Complete Chloroplast Genome Structure and Characterization of Syringa villosa subsp. wolfii

doi:10.7525/j.issn.1673-5102.2023.01.013

Abstract

Abstract:

To clarify the basic characteristics of the complete chloroplast genome of Syringa villosa subsp. wolfii， the sequence information of chloroplast genome was analyzed by high-throughput sequencing technology， and its systematic evolution position was discussed. The results showed that：（1）The total length of the S. villosa subsp. wolfii chloroplast genome was 156 517 bp， which had a typical tetrad structure and had 131 functional genes， including 36 tRNA genes， 8 rRNA genes and 87 protein-coding genes respectively. （2）The relative synonymous codon usage（RSCU） analysis of the protein-coding region of the chloroplast genome showed that there were 31 codons with RSCU>1， of which 21 ended with A/U base； and there were 34 codons with RSCU<1， including 22 codons ending with G/C base. （3）In the chloroplast genome of S. villosa subsp. wolfii， 334 scattered repeats were detected， including 170 forward repeats and 164 palindromic repeats， and 227 SSR loci were discovered， and PCR primers were designed successfully for 226 of these loci. （4）Phylogenetic tree analysis based on the maximum likelihood method showed that S. villosa subsp. wolfii was the most closely to the S. yunnanensis. In this study， repeated sequences， IR boundaries and phylogeny of chloroplast genome of S. villosa subsp. wolfii were analyzed to provide reference data for molecular markers， phylogenetic classification， species identification and evaluation and DNA barcode development.

Key words: Syringa villosa subsp. wolfii, chloroplast genome, RSCU, sequence repeats, phylogeny

CLC Number:

S685.26

Yongchang LU, Xin ZHANG, Luyan ZHANG, Jiuli WANG. Complete Chloroplast Genome Structure and Characterization of Syringa villosa subsp. wolfii[J]. Bulletin of Botanical Research, 2023, 43(1): 120-130.

Figures/Tables 10

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氨基酸 Amino acid	密码子 Codon	数量 No.	密码子相对使用度 Relative synonymous codon usage	氨基酸 Amino acid	密码子 Codon	数量 No.	密码子相对使用度 Relative synonymous codon usage
Ter	UAA	45	1.551 6	Met	GUG	1	0.004 5
Ter	UAG	24	0.827 7	Met	UUG	1	0.004 5
Ter	UGA	18	0.620 7	Asn	AAC	291	0.474 4
Ala	GCA	388	1.153 2	Asn	AAU	936	1.525 6
Ala	GCC	226	0.671 6	Pro	CCA	338	1.206 0
Ala	GCG	139	0.413 2	Pro	CCC	213	0.760 0
Ala	GCU	593	1.762 4	Pro	CCG	140	0.499 6
Cys	UGC	74	0.510 4	Pro	CCU	430	1.534 4
Cys	UGU	216	1.489 6	Gln	CAA	672	1.501 6
Asp	GAC	198	0.381 6	Gln	CAG	223	0.498 4
Asp	GAU	840	1.618 4	Arg	AGA	497	1.862 4
Glu	GAA	1 053	1.476 8	Arg	AGG	175	0.655 8
Glu	GAG	373	0.523 2	Arg	CGA	359	1.345 2
Phe	UUC	516	0.724 2	Arg	CGC	94	0.352 2
Phe	UUU	909	1.275 8	Arg	CGG	128	0.480 0
Gly	GGA	713	1.616 8	Arg	CGU	348	1.304 4
Gly	GGC	164	0.372 0	Ser	AGC	125	0.375 6
Gly	GGG	324	0.734 8	Ser	AGU	401	1.204 2
Gly	GGU	563	1.276 8	Ser	UCA	381	1.144 2
His	CAC	128	0.433 8	Ser	UCC	324	0.973 2
His	CAU	462	1.566 2	Ser	UCG	192	0.576 6
Ile	AUA	675	0.928 8	Ser	UCU	575	1.726 8
Ile	AUC	445	0.612 3	Thr	ACA	397	1.205 6
Ile	AUU	1 060	1.458 6	Thr	ACC	249	0.756 4
Lys	AAA	1 041	1.494 6	Thr	ACG	140	0.425 2
Lys	AAG	352	0.505 4	Thr	ACU	531	1.612 8
Leu	CUA	389	0.866 4	Val	GUA	515	1.490 4
Leu	CUC	179	0.398 4	Val	GUC	181	0.524 0
Leu	CUG	190	0.423 0	Val	GUG	183	0.529 6
Leu	CUU	586	1.305 0	Val	GUU	503	1.456 0
Leu	UUA	800	1.782 0	Trp	UGG	427	1.000 0
Leu	UUG	550	1.225 2	Tyr	UAC	201	0.425 0
Met	AUG	645	2.990 7	Tyr	UAU	745	1.575 0

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