scholarly journals Characterization of the Chloroplast Genome Sequence of Acer miaotaiense: Comparative and Phylogenetic Analyses

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1740 ◽  
Author(s):  
Jiantao Zhao ◽  
Yao Xu ◽  
Linjie Xi ◽  
Junwei Yang ◽  
Hongwu Chen ◽  
...  
Keyword(s):  
Endangered Species ◽  
Chloroplast Genome ◽  
Microsatellite Loci ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Protein Coding ◽  
Useful Knowledge ◽  
Synonymous Mutations ◽  
Repeat Units ◽  
Chloroplast Genome Sequence

Acer miaotaiense is an endangered species within the Aceraceae family, and has only a few small natural distributions in China’s Qingling Mountains and Bashan Mountains. Comparative analyses of the complete chloroplast genome could provide useful knowledge on the diversity and evolution of this species in different environments. In this study, we sequenced and compared the chloroplast genome of Acer miaotaiense from five ecological regions in the Qingling and Mashan Regions of China. The size of the chloroplast genome ranged from 156,260 bp to 156,204 bp, including two inverted repeat regions, a small single-copy region, and a large single-copy region. Across the whole chloroplast genome, there were 130 genes in total, and 92 of them were protein-coding genes. We observed four genes with non-synonymous mutations involving post-transcriptional modification (matK), photosynthesis (atpI), and self-replication (rps4 and rpl20). A total of 415 microsatellite loci were identified, and the dominant microsatellite types were composed of dinucleotide and trinucleotide motifs. The dominant repeat units were AT and AG, accounting for 37.92% and 31.16% of the total microsatellite loci, respectively. A phylogenetic analysis showed that samples with the same altitude (Xunyangba, Ningshan country, and Zhangliangmiao, Liuba country) had a strong bootstrap value (88%), while the remaining ones shared a similar longitude. These results provided clues about the importance of longitude/altitude for the genetic diversity of Acer miaotaiense. This information will be useful for the conservation and improved management of this endangered species.

scholarly journals Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 744
Author(s):  
Yunyan Zhang ◽  
Yongjing Tian ◽  
David Y. P. Tng ◽  
Jingbo Zhou ◽  
Yuntian Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Eastern China ◽  
Chloroplast Microsatellites ◽  
Endangered Tree ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications ◽  
Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

scholarly journals Complete chloroplast genome sequence of a vegetative Bermudagrass cultivar Tifeagle (Cynodon dactylon × Cynodon transvaalensis)

2019 ◽  
Vol 48 (4) ◽  
pp. 1083-1089
Author(s):  
Yancai Shi ◽  
Shaofeng Jiang ◽  
Shilian Huang
Keyword(s):  
Chloroplast Genome ◽  
Cynodon Dactylon ◽  
Single Copy ◽  
Rrna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Common Bermudagrass ◽  
Trampling Tolerance ◽  
Small Single Copy

Hybrid (Cynodonn dactylon × C. transvaalensis) is a widely distributed turfgrass and shows a great value of environment, horticulture and economic. Though, the chloroplast genome of C. dactylon has been reported, it might be helpful finding reasons that triploid bermudagrass shows a better drought and trampling tolerance than common bermudagrass through comparing chloroplast genome analysis. The present results showed the complete chloroplast genome of the C. dactylon × C. transvaalensis is 134655 bp in length. The tetramerous genome contained a large single copy (LSC) region (79,998 bp), a small single copy (SSC) region (12,517 bp), and a pair of inverted repeat (IR) regions (42,140 bp). In the chloroplast genome, 116 genes were predicted, including 83 protein-coding, 29 tRNA and 4 rRNA genes. Furthermore, a total of 80 repeat sequences were identified. Only 0.23% intergenicnon-collinear sequences were found between the chloroplast genome of Cynodon dactylon × C. transvaalensis and Cynodon dactylon.

