scholarly journals Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6244 ◽  
Author(s):  
Simon Pfanzelt ◽  
Dirk C. Albach ◽  
K. Bernhard von Hagen
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Single Copy ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Sequence Comparisons ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence

Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.

scholarly journals Determination of the evolutionary pressure onCamellia oleiferaon Hainan Island using the complete chloroplast genome sequence

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7210 ◽  
Author(s):  
Wan Zhang ◽  
Yunlin Zhao ◽  
Guiyan Yang ◽  
Jiao Peng ◽  
Shuwen Chen ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Evolutionary History ◽  
Evolutionary Relationship ◽  
Hainan Island ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Phylogenetic Studies ◽  
Chloroplast Genome Sequence

Camellia oleiferais one of the four largest woody edible oil plants in the world with high ecological and medicinal values. Due to frequent interspecific hybridization, it was difficult to study its genetics and evolutionary history. This study usedC. oleiferathat was collected on Hainan Island to conduct our research. The unique island environment makes the quality of tea oil higher than that of other species grown in the mainland. Moreover, a long-term geographic isolation might affect gene structure. In order to better understand the molecular biology of this species, protect excellent germplasm resources, and promote the population genetics and phylogenetic studies ofCamelliaplants, high-throughput sequencing technology was used to obtain the chloroplast genome sequence of HainanC. oleifera. The results showed that the whole chloroplast genome ofC. oleiferain Hainan was 156,995 bp in length, with a typical quadripartite structure of a large single copy (LSC) region of 86,648 bp, a small single copy (SSC) region of 18,297 bp, and a pair of inverted repeats (IRs) of 26,025 bp. The whole genome encoded a total of 141 genes (115 different genes), including 88 protein-coding genes, 45 tRNA genes, and eight rRNA genes. Among these genes, nine genes contained one intron, two genes contained two introns, and four overlapping genes were also detected. The total GC content of HainanC. oleifera’s chloroplast genome was 37.29%. The chloroplast genome structure characteristics of HainanC. oleiferawere compared with mainlandC. oleiferaand those of the other eight closely related Theaceae species; it was found that the contractions and expansions of the IR/LSC and IR/SSC regions affected the length of chloroplast genome. The chloroplast genome sequences of these Theaceae species were highly similar. A comparative analysis indicated that the Theaceae species were conserved in structure and evolution. A total of 51 simple sequence repeat (SSR) loci were detected in the chloroplast genome of HainanC. oleifera, and allCamelliaplants did not have pentanucleotide repeats, which could be used as a good marker in phylogenetic studies. We also detected seven long repeats, the base composition of all repeats was biased toward A/T, which was consistent with the codon bias. It was found that HainanC. oleiferahad a similar evolutionary relationship withC. crapnelliana, through the use of codons and phylogenetic analysis. This study can provide an effective genomic resource for the evolutionary history of Theaceae family.

scholarly journals Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya)

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Junling Cao ◽  
Dan Jiang ◽  
Zhenyu Zhao ◽  
Subo Yuan ◽  
Yujun Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complete Chloroplast Genome ◽  
Genomic Resources ◽  
Chinese Yam ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Simple Sequence

Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs). Seventy simple sequence repeats (SSRs) were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

scholarly journals The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

2021 ◽  
Vol 51 (3) ◽  
pp. 326-331
Author(s):  
Sung-Dug OH ◽  
Seong-Kon LEE ◽  
Doh-Won YUN ◽  
Hyeon-Jin SUN ◽  
Hong-Gyu KANG ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Single Copy ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Intraspecific Variations

The complete chloroplast genome of Zoysia macrostachya Franch. & Sav. isolated in Korea is 135,902 bp long (GC ratio is 38.4%) and has four subregions; 81,546 bp of large single-copy (36.3%) and 12,586 bp of small single-copy (32.7%) regions are separated by 20,885 bp of inverted repeat (44.1%) regions, including 130 genes (83 protein-coding genes, eight rRNAs, and 39 tRNAs). Thirty-nine single nucleotide polymorphisms and 11 insertions and deletion (INDEL) regions were identified from two Z. macrostachya chloroplast genomes, the smallest among other Zoysia species. Phylogenetic trees show that two Z. macrostachya chloroplast genomes are clustered into a single clade. However, we found some incongruency with regard to the phylogenetic position of the Z. macrostachya clade. Our chloroplast genome provides insights into intraspecific variations and species delimitation issues pertaining to the Zoysia species.

scholarly journals Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

2019 ◽  
Vol 20 (23) ◽  
pp. 5940
Author(s):  
Xinbo Pang ◽  
Hongshan Liu ◽  
Suran Wu ◽  
Yangchen Yuan ◽  
Haijun Li ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Species Identification ◽  
Genome Sequence ◽  
Dna Barcode ◽  
Single Copy ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Quercus Species ◽  
Chloroplast Genome Sequence

Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.

scholarly journals Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

2021 ◽  
Author(s):  
Jianjian Li ◽  
Junqin Zong ◽  
Haoran Wang ◽  
Jingjing Wang ◽  
Hailin Guo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Genome Sequence ◽  
Warm Season ◽  
Single Copy ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Complete Chloroplast Genome ◽  
Eremochloa Ophiuroides ◽  
Cp Genome

