Structure and variation analyses of chloroplast genomes in Carpinus

doi:10.12302/j.issn.1000-2006.202009007

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2021, Vol. 45 ›› Issue (2): 25-34.doi: 10.12302/j.issn.1000-2006.202009007

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Structure and variation analyses of chloroplast genomes in Carpinus

ZHAO Runan¹(), CHU Xiaojie², LIU Wei¹, HE Qianqian¹, ZHU Zunling¹^,³^,^*()

1. Co-Innovation Center for the Sustainable Forestry in Southern China, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
2. College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
3. College of Art and Design, Nanjing Forestry University, Nanjing 210037, China

Received:2020-09-02 Accepted:2020-11-16 Online:2021-03-30 Published:2021-04-09
Contact: ZHU Zunling E-mail:zhao-rn@njfu.edu.cn;zhuzunling@njfu.edu.cn

Abstract

Abstract:

【Objective】Chloroplasts are the organelles responsible for the photosynthesis in green plants. The chloroplast genome structure and gene composition of higher plants are relatively conservative, but can show different degrees of variation due to hybridization, evolution and gene introgression. It contains a significant amount of DNA information, which is used in species classification, phylogeny and origin. Carpinus is one of the most evolved genus in the Betulaceae family. Although the chloroplast genomes of more than ten species of Carpinus have been sequenced and assembled, only a few of these have been fully studied. Therefore, this study aimed to understand the chloroplast genome gene composition and structural characteristics of Carpinus, reveal the contraction and expansion of the inverted repeat (IR) region boundary, and lay a foundation for further studies on phylogenetic relationships, species identification, genome evolution and resource utilization and provide a reference for the development of Carpinus DNA barcoding. 【Method】GeSeq was used to annotate the chloroplast genome with Ostrya rehdariana as the reference genome. Then, the number of genes, genomic DNA base composition (GC) content, large single copy (LSC), small single copy (SSC) and two IR regions of the chloroplast genomes of 16 Carpinus species were obtained. The structure, boundary contraction and expansion, and sequence variation were then compared by using OGDRAW, IRscope and mVISTA programs. The phylogenetic relationship of Carpinus was analyzed with Quercus acutissima as an outgroup. 【Result】We found that the chloroplast genomes of 16 species were circular, double-stranded, which were tetrads containing one LSC and SSC and two IRs. The difference in genome size was small, and the maximum difference was only 1 902 bp. The differences in IR region length and GC content among species were small. The gene sequence length and composition were relatively conservative, with the number of rRNAs (8) as the most conservative; however, there was significant diversity at the four boundaries. There were differences in the non-coding regions, and the degree of variation was high; however, the difference in gene coding region was small and highly conservative. Among the four parts of the chloroplast genome, the LSC region had the highest degree of variation, while the IRa region had the lowest. There were significant differences in the coding regions of psbA, rps16, atpA, rps19, ndhF, ndhI and ycf1 genes. In addition, the non-coding regions of the intergenic regions of ycf3-trnS, trnS-rps4, trnH-psbA, psbZ-trnfM, matK-rps16, rps16-trnQ, trnQ-psbK, ccsA-ndhD, accD-psaI, ndhC-trnV, trnT-trnL, trnF-ndhJ, atpB-rbcL, trnT-psbD, trnE-trnT, trnD-trnY, and rpl32-trnL were significantly different. In addition, the coding region length of most genes was very conservative, and the variation of coding gene length of proteins containing introns originated from the change in intron length or coding region length. The phylogenetic tree supported a division of Carpinus and Distegocarpus sections. In addition, due to the significant geographical isolation,C. caroliniana and C. betulus showed a relatively distant phylogenetic relationship with other species of Carpinus. 【Conclusion】The chloroplast genome of Carpinus was highly conservative with little gene sequence differences; no large-scale inversion or gene rearrangement was detected. However, the IRs and SC boundaries had significant diversity. In addition, some genes with significant differences in coding or non-coding regions may provide a reference for developing new DNA barcodes of Carpinus species.

