scholarly journals The complete chloroplast genome provides insight into the polymorphism and adaptive evolution of Garcinia paucinervis

2021 ◽  
Vol 35 (1) ◽  
pp. 377-391
Author(s):  
Yifei Wang ◽  
Bo Zhao ◽  
Zhaocen Lu ◽  
Yancai Shi ◽  
Jingjian Li
Keyword(s):  
Chloroplast Genome ◽  
Adaptive Evolution ◽  
Complete Chloroplast Genome ◽  
Garcinia Paucinervis ◽  
Insight Into

scholarly journals The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng

2015 ◽  
Vol 5 ◽  
Author(s):  
Yongbing Zhao ◽  
Jinlong Yin ◽  
Haiyan Guo ◽  
Yuyu Zhang ◽  
Wen Xiao ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Panax Ginseng ◽  
Complete Chloroplast Genome ◽  
Insight Into

scholarly journals The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene

2019 ◽  
Author(s):  
Qiwen Zhong ◽  
Shipeng Yang ◽  
Xuemei Sun ◽  
Lihui Wang ◽  
Yi Li
Keyword(s):  
Chloroplast Genome ◽  
Adaptive Evolution ◽  
Jerusalem Artichoke ◽  
Single Copy ◽  
Reverse Direction ◽  
Evolutionary Analysis ◽  
Helianthus Tuberosus ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Coding Regions

Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China which has become an emerging economic crop with rapid development. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (LSC, 83,981 bp), and a small single-copy region (SSC, 18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased towards A/T bases. 32 SSRs were distributed in the non-coding regions. Comparative analysis of the chloroplast genome sequence of Jerusalem artichoke and other species of the composite family revealed the chloroplast genome sequences of plants of the composite family to be highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. Phylogenetic analysis showed Helianthus petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution and has the potential to be used as a phylogenetic reconstruction locus in the composite family. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family, and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.

scholarly journals The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene

2019 ◽  
Author(s):  
Qiwen Zhong ◽  
Shipeng Yang ◽  
Xuemei Sun ◽  
Lihui Wang ◽  
Yi Li
Keyword(s):  
Chloroplast Genome ◽  
Adaptive Evolution ◽  
Jerusalem Artichoke ◽  
Single Copy ◽  
Reverse Direction ◽  
Evolutionary Analysis ◽  
Helianthus Tuberosus ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Coding Regions

Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China which has become an emerging economic crop with rapid development. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (LSC, 83,981 bp), and a small single-copy region (SSC, 18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased towards A/T bases. 32 SSRs were distributed in the non-coding regions. Comparative analysis of the chloroplast genome sequence of Jerusalem artichoke and other species of the composite family revealed the chloroplast genome sequences of plants of the composite family to be highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. Phylogenetic analysis showed Helianthus petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution and has the potential to be used as a phylogenetic reconstruction locus in the composite family. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family, and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.

scholarly journals The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7596 ◽  
Author(s):  
Qiwen Zhong ◽  
Shipeng Yang ◽  
Xuemei Sun ◽  
Lihui Wang ◽  
Yi Li
Keyword(s):  
Chloroplast Genome ◽  
Adaptive Evolution ◽  
Jerusalem Artichoke ◽  
Single Copy ◽  
Reverse Direction ◽  
Evolutionary Analysis ◽  
Helianthus Tuberosus ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Coding Regions

Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China, and it has become an emerging economic crop that is rapidly developing. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (83,981 bp), and a small single-copy region (18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. A total of 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 32 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the Jerusalem artichoke and other species of the composite family revealed that the chloroplast genome sequences of plants of the composite family were highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. A phylogenetic analysis showed that H. petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.

scholarly journals Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 441
Author(s):  
Shixiong Ding ◽  
Xiang Dong ◽  
Jiaxin Yang ◽  
Chunce Guo ◽  
Binbin Cao ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Adaptive Evolution ◽  
Single Copy ◽  
Evolutionary Conservation ◽  
Central China ◽  
Rrna Genes ◽  
Trna Genes ◽  
Complete Chloroplast Genome ◽  
Genome Features

Clethra fargesii, an essential ecological and endemic woody plant of the genus Clethra in Clethraceae, is widely distributed in Central China. So far, there have been a paucity of studies on its chloroplast genome. In the present study, we sequenced and assembled the complete chloroplast genome of C. fargesii. We also analyzed the chloroplast genome features and compared them to Clethra delavayi and other closely related species in Ericales. The complete chloroplast genome is 157,486 bp in length, including a large single-copy (LSC) region of 87,034 bp and a small single-copy (SSC) region of 18,492 bp, separated by a pair of inverted repeat (IR) regions of 25,980 bp. The GC content of the whole genome is 37.3%, while those in LSC, SSC, and IR regions are 35.4%, 30.7%, and 43.0%, respectively. The chloroplast genome of C. fargesii encodes 132 genes in total, including 87 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. A total of 26,407 codons and 73 SSRs were identified in C. fargesii chloroplast genome. Additionally, we postulated and demonstrated that the structure of the chloroplast genome in Clethra species may present evolutionary conservation based on the comparative analysis of genome features and genome alignment among eight Ericales species. The low Pi values revealed evolutionary conservation based on the nucleotide diversity analysis of chloroplast genome in two Clethra species. The low selection pressure was shown by a few positively selected genes by adaptive evolution analysis using 80 coding sequences (CDSs) of the chloroplast genomes of two Clethra species. The phylogenetic tree showed that Clethraceae and Ericaceae are sister clades, which reconfirm the previous hypothesis that Clethra is highly conserved in the chloroplast genome using 75 CDSs of chloroplast genome among 40 species. The genome information and analysis results presented in this study are valuable for further study on the intraspecies identification, biogeographic analysis, and phylogenetic relationship in Clethraceae.

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