四川山胡椒叶绿体基因组特征及山胡椒属系统发育

doi:10.11707/j.1001-7488.20211217

Abstract

Abstract:

Objective: Lindera setchuenensis has important medicinal value. Researches of chloroplast genome possess essential theoretical and practical significance for species identification, analysis of genetic diversity and resource protection of the genus Lindera. Method: The complete chloroplast genome of L. setchuenensis was sequenced based on Illumina HiSeq 2000 platform, and was assembled through de novo. The genome structure, gene composition, repeats and phylogeny were analyzed. Result: The chloroplast genome of L. setchuenensis exhibited a typical quadripartite structure. A total of 125 functional genes were detected, including 81 protein coding genes, 36 tRNA genes, and eight rRNA genes. Frequency of guanine and cytosine bases(GC3s) of the genome encoding genes was 27.96%, 20 codons were ended with A/U(T) among 21 optimal codons. Among the 27 pairs of long repeats, forward repeats and palindromic repeats accounted for 44% and 41% respectively, and the length of 30 bp and 33 bp accounted for 44% and 30% respectively. Among the 181 SSRs, 68% were A/T repeats and 55% were located in the intergenic regions. Comparing the chloroplast genomes of the genus Lindera, it was indicated that six hyper-variable loci, petA-psbJ, trnH-psbA, petK-psbI, ccsA-ndhD, rpl32-trnL, and ycf1, could potentially be used as DNA barcodes candidates for species identification. Phylogenetic analysis revealed that the genus Lindera was divided into five clades. L. setchuenensis presented the closest relationship with L. megaphylla. Conclusion: The structure of chloroplast genome of L. setchuenensis is conservative and prefers codons ending with A or U(T). The hyper-variable regions and SSR loci can be used as DNA barcoding for species identification. The results provide a basis for the development of molecular markers, phylogeny and breeding of elite varieties of Lindera plants.

Key words: Lindera setchuenensis, codon usage bias, SSR, phylogeny, mutational hotspots

CLC Number:

S718.46

Chao Liu,Lizhou Tang,Lihong Han. Characterization of the Chloroplast Genome of Lindera setchuenensis and Phylogenetics of the Genus Lindera[J]. Scientia Silvae Sinicae, 2021, 57(12): 167-174.

Figures/Tables 7

Fig.1

Table 1

Relative synonymous codon usage of genes in the chloroplast genome of Lindera setchuenensis"

氨基酸 Amino acid	密码子 Codon	相对同义密码子使用度 Relative synonymous codon usage			氨基酸 Amino acid	密码子 Codon	相对同义密码子使用度 Relative synonymous codon usage
氨基酸 Amino acid	密码子 Codon	基因组 Genome	高表达基因 High expression gene	低表达基因 Low expression gene	氨基酸 Amino acid	密码子 Codon	基因组 Genome	高表达基因 High expression gene	低表达基因 Low expression gene
蛋氨酸 Met	ATG	1.00	1.00	1.00	色氨酸 Trp	TGG	1.00	1.00	1.00
丙氨酸	GCA	1.15	1.04	1.16	脯氨酸	CCA^**	1.10	1.19	0.89
Ala	GCC	0.65	0.46	0.99	Pro	CCC	0.89	1.05	1.22
	GCG	0.43	0.12	0.41		CCG	0.52	0.07	0.50
	GCT^***	1.77	2.38	1.45		CCT^**	1.50	1.68	1.39
半胱氨酸	TGC	0.51	0.29	0.62	谷氨酰胺	CAA^*	1.47	1.37	1.29
Cys	TGT^**	1.50	1.71	1.39	Gln	CAG	0.53	0.63	0.71
天冬氨酸	GAC	0.43	0.50	0.62	精氨酸	AGA^*	1.80	2.08	1.78
Asp	GAT^*	1.58	1.50	1.38	Arg	AGG	0.70	0.46	0.86
谷氨酸	GAA^*	1.48	1.62	1.38		CGA^*	1.35	1.44	1.19
Glu	GAG	0.52	0.38	0.62		CGC	0.36	0.23	0.53
苯丙氨酸	TTC	0.82	1.12	0.87		CGG	0.43	0.17	0.33
Phe	TTT	1.18	0.88	1.13		CGT^*	1.36	1.62	1.32
甘氨酸	GGA^*	1.56	1.56	1.43	丝氨酸	AGC	0.34	0.44	0.48
Gly	GGC	0.46	0.49	0.39	Ser	AGT	1.17	1.39	1.26
	GGG	0.72	0.44	0.79		TCA	1.24	0.66	1.08
	GGT^*	1.26	1.51	1.39		TCC	1.05	1.02	1.08
组氨酸	CAC	0.48	0.64	0.67		TCG	0.63	0.44	0.54
His	CAT	1.52	1.36	1.33		TCT^**	1.57	2.05	1.56
异亮氨酸	ATA	0.91	0.80	0.97	苏氨酸	ACA	1.15	0.94	1.30
Ile	ATC	0.65	0.70	0.62	Thr	ACC	0.83	1.18	0.85
	ATT^*	1.44	1.50	1.41		ACG	0.48	0.18	0.34
赖氨酸	AAA	1.48	1.48	1.49		ACT^*	1.54	1.71	1.52
Lys	AAG	0.52	0.53	0.52	缬氨酸	GTA^*	1.42	1.68	1.52
亮氨酸	CTA	0.89	0.87	0.79	Val	GTC	0.52	0.70	0.64
Leu	CTC	0.44	0.40	0.23		GTG	0.63	0.32	0.69
	CTG	0.44	0.20	0.45		GTT^*	1.43	1.30	1.15
	CTT	1.22	1.33	1.59	络氨酸	TAC	0.44	0.55	0.49
	TTA^*	1.76	1.73	1.64	Tyr	TAT	1.56	1.46	1.51
	TTG^*	1.27	1.47	1.30	终止	TAA^***	1.37	2.10	1.20
天冬酰胺	AAC	0.48	0.77	0.29	密码子 TER	TAG	0.76	0.30	1.20
Asn	AAT	1.52	1.23	1.71	密码子 TER	TGA	0.87	0.60	0.60

Table 1

Fig.2

Fig.3

Fig.4

Fig.5

Fig.6

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Characterization of the Chloroplast Genome of Lindera setchuenensis and Phylogenetics of the Genus Lindera

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