Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae

Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L . ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L . ruprechtiana was ide...

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Veröffentlicht in:	PloS one Jg. 17; H. 1; S. e0262813
Hauptverfasser:	Gu, Lei, Hou, Yunyan, Wang, Guangyi, Liu, Qiuping, Ding, Wei, Weng, Qingbei
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	United States Public Library of Science 25.01.2022 Public Library of Science (PLoS)
Schlagworte:	Biology and Life Sciences Caprifoliaceae Caprifoliaceae - genetics Chloroplasts Comparative analysis Computer and Information Sciences Conserved Sequence - genetics Cytochrome Cytochrome b Cytochromes Engineering and Technology Flowers & plants Genes Genes, Plant - genetics Genetic aspects Genetic testing Genome, Chloroplast - genetics Genomes Identification and classification Inverted repeat Life sciences Lonicera - genetics Lonicera ruprechtiana Microsatellite Repeats - genetics NADH NADH dehydrogenase Nicotinamide adenine dinucleotide Photosynthesis - genetics Photosystem Phylogenetics Phylogeny Plant mitochondria Sequence Analysis, DNA Species Whole genome sequencing China United States > US
ISSN:	1932-6203, 1932-6203
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Abstract	Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L . ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L . ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L . ruprechtiana was closely related to Lonicera insularis . Comparison of IR regions revealed that the cp genome of L . ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3 , and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L . ruprechtiana evolution.
AbstractList	Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution. Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L . ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L . ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L . ruprechtiana was closely related to Lonicera insularis . Comparison of IR regions revealed that the cp genome of L . ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3 , and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L . ruprechtiana evolution. Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution.Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution.
Audience	Academic
Author	Weng, Qingbei Wang, Guangyi Gu, Lei Ding, Wei Liu, Qiuping Hou, Yunyan
AuthorAffiliation	Institute for Biological Research, University of Belgrade, SERBIA 2 Colleage of plant protection, Southwest University, Chongqing, China 1 School of Life Sciences, Guizhou Normal University, Guiyang, China 3 Qiannan Normal University for Nationalities, Duyun, China
AuthorAffiliation_xml	– name: 1 School of Life Sciences, Guizhou Normal University, Guiyang, China – name: 2 Colleage of plant protection, Southwest University, Chongqing, China – name: 3 Qiannan Normal University for Nationalities, Duyun, China – name: Institute for Biological Research, University of Belgrade, SERBIA
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CitedBy_id	crossref_primary_10_1080_23802359_2023_2239386 crossref_primary_10_3390_genes14030548 crossref_primary_10_1080_23802359_2023_2180309 crossref_primary_10_48130_mpb_0024_0008 crossref_primary_10_3390_d15020197
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Snippet	Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship... Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship...
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SubjectTerms	Biology and Life Sciences Caprifoliaceae Caprifoliaceae - genetics Chloroplasts Comparative analysis Computer and Information Sciences Conserved Sequence - genetics Cytochrome Cytochrome b Cytochromes Engineering and Technology Flowers & plants Genes Genes, Plant - genetics Genetic aspects Genetic testing Genome, Chloroplast - genetics Genomes Identification and classification Inverted repeat Life sciences Lonicera - genetics Lonicera ruprechtiana Microsatellite Repeats - genetics NADH NADH dehydrogenase Nicotinamide adenine dinucleotide Photosynthesis - genetics Photosystem Phylogenetics Phylogeny Plant mitochondria Sequence Analysis, DNA Species Whole genome sequencing
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Title	Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae
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