Complete Chloroplast Genome Sequence and Characteristics Analysis of Carya illinoinensis

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

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (8): 1772-1784.doi: 10.16420/j.issn.0513-353x.2021-0389

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Complete Chloroplast Genome Sequence and Characteristics Analysis of Carya illinoinensis

JIANG Sisi¹, YUAN Jun¹, ZHOU Wenjun¹, NIU Genhua², ZHOU Junqin¹^,^*()

1. Key Lab of Cultivation and Protection for Non-wood Forest Trees of Education Ministry,Central South University of Forestry and Technology,Changsha 410004,China
2. Texas A & M AgriLife Research Center,Dallas TX 75252,USA

Received:2021-12-21 Revised:2022-03-08 Online:2022-08-25 Published:2022-09-05
Contact: ZHOU Junqin E-mail:zhoujunqin@csuft.edu.cn

Abstract

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

CLC Number:

S664.1

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.

Figures/Tables 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

Complete Chloroplast Genome Sequence and Characteristics Analysis of Carya illinoinensis

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密码子Codon	氨基酸 Amino acid	频率/% Frequency			数量 Number			RSCU
密码子Codon	氨基酸 Amino acid	金华 Jinhua	波尼 Pawnee	实生单株 Seedling individual	金华 Jinhua	波尼 Pawnee	实生单株 Seedling individual	金华 Jinhua	波尼 Pawnee	实生单株 Seedling individual
GCA	A	1.454	1.426	1.454	715	729	715	1.130	1.140	1.130
GCC	A	0.679	0.665	0.679	334	340	334	0.530	0.530	0.530
GCG	A	0.596	0.585	0.592	293	299	291	0.460	0.470	0.460
GCT	A	2.408	2.348	2.408	1 184	1 200	1 184	1.870	1.870	1.880
TGC	C	0.334	0.333	0.334	164	170	164	0.560	0.560	0.560
TGT	C	0.860	0.855	0.860	423	437	423	1.440	1.440	1.440
GAC	D	0.810	0.802	0.810	398	410	398	0.400	0.390	0.400
GAT	D	3.259	3.272	3.259	1 602	1 672	1 602	1.600	1.610	1.600
GAA	E	3.897	3.996	3.897	1 916	2 042	1 916	1.490	1.500	1.490
GAG	E	1.328	1.336	1.332	653	683	655	0.510	0.500	0.510
TTC	F	2.018	2.015	2.018	992	1 030	992	0.690	0.680	0.690
TTT	F	3.794	3.872	3.794	1 865	1 979	1 865	1.310	1.320	1.310
GGA	G	2.532	2.499	2.532	1 245	1 277	1 245	1.590	1.600	1.590
GGC	G	0.712	0.701	0.712	350	358	350	0.450	0.450	0.450
GGG	G	0.970	0.961	0.970	477	491	477	0.610	0.620	0.610
GGT	G	2.140	2.090	2.140	1 052	1 068	1 052	1.350	1.340	1.350
CAC	H	0.547	0.546	0.547	269	279	269	0.450	0.450	0.450
CAT	H	1.906	1.869	1.906	937	955	937	1.550	1.550	1.550
ATA	I	2.888	2.947	2.893	1 420	1 506	1 422	0.990	1.000	0.990
ATC	I	1.621	1.622	1.621	797	829	797	0.550	0.550	0.550
ATT	I	4.274	4.283	4.274	2 101	2 189	2 101	1.460	1.450	1.460
AAA	K	3.995	4.133	3.995	1 964	2 112	1 964	1.450	1.450	1.450