scholarly journals The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1405
Author(s):  
Gurusamy Raman ◽  
SeonJoo Park
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Gene Evolution ◽  
Single Copy ◽  
Specific Marker ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genome Sequence

The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

scholarly journals Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Lu Wang ◽  
Na He ◽  
Yao Li ◽  
Yanming Fang ◽  
Feilong Zhang
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Evolutionary Patterns ◽  
Closely Related Species ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Cp Genome ◽  
Rna Genes ◽  
Toxicodendron Vernicifluum

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

scholarly journals Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2426 ◽  
Author(s):  
Xiaofeng Shen ◽  
Shuai Guo ◽  
Yu Yin ◽  
Jingjing Zhang ◽  
Xianmei Yin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Chinese Herb ◽  
Single Copy ◽  
Future Research ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Rna Genes ◽  
Small Single Copy

We sequenced and analyzed the complete chloroplast genome of Aster tataricus (family Asteraceae), a Chinese herb used medicinally to relieve coughs and reduce sputum. The A. tataricus chloroplast genome was 152,992 bp in size, and harbored a pair of inverted repeat regions (IRa and IRb, each 24,850 bp) divided into a large single-copy (LSC, 84,698 bp) and a small single-copy (SSC, 18,250 bp) region. Our annotation revealed that the A. tataricus chloroplast genome contained 115 genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. In addition, 70 simple sequence repeats (SSRs) were detected in the A. tataricus chloroplast genome, including mononucleotides (36), dinucleotides (1), trinucleotides (23), tetranucleotides (1), pentanucleotides (8), and hexanucleotides (1). Comparative chloroplast genome analysis of three Aster species indicated that a higher similarity was preserved in the IR regions than in the LSC and SSC regions, and that the differences in the degree of preservation were slighter between A. tataricus and A. altaicus than between A. tataricus and A. spathulifolius. Phylogenetic analysis revealed that A. tataricus was more closely related to A. altaicus than to A. spathulifolius. Our findings offer valuable information for future research on Aster species identification and selective breeding.

scholarly journals Complete chloroplast genome sequence and structural analysis of the medicinal plant Lycium chinense Mill

2018 ◽  
Author(s):  
Zerui Yang ◽  
Yuying Huang ◽  
Xiasheng Zheng ◽  
Song Huang ◽  
Lingling Liang
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Start Codon ◽  
Lycium Chinense ◽  
Protein Coding ◽  
Engineering Research ◽  
Complete Sequences ◽  
Chloroplast Genome Sequence ◽  
Cp Genome

Lycium chinense Mill, an important Chinese herbal medicine, is emphasized as a healthy food and is widely used as a dietary supplement. Here we sequenced and analyzed the complete chloroplast (CP) genome of the L. chinense, which is 155,756 bp in length and with 37.8% GC content. This CP genome consists of a pair of inverted repeat regions (IRa and IRb) of 25,476 bp, separated by a large single-copy region (LSC) and a small single-copy region (SSC), with length of 86,595 and 18,209 bp, respectively. Annotation results revealed that the L. chinense CP genome contains 114 genes, 16 of which are duplicated genes. Most of the 85 protein-coding genes have a usual ATG start codon, except for 3 genes including rps12, psbL and ndhD. Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to the high AT content of the chloroplast genome. Revealing of the complete sequences and annotation of the L. chinense chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.

scholarly journals Complete Chloroplast Genome Sequence of Fortunella venosa (Champ. ex Benth.) C.C.Huang (Rutaceae): Comparative Analysis, Phylogenetic Relationships, and Robust Support for Its Status as an Independent Species

Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 996
Author(s):  
Ting Wang ◽  
Ren-Ping Kuang ◽  
Xiao-Hui Wang ◽  
Xiao-Li Liang ◽  
Vincent Okelo Wanga ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Taxonomic Status ◽  
Single Copy ◽  
Ring Structure ◽  
Protein Coding ◽  
Coding Regions ◽  
Second Generation Sequencing ◽  
Chloroplast Genome Sequence ◽  
Independent Species