Abstract Background: Chloroplast (cp) genome sequence data could provide valuable information for molecular taxonomy and phylogenetic reconstruction among plant species and individuals. However, as one of the most important warm-season turfgrasses widely used in USA and China, cp genome characteristics and phylogenetic position of centipedegrass (Eremochloa ophiuroides) were poorly understood.Results: In this study, we determined the complete chloroplast genome sequences of E. ophiuroides using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, and has a typical quadripartite structure consisting of a pair of inverted repeat (IR) regions of 22,230 bp each separated by a large single copy (LSC) region of 82,081 bp and a small single copy (SSC) region of 12,566 bp. The nucleotide composition of E. ophiuroides cp genome is asymmetric with an overall A + T content of 61.60%. It encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes including 77 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Analysis of the repetitive sequences revealed that E. ophiuroides cp genome contains 51 tandem repeats including 29 forward, 20 palindromic and 2 reverse repeats, and 197 simple sequence repeats (SSRs) which were mainly composed of adenine (A) and thymine (T) bases. Comparison of the E. ophiuroides complete cp genome with the genomes of other seven Gramineae species showed a high degree of collinearity among Gramineae plants. Phylogenetic analysis showed that E. ophiuroides was closely related to E. ciliaris and E. eriopoda, and was placed in a clade with the two Eremochloa species and Mnesithea helferi within the subtribe Rottboelliinae, which clarified evolutionary status of E. ophiuroides in tribe Andropogoneae and also authenticated the current taxonomy of the tribe Andropogoneae.Conclusions: The present study provides the complete structure of the E. ophiuroides cp genome, and preliminarily ascertains the phylogenetic position of E. ophiuroides in tribe Andropogonodae. This will be of value to grass taxa identification, phylogenetic resolution, population structure and biodiversity, novel gene discovery and functional genomic studies for the genus Eremochloa.

scholarly journals Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

2021 ◽  
Author(s):  
Junqin Zong ◽  
Haoran Wang ◽  
Jingjing Wang ◽  
Hailin Guo ◽  
Jingbo Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Genome Sequence ◽  
Warm Season ◽  
Single Copy ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Complete Chloroplast Genome ◽  
Eremochloa Ophiuroides ◽  
Cp Genome

Abstract Background: Chloroplast (cp) genome sequence data could provide valuable information for molecular taxonomy and phylogenetic reconstruction among plant species and individuals. However, as one of the most important warm-season turfgrasses widely used in USA and China, cp genome characteristics and phylogenetic position of centipedegrass (Eremochloa ophiuroides) were poorly understood.Results: In this study, we determined the complete chloroplast genome sequences of E. ophiuroides using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, and has a typical quadripartite structure consisting of a pair of inverted repeat (IR) regions of 22,230 bp each separated by a large single copy (LSC) region of 82,081 bp and a small single copy (SSC) region of 12,566 bp. The nucleotide composition of E. ophiuroides cp genome is asymmetric with an overall A + T content of 61.60%. It encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes including 77 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Analysis of the repetitive sequences revealed that E. ophiuroides cp genome contains 51 tandem repeats including 29 forward, 20 palindromic and 2 reverse repeats, and 197 simple sequence repeats (SSRs) which were mainly composed of adenine (A) and thymine (T) bases. Comparison of the E. ophiuroides complete cp genome with the genomes of other seven Gramineae species showed a high degree of collinearity among Gramineae plants. Phylogenetic analysis showed that E. ophiuroides was closely related to E. ciliaris and E. eriopoda, and was placed in a clade with the two Eremochloa species and Mnesithea helferi within the subtribe Rottboelliinae, which clarified evolutionary status of E. ophiuroides in tribe Andropogoneae and also authenticated the current taxonomy of the tribe Andropogoneae.Conclusions: The present study provides the complete structure of the E. ophiuroides cp genome, and preliminarily ascertains the phylogenetic position of E. ophiuroides in tribe Andropogonodae. This will be of value to grass taxa identification, phylogenetic resolution, population structure and biodiversity, novel gene discovery and functional genomic studies for the genus Eremochloa.

scholarly journals The complete chloroplast genome sequence of an endemic monotypic genusHagenia(Rosaceae): structural comparative analysis, gene content and microsatellite detection

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2846 ◽  
Author(s):  
Andrew W. Gichira ◽  
Zhizhong Li ◽  
Josphat K. Saina ◽  
Zhicheng Long ◽  
Guangwan Hu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Genome Sequence ◽  
Gene Content ◽  
Rrna Genes ◽  
Inverted Repeats ◽  
Translational Initiation ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence

Hageniais an endangered monotypic genus endemic to the topical mountains of Africa. The only species,Hagenia abyssinica(Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence ofH. abyssinica.The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696).H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing inH. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placedHageniain Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

scholarly journals Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 61 ◽  
Author(s):  
Huyen-Trang Vu ◽  
Ngan Tran ◽  
Thanh-Diem Nguyen ◽  
Quoc-Luan Vu ◽  
My-Huyen Bui ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Complete Chloroplast Genome ◽  
Critically Endangered Species ◽  
Plastid Genomes ◽  
Chloroplast Genomes

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

scholarly journals Chloroplast Genome Sequence ofArabidopsis thalianaAccession Landsbergerecta, Assembled from Single-Molecule, Real-Time Sequencing Data

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Kai Bernd Stadermann ◽  
Daniela Holtgräwe ◽  
Bernd Weisshaar
Keyword(s):  
Arabidopsis Thaliana ◽  
High Resolution ◽  
Chloroplast Genome ◽  
Real Time ◽  
Genome Sequence ◽  
Single Molecule ◽  
Sequencing Data ◽  
Data Set ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence

A publicly available data set from Pacific Biosciences was used to create an assembly of the chloroplast genome sequence of theArabidopsis thalianagenotype Landsbergerecta. The assembly is solely based on single-molecule, real-time sequencing data and hence provides high resolution of the two inverted repeat regions typically contained in chloroplast genomes.

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