Comparative chloroplast genomics of the important resource plant Kadsura coccinea

doi:10.12302/j.issn.1000-2006.202404014

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (6): 71-78.doi: 10.12302/j.issn.1000-2006.202404014

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Comparative chloroplast genomics of the important resource plant Kadsura coccinea

ZHAI Xuechang¹(), PENG Li¹, YAN Haifei²^,^*(), ZHU Kefan³, ZHANG Shuyan²^,⁴, ZHANG Caiyun⁵, LU Xiankai²

1. Jiangxi Environmental Engineering Vocational College, Ganzhou 341000, China
2. Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
3. Xinfeng County Seed Farm of Jiangxi Province, Ganzhou 341624, China
4. College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
5. Guangdong Food and Drug Vocational College, Guangzhou 510520, China

Received:2024-04-10 Revised:2024-09-05 Online:2024-11-30 Published:2024-12-10
Contact: YAN Haifei E-mail:xuechangzhai@163.com;yanhaifei@scbg.ac.cn

Abstract

Abstract:

【Objective】This study aims to investigate the chloroplast genomes and SSR loci of Kadsura coccinea, an important plant resource in China, to establish a basis for assessing its genetic diversity and germplasm resources.【Method】The study obtained and analyzed the chloroplast genomes of five individuals of K. coccinea through genetical annotation, nucleotide polymorphism analysis, and SSR analysis using bioinformatics methods. Additionally, the phylogenetic analysis of Kadsura were reconstructed using two Schisandra spp. as outgroups.【Result】The chloroplast genome of K. coccinea showed a typical quadripartite structure, with genome lengths ranging from 145 413 to 145 903 base pairs (bp). The large single-copy region (LSC) spaned from 94 457 to 94 757 bp, while the small single-copy region (SSC) encompassed 18 032 to 18 047 bp. It encodes a total of 125 genes, including 82 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. The genome had a total GC content of 39.7% and demonstrated substantial nucleotide polymorphisms (P_i > 0.03) in the intergenic regions of petN-psbM and trnS-GCU-trnG-UCC. A total of 212 single sequence repeat (SSR) loci were identified across the chloroplast genomes of this species. Mononucleotide repeats were the most prevalent, followed by trinucleotide repeats, and pentanucleotide repeats were the least frequent. Among these loci, 24 polymorphic SSR loci were found among five individuals of K. coccinea, indicating their potential utility in future. Phylogenetic analysis robustly clusters K. coccinea individuals into a distinct group, revealing no close relationship with other congeneric species.【Conclusion】This study presents the first systematic comparison of chloroplast genomes among multiple K. coccinea individuals. Our findings identified highly variable regions and SSR loci that can be valuable for evaluating the genetic diversity and germplasm resource of this species.

Key words: Kadsura coccinea, plastid genome, genetic diversity, SSR loci, phylogeny

CLC Number:

S718
Q754

ZHAI Xuechang, PENG Li, YAN Haifei, ZHU Kefan, ZHANG Shuyan, ZHANG Caiyun, LU Xiankai. Comparative chloroplast genomics of the important resource plant Kadsura coccinea[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2024, 48(6): 71-78.

Figures/Tables 6

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编号 No.	物种 species	总长/bp genome size	大单拷贝区长度/bp LSC size	重复区长度/bp IR size	小单拷贝区长度/bp SSC size	GC占比/% GC proportion	总基因数 gene number	蛋白质编码基因数 number of protein- coding genes	rRNA 基因数 number of rRNA genes	tRNA 基因数 number of tRNA genes
HLH-1A	黑老虎	145 617	94 481	16 552	18 032	39.7	125	82	8	35
HLH-2A	黑老虎	145 617	94 481	16 552	18 032	39.7	125	82	8	35
MN480469	黑老虎	145 608	94 457	16 552	18 047	39.7	125	82	8	35
MT934443	黑老虎	145 413	94 511	16 431	18 040	39.7	125	82	8	35
NC_057265	中泰南五味子	145 903	94 757	16 552	18 042	39.7	125	82	8	35
NC_057266	异形南五味子	153 289	85 774	24 657	18 201	39.6	129	84	8	37
NC_050348	异形南五味子	153 201	85 774	24 656	18 115	39.6	129	84	8	37
MW801021	南五味子	153 106	85 593	24 670	18 173	39.6	129	84	8	37

类别category	基因功能gene function	基因gene
光合作用相关 photosynthesis	二磷酸核酮糖羧化酶大亚基	rbcL
	光系统Ⅰ	psaA、psaB、psaC、psaI、psaJ
	光系统Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbJ、 psbK、psbL、psbM、psbN、psbT、psbZ
	ATP合酶	atpA、atpB、atpE、atpF^、atpH、atpI*
	细胞色素b/f复合体	petA、petB^、petD^、petG、petL、petN
	NADPH脱氢酶	ndhA^、ndhB^(2)、ndhC、ndhD、ndhE、 ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK
	细胞色素c	ccsA
自身表达相关 self-replication	RNA聚合酶	rpoA、rpoB、rpoC1^、rpoC2*
	核糖体蛋白	rpl2^、rpl14、rpl16、rpl20、rpl22、rpl23、rpl32、rpl33、rpl36、 rps2、rps3、rps4、rps7(2)、rps8、rps11、rps12^(2)、rps14、 rps15、rps16^、rps18、rps19*
	翻译起始因子	infA
RNA相关 RNA-related	核糖体RNAs	rrn4.5(2)、rrn5(2)、rrn16(2)、rrn23(2)
	转运RNAs	trnA-UGC^(2)、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、 trnfM-CAU、trnG-GCC、trnG-UCC^、trnH-GUG、trnI-CAU、trnI-GAU^(2)、 trnK-UUU^、trnL-CAA、trnL-UAA^、trnL-UAG、trnM-CAU、trnN-GUU(2)、 trnP-UGG、trnQ-UUG、trnR-ACG(2)、trnR-UCU、trnS-CGA、trnS-GCU、 trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、trnV-GAC(2)、trnV-UAC^、 trnW-CCA、trnY-GUA
	ATP依赖型蛋白酶	clpP^**
其他 others	成熟酶	matK
	乙酰辅酶A羧化酶亚基	accD
	外膜蛋白基因	cemA
	保守的开放阅读框	ycf1(2)、ycf2、ycf3^*、ycf*4

Comparative chloroplast genomics of the important resource plant Kadsura coccinea

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