AAG	K	1.511	1.552	1.507	743	793	741	0.550	0.550	0.550
CTA	L	1.336	1.333	1.332	657	681	655	0.760	0.760	0.760
CTC	L	0.755	0.757	0.755	371	387	371	0.430	0.430	0.430
CTG	L	0.675	0.681	0.675	332	348	332	0.390	0.390	0.390
CTT	L	2.258	2.227	2.258	1 110	1 138	1 110	1.290	1.280	1.290
TTA	L	3.242	3.260	3.242	1 594	1 666	1 594	1.850	1.870	1.850
TTG	L	2.246	2.199	2.246	1 104	1 124	1 104	1.280	1.260	1.280
ATG	M	2.244	2.225	2.244	1 103	1 137	1 103	1.000	1.000	1.000
AAC	N	1.153	1.156	1.153	567	591	567	0.470	0.460	0.470
AAT	N	3.794	3.837	3.802	1 865	1 961	1 869	1.530	1.540	1.530
密码子Codon	氨基酸 Amino acid	频率/% Frequency			数量 Number			RSCU
密码子Codon	氨基酸 Amino acid	金华 Jinhua	波尼 Pawnee	实生单株 Seedling individual	金华 Jinhua	波尼 Pawnee	实生单株 Seedling individual	金华 Jinhua	波尼 Pawnee	实生单株 Seedling individual
CCA	P	1.168	1.155	1.168	574	590	574	1.140	1.130	1.140
CCC	P	0.816	0.816	0.816	401	417	401	0.800	0.800	0.800
CCG	P	0.633	0.640	0.633	311	327	311	0.620	0.630	0.620
CCT	P	1.479	1.477	1.479	727	755	727	1.440	1.450	1.440
CAA	Q	2.805	2.820	2.805	1 379	1 441	1 379	1.550	1.560	1.550
CAG	Q	0.818	0.806	0.818	402	412	402	0.450	0.440	0.450
AGA	R	1.827	1.828	1.827	898	934	898	1.810	1.820	1.810
AGG	R	0.716	0.704	0.716	352	360	352	0.710	0.700	0.710
CGA	R	1.367	1.374	1.367	672	702	672	1.350	1.370	1.350
CGC	R	0.393	0.389	0.393	193	199	193	0.390	0.390	0.390
CGG	R	0.472	0.458	0.472	232	234	232	0.470	0.460	0.470
CGT	R	1.288	1.274	1.288	633	651	633	1.270	1.270	1.270
AGC	S	0.535	0.538	0.535	263	275	263	0.420	0.420	0.420
AGT	S	1.530	1.511	1.526	752	772	750	1.200	1.190	1.200
TCA	S	1.526	1.542	1.526	750	788	750	1.200	1.220	1.200
TCC	S	1.202	1.192	1.202	591	609	591	0.940	0.940	0.940
TCG	S	0.738	0.726	0.738	363	371	363	0.580	0.570	0.580
TCT	S	2.126	2.107	2.126	1 045	1 077	1 045	1.670	1.660	1.670
ACA	T	1.471	1.493	1.471	723	763	723	1.220	1.230	1.220
ACC	T	0.828	0.828	0.828	407	423	407	0.690	0.680	0.690
ACG	T	0.531	0.530	0.531	261	271	261	0.440	0.440	0.440
ACT	T	1.991	1.998	1.991	979	1 021	979	1.650	1.650	1.650
GTA	V	1.983	1.970	1.983	975	1 007	975	1.530	1.530	1.530
GTC	V	0.631	0.638	0.631	310	326	310	0.490	0.500	0.490
GTG	V	0.677	0.663	0.677	333	339	333	0.520	0.520	0.520
GTT	V	1.906	1.869	1.906	937	955	937	1.470	1.450	1.470
TGG	W	1.855	1.847	1.855	912	944	912	1.000	1.000	1.000
TAC	Y	0.767	0.753	0.767	377	385	377	0.410	0.400	0.410
TAT	Y	3.015	3.021	3.015	1 482	1 544	1 482	1.590	1.600	1.590
TAA	*	0.283	0.276	0.283	139	141	139	1.260	1.270	1.260
TAG	*	0.205	0.198	0.205	101	101	101	0.920	0.910	0.920
TGA	*	0.185	0.178	0.185	91	91	91	0.830	0.820	0.830

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