Key words: Carpinus, chloroplast genome, variation, evolution, phylogeny

CLC Number:

Q941

ZHAO Runan, CHU Xiaojie, LIU Wei, HE Qianqian, ZHU Zunling. Structure and variation analyses of chloroplast genomes in Carpinus[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2021, 45(2): 25-34.

Figures/Tables 7

Table 1

Fig.1

Table 2

Fig.2

Fig.3

Table 3

Length of the coding region and the intron-containing gene in chloroplast genome of 16 species in Carpinusbp"

树种 species	rps16		atpF		rpoC1		ycf3		clpP		petB		petD		rpl16		rpl2		ndhB		ndhA
树种 species	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length	编码区长 coding region length	基因全长 gene length
川黔千金榆 C. fangiana	258	1 132	555	1 304	2 058	2 871	507	2 002	591	2 014	648	1 372	483	1 103	408	1 481	825	1 513	1 539	2 225	1 095	2 292
千金榆 C. cordata	258	1 132	555	1 304	2 058	2 885	507	2 002	591	2 015	648	1 441	483	1 103	408	1 498	825	1 513	1 539	2 225	1 095	2 293
天台鹅耳枥 C. tientaiensis	258	1 132	555	1 305	2 058	2 870	507	2 008	591	2 013	-	-	483	1 103	408	1 484	825	1 513	1 539	2 225	1 095	2 292
普陀鹅耳枥 C. putoensis	258	1 132	555	1 306	2 058	2 869	507	2 008	591	2 015	-	-	483	1 103	408	1 316	825	1 513	1 539	2 225	1 095	2 287
太鲁阁鹅耳枥 C. hebestroma	240	1 132	558	1 307	2 052	2 879	510	2 002	591	2 013	648	1 445	483	1 103	408	1 483	864	1 513	1 539	2 225	1 092	2 283
紫脉鹅耳枥 C. purpurinervis	240	1 132	558	1 303	2 052	2 869	510	2 007	591	2 014	648	1 441	483	1 103	408	1 483	864	1 513	1 539	2 225	1 092	2 292
宝华鹅耳枥 C. oblongifolia	240	1 132	558	1 306	2 052	2 870	510	2 002	591	2 012	648	1 445	483	1 103	408	1 483	864	1 513	1 539	2 225	1 092	2 291
岩生鹅耳枥 C. rupestris	258	1 132	555	1 304	2 058	2 869	507	2 008	591	2 013	648	1 441	483	1 103	408	1 483	825	1 513	1 539	2 225	1 095	2 292
多脉鹅耳枥 C. polyneura	258	1 132	555	1 306	2 058	2 870	507	1 995	591	2 012	648	1 445	483	1 103	408	1 483	825	1 513	1 539	2 225	1 095	2 290
云南鹅耳枥 C. monbeigiana	258	1 132	555	1 305	2 058	2 870	507	2 002	591	2 011	648	1 445	483	1 103	408	1 483	825	1 513	1 539	2 225	1 095	2 298
昌化鹅耳枥 C. tschonoskii	240	1 132	558	1 307	2 052	2 871	510	2 002	591	2 012	648	1 445	483	1 103	408	1 483	864	1 513	1 539	2 225	1 092	2 289
川陕鹅耳枥 C. fargesiana	240	1 132	558	1 305	2 052	2 870	510	2 000	591	2 011	648	1 445	483	1 103	408	1 483	864	1 513	1 539	2 225	1 092	2 291
美洲鹅耳枥 C. caroliniana	240	1 132	558	1 308	2 052	2 871	510	2 001	591	2 010	648	1 441	483	1 103	408	1 489	864	1 513	1 539	2 225	1 092	2 303
欧洲鹅耳枥 C. betulus	240	1 132	558	1 306	2 052	2 871	510	2 001	591	2 015	648	1 449	483	1 103	408	1 478	864	1 513	1 539	2 225	1 092	2 289
疏花鹅耳枥 C. laxiflora	240	1 132	558	1 308	2 052	2 870	507	2 002	591	2 009	648	1 445	483	1 103	411	1 483	864	1 513	1 539	2 225	1 092	2 302
雷公鹅耳枥 C. viminea	240	1 132	558	1 304	2 052	2 869	510	2 008	591	2 013	648	1 441	483	1 103	408	1 483	864	1 513	1 539	2 225	1 092	2 293