Fortunella venosa (Rutaceae) is an endangered species endemic to China and its taxonomic status has been controversial. The genus Fortunella contains a variety of important economic plants with high value in food, medicine, and ornamental. However, the placement of Genus Fortunella into Genus Citrus has led to controversy on its taxonomy and Systematics. In this present research, the Chloroplast genome of F. venosa was sequenced using the second-generation sequencing, and its structure and phylogenetic relationship analyzed. The results showed that the Chloroplast genome size of F. venosa was 160,265 bp, with a typical angiosperm four-part ring structure containing a large single copy region (LSC) (87,597 bp), a small single copy region (SSC) (18,732 bp), and a pair of inverted repeat regions (IRa\IRb) (26,968 bp each). There are 134 predicted genes in Chloroplast genome, including 89 protein-coding genes, 8 rRNAs, and 37 tRNAs. The GC-content of the whole Chloroplast genome was 43%, with the IR regions having a higher GC content than the LSC and the SSC regions. There were no rearrangements present in the Chloroplast genome; however, the IR regions showed obvious contraction and expansion. A total of 108 simple sequence repeats (SSRs) were present in the entire chloroplast genome and the nucleotide polymorphism was high in LSC and SSC. In addition, there is a preference for codon usage with the non-coding regions being more conserved than the coding regions. Phylogenetic analysis showed that species of Fortunella are nested in the genus of Citrus and the independent species status of F. venosa is supported robustly, which is significantly different from F. japonica. These findings will help in the development of DNA barcodes that can be useful in the study of the systematics and evolution of the genus Fortunella and the family Rutaceae.

scholarly journals Complete chloroplast genome sequence and structural analysis of the medicinal plant Lycium chinense Mill

2018 ◽  
Author(s):  
Zerui Yang ◽  
Yuying Huang ◽  
Xiasheng Zheng ◽  
Song Huang ◽  
Lingling Liang
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Start Codon ◽  
Lycium Chinense ◽  
Protein Coding ◽  
Engineering Research ◽  
Complete Sequences ◽  
Chloroplast Genome Sequence ◽  
Cp Genome

Lycium chinense Mill, an important Chinese herbal medicine, is emphasized as a healthy food and is widely used as a dietary supplement. Here we sequenced and analyzed the complete chloroplast (CP) genome of the L. chinense, which is 155,756 bp in length and with 37.8% GC content. This CP genome consists of a pair of inverted repeat regions (IRa and IRb) of 25,476 bp, separated by a large single-copy region (LSC) and a small single-copy region (SSC), with length of 86,595 and 18,209 bp, respectively. Annotation results revealed that the L. chinense CP genome contains 114 genes, 16 of which are duplicated genes. Most of the 85 protein-coding genes have a usual ATG start codon, except for 3 genes including rps12, psbL and ndhD. Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to the high AT content of the chloroplast genome. Revealing of the complete sequences and annotation of the L. chinense chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.

scholarly journals Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 476 ◽  
Author(s):  
Shabina Iram ◽  
Muhammad Qasim Hayat ◽  
Muhammad Tahir ◽  
Alvina Gul ◽  
Abdullah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Cost Effective ◽  
Single Copy ◽  
Protein Coding ◽  
Important Species ◽  
Mutational Hotspots ◽  
Genome Features ◽  
Artemisia Scoparia ◽  
Chloroplast Genome Sequence

Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.

scholarly journals The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2734 ◽  
Author(s):  
Xin Yao ◽  
Ying-Ying Liu ◽  
Yun-Hong Tan ◽  
Yu Song ◽  
Richard T. Corlett
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Phylogenomic Analysis ◽  
Trna Genes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genome Sequence

Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome forHelwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels. TheHelwingiagenome consists of 158,362 bp containing a pair of inverted repeat (IR) regions of 25,996 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

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