD	+	82 418	82 418	82 360	83 526	83 526	83 468	9	626	474
rpl16	-	87 056	87 056	86 998	88 382	88 382	88 324	9	919	399
rpl2	-	90 103	90 103	90 045	91 625	91 625	91 567	391	698	434
ndhB	-	100 446	100 446	100 388	102 670	102 670	102 612	775	686	764
trnI-GAU	+	108 073	108 073	108 015	109 099	109 099	109 041	37	955	35
trnA-UGC	+	109 164	109 164	109 106	110 043	110 043	109 985	38	807	35
ndhA	-	125 970	127 762	125 912	128 253	130 045	128 195	553	1 192	539
trnA-UGC	-	140 799	142 591	140 742	141 678	143 470	141 621	38	807	35
trnI-GAU	-	141 743	143 535	141 686	142 769	144 561	142 712	37	955	35
ndhB	+	148 172	149 964	148 115	150 396	152 188	150 339	775	686	764
rpl2	+	159 217	161 009	159 160	160 739	162 531	160 682	391	698	434