Table 3

Fig.4

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种名 species	GenBank登录号 GenBank No.	种名 species	GenBank登录号 GenBank No.
川黔千金榆C. fangiana	MG386371.1	多脉鹅耳枥C. polyneura	NC_039998.1
千金榆C. cordata	NC_036723.1	云南鹅耳枥C. monbeigiana	NC_039997.1
天台鹅耳枥C. tientaiensis	NC_034910.1	昌化鹅耳枥C. tschonoskii	NC_039938.1
普陀鹅耳枥C. putoensis	NC_033503.1	川陕鹅耳枥C. fargesiana	NC_039937.1
太鲁阁鹅耳枥C. hebestroma	NC_038131.1	美洲鹅耳枥C. caroliniana	NC_039935.1
紫脉鹅耳枥C. purpurinervis	NC_038093.1	欧洲鹅耳枥C. betulus	NC_039934.1
宝华鹅耳枥C. oblongifolia	MG720817.1	疏花鹅耳枥C. laxiflora	MK425701.1
岩生鹅耳枥C. rupestris	NC_039999.1	雷公鹅耳枥C. viminea	NC_039939.1

树种 speices	基因组大小/bp genome size	GC含量/% GC content	rRNA	tRNA	蛋白编码基因数 protein coding gene	总基因数 total genes	LSS/ bp	SSC/ bp	IR_a/bp	IR_b/bp
川黔千金榆 C. fangiana	158 787	36.50	8	31	86	126	88 168	18 537	26 041	26 041
千金榆 C. cordata	159 157	36.50	8	30	86	125	88 525	18 556	26 038	26 038
天台鹅耳枥 C. tientaiensis	160 104	36.40	8	29	86	124	89 445	18 588	26 035	26 036
普陀鹅耳枥 C. putoensis	159 673	36.40	8	29	85	122	89 019	18 565	26 043	26 046
太鲁阁鹅耳枥 C. hebestroma	159 231	36.50	8	30	85	123	88 168	18 872	26 095	26 096
紫脉鹅耳枥 C. purpurinervis	159 145	36.50	8	29	86	123	88 186	18 800	26 079	26 079
宝华鹅耳枥 C. oblongifolia	159 086	36.50	8	30	86	124	88 190	18 763	26 066	26 067
岩生鹅耳枥 C. rupestris	158 888	36.40	8	29	86	123	87 972	18 779	26 068	26 069
多脉鹅耳枥 C. polyneura	159 400	36.40	8	30	86	124	88 516	18 764	26 060	26 060
云南鹅耳枥 C. monbeigiana	159 450	36.40	8	30	86	124	88 553	18 775	26 061	26 061
昌化鹅耳枥 C. tschonoskii	159 505	36.40	8	30	86	124	88 616	18 758	26 065	26 066
川陕鹅耳枥 C. fargesiana	159 484	36.40	8	30	86	124	88 519	18 814	26 075	26 076
美洲鹅耳枥 C. caroliniana	160 151	36.30	8	31	86	125	88 555	18 517	26 542	26 543
欧洲鹅耳枥 C. betulus	160 583	36.40	8	29	86	123	88 282	17 184	27 567	27 568
疏花鹅耳枥 C. laxiflora	159 225	36.50	8	30	86	124	88 359	18 764	26 066	26 066
雷公鹅耳枥 C. viminea	158 681	36.50	8	29	86	123	87 808	18 808	26 032	26 033

Structure and variation analyses of chloroplast genomes in Carpinus

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