scholarly journals Complete Chloroplast Genome of Fokienia hodginsii (Dunn) Henry et Thomas: Insights into Repeat Regions Variation and Phylogenetic Relationships in Cupressophyta

Forests ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 528 ◽  
Author(s):  
Mingyue Zang ◽  
Qian Su ◽  
Yuhao Weng ◽  
Lu Lu ◽  
Xueyan Zheng ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Tandem Repeats ◽  
Genomic Structure ◽  
Gc Content ◽  
Reference Value ◽  
Complete Sequence ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
History Of

Fokienia hodginsii (Dunn) Henry et Thomas is a relic gymnosperm with broad application value. It is a fit candidate when choosing species for the construction of artificial forests. We determined the complete chloroplast genome sequence of F. hodginsii, which is 129,534 bp in length and encodes 83 protein genes, 33 transfer RNA (tRNA) genes, as well as four ribosomal RNA genes. The GC content of the complete sequence and protein coding regions is 34.8% and 36.2%, respectively. We identified 11 tandem repeats, 11 forward repeats, and three palindromic repeats and classified them by size. Following our microsatellite analysis, a total number of 73 simple sequence repeats were detected, preferentially within the intergenic space. Being a member of Cupressophyta, F. hodginsii owns several common characters; the trnR-CCG gene has been deleted, while the trnI-CAU and trnQ-UUG genes have been duplicated. Moreover, the accD gene, which encodes acetyl-CoA carboxylase, contains 771 codons in F. hodginsii, similar to Cryptomeria japonica (L. F.) D. Don, further supporting the diversity of accD and its size expansion in Cupressophyta. Concerning the loss of inverted repeat (IR) regions, the 86-bp sequence with the duplicated trnI-CAU gene is inferred to be the footprint of IR contraction. Phylogenetically, F. hodginsii is placed as a sister taxon to Chamaecyparis hodginsii (Dunn) Rushforth. This work offers meaningful guidance as well as reference value to the breeding research and improvement of F. hodginsii. Moreover, it gives us a better understanding of the genomic structure and evolutionary history of gymnosperms, especially coniferales.

scholarly journals Application of chloroplast genome to resolve the taxonomy and phylogenetic relationships of invasive dioecious weeds in Amaranthus (Amaranthaceae)

2019 ◽  
Author(s):  
Han Xu
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Rrna Genes ◽  
Alien Invasive Species ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Intergenic Spacers ◽  
Phylogenetic Studies ◽  
Hybrid Complex

Abstract Backgroud: Amaranthus palmeri, A. tuberculatus and A. arenicola are alien invasive dioecious amaranths originated from North America which have similar morphology and complex taxonomic relationship with their relatives. To search for effective molecular methods and accurate species boundary for detecting the alien invasive species, we sequenced whole chloroplast genome of 6 amaranths species, of which A. palmeri , A. arenicola , A. retroflexus and A. dubius are the first reports.Results: The complete chloroplast genome of 6 species has a circular molecular structure of 150,454 to 150,939 bp in length with 36.6% of GC content and contains a total of 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. There are a total of 802 parsimony-informative (PI) sites within genes and intergenic spacers. The rpl22-rps19 , ndhG-I , rpl 32- trnLUAG , trnPUGG-psaJ and ccsA - ndhD are the hotspots in the genus. And the 1,601 bp fragment from rpl32 to psaC has contained maximum variants with 82 PI sites. A. arenicola differs from A. tuberculatus with 19 PI sites located in 14 genes and spacers separately. The regions for differentiate A. dubius , A. hypochondriacus and A. caudatus of the Hybrid complex only fasten on 2 coding genes and 5 intergenic spacers. The patristic distances (0.00001-0.00005) among the three species are approximate to the distance (0.00005) between individuals of A. tuberculatus . Conformed to dioecious and monoecious distinctions but different with previous phylogenetic studies, A. palmeri clustered with A. arenicola and A. tuberculatus and formed a stable clade of subgen. Acnida .Conclusion: The chloroplast genome has played a role in offering enough information for discrimination and phylogenetic relationship among the Amaranthus subgen. Acnida . The most valuable regions of chloroplast genome in Amaranthus are intergenic spacers and could differentiate A. arenicola from A. tuberculatus better. Subsequently, much more Amaranthus species should be sequenced and analyzed complementally in the future.

scholarly journals Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1354
Author(s):  
Slimane Khayi ◽  
Fatima Gaboun ◽  
Stacy Pirro ◽  
Tatiana Tatusova ◽  
Abdelhamid El Mousadik ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Important Species ◽  
Complete Chloroplast Genome ◽  
Argania Spinosa ◽  
Protein Coding Genes ◽  
Cp Genome

Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.

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 The complete chloroplast genome sequence of American elm (Ulmus americana) and comparative genomics of related species

2020 ◽  
Author(s):  
Aziz Ebrahimi ◽  
Jennifer D. Antonides ◽  
Cornelia C. Pinchot ◽  
James M. Slavicek ◽  
Charles E. Flower ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Natural Populations ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Ulmus Americana ◽  
Important Species ◽  
Complete Chloroplast Genome ◽  
American Elm ◽  
Chloroplast Genomes

ABSTRACTAmerican elm, Ulmus americana L., was cultivated widely in USA and Canada as a landscape tree, but the genome of this important species is poorly characterized. For the first time, we describe the sequencing and assembly of the chloroplast genomes of two American elm genotypes (RV16 and Am57845). The complete chloroplast genome of U. americana ranged from 158,935-158,993 bp. The genome contains 127 genes, including 85 protein-coding genes, 34 tRNA genes and 8 rRNA genes. Between the two American elm chloroplasts we sequenced, we identified 240 sequence variants (SNPs and indels). To evaluate the phylogeny of American elm, we compared the chloroplast genomes of two American elms along with seven Asian elm species and twelve other chloroplast genomes available through the NCBI database. As expected, Ulmus was closely related to Morus and Cannabis, as all three genera are assigned to the Urticales. Comparison of American elm with Asian elms revealed that trnH was absent from the chloroplast of American elm but not most Asian elms; conversely, petB, petD, psbL, trnK, and rps16 are present in the American elm but absent from all Asian elms. The complete chloroplast genome of U. americana will provide useful genetic resources for characterizing the genetic diversity of U. americana and potentially help to conserve natural populations of American elm.

scholarly journals Characterization of the complete chloroplast genome sequence and phylogenetic analysis of B. oleracea var. italica

2020 ◽  
Author(s):  
Zhenchao Zhang ◽  
Zhongliang Dai ◽  
Yuemei Yao ◽  
Yongfei Pan ◽  
Guosheng Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Genomic Structure ◽  
Gc Content ◽  
Single Copy ◽  
Biological Research ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Functional Components

Abstract Backgrounds: Broccoli (Brassica. oleracea var. italica L.) is known as one of the most nutritionally rich vegetables, as well as rich in functional components that benefit to health. The main purposes of this research were sequencing, assembling and annotation of chloroplast genome of broccoli based on Illumina HiSeq2500 sequencing platform. Results: The size of the broccoli cp genome is 153,364 bp, including two inverted repeat (IR) regions of 26,197 bp each, separated by a small single copy (SSC) region of 17,834 bp and a large single copy (LSC) region of 83,136 bp. The GC content of the complete genome is 36.36%, while those of SSC, LSC, and IR are 29.1%, 34.15% and 42.35%, respectively. It harbors 134 functional genes, including 87 protein-coding genes, 39 tRNAs and 8 rRNAs, with 31 duplicates in the IRs. The most abundant amino acid in the protein-coding genes is leucine, while the least is cysteine. Codon usage frequency showed bias for A/T-ending codons in the cp genome. In the repeat structure analysis, a total of 34 repeat sequences and 291 simple sequence repeat (SSRs) were detected in the work. Although cp genomic structure and size are highly conserved, the SC-IR boundary regions are variable between the 7 cp genomes. The phylogenetic relationships based on complete cp genome from 9 species suggest that B. oleracea var. italica is closely related to Brassica juncea. Conclusions: The complete cp genome sequence was obtained and annotated for broccoli for the first time. The information acquired from this research will be useful for further species identification, population genetics and biological research of broccoli.

scholarly journals The Complete Chloroplast Genome of Critically Endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and Phylogenetic Analysis

2021 ◽  
Author(s):  
yanjiang liu ◽  
Xiao Zhu ◽  
Mingli Wu ◽  
Xue Xu ◽  
Zhaoxia Dai ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gc Content ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Usage Frequency ◽  
Cp Genome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Simple Sequence

Abstract Chimonobambusa hirtinoda is a threatened species and only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used obtained the complete chloroplast (cp) genome sequence of C. hirtinoda, and then the sequence was assembled and analyze for phylogenetic and evolutionary. We also analyzed comparing the cp genome among Chimonobambusa species with previously published. The complete cp genome of C. hirtinoda has the total length of 139, 561 bp, 38.90% GC content was detected. A total of 130 genes were founded in the cp genome, including 85 protein coding genes, 37 tRNA genes, 8 rRNA. Some genes are missing and the introns occur lost in the cp genome of C. hirtinoda. A total of 48 simple sequence repeat (SSR) were detected and by measuring the codon usage frequency of amino acids, the A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained. Furthermore, phylogenetic analysis using complete cp sequences, matk gene exhibited genetic relationship within the Chimonobambusa genus.

scholarly journals Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae

2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Samaila S. Yaradua ◽  
Dhafer A. Alzahrani ◽  
Enas J. Albokhary ◽  
Abidina Abba ◽  
Abubakar Bello
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Cp Genome

The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.

scholarly journals Structural and Comparative Analysis of the Complete Chloroplast Genome of Pyrus hopeiensis—“Wild Plants with a Tiny Population”—and Three Other Pyrus Species

2018 ◽  
Vol 19 (10) ◽  
pp. 3262 ◽  
Author(s):  
Yongtan Li ◽  
Jun Zhang ◽  
Longfei Li ◽  
Lijuan Gao ◽  
Jintao Xu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Population Decline ◽  
Gc Content ◽  
Single Copy ◽  
Wild Plants ◽  
Similar Degree ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
History Of

Pyrus hopeiensis is a valuable wild resource of Pyrus in the Rosaceae. Due to its limited distribution and population decline, it has been listed as one of the “wild plants with a tiny population” in China. To date, few studies have been conducted on P. hopeiensis. This paper offers a systematic review of P. hopeiensis, providing a basis for the conservation and restoration of P. hopeiensis resources. In this study, the chloroplast genomes of two different genotypes of P. hopeiensis, P. ussuriensis Maxin. cv. Jingbaili, P. communis L. cv. Early Red Comice, and P. betulifolia were sequenced, compared and analyzed. The two P. hopeiensis genotypes showed a typical tetrad chloroplast genome, including a pair of inverted repeats encoding the same but opposite direction sequences, a large single copy (LSC) region, and a small single copy (SSC) region. The length of the chloroplast genome of P. hopeiensis HB-1 was 159,935 bp, 46 bp longer than that of the chloroplast genome of P. hