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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Published in:PloS one Vol. 17; no. 1; p. e0262813
Main Authors: Gu, Lei, Hou, Yunyan, Wang, Guangyi, Liu, Qiuping, Ding, Wei, Weng, Qingbei
Format: Journal Article
Language:English
Published: United States Public Library of Science 25.01.2022
Public Library of Science (PLoS)
Subjects:
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
Online Access:Get full text
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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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  surname: Gu
  fullname: Gu, Lei
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  fullname: Weng, Qingbei
BackLink https://www.ncbi.nlm.nih.gov/pubmed/35077482$$D View this record in MEDLINE/PubMed
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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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StartPage e0262813
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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http://dx.doi.org/10.1371/journal.pone.0262813
Volume 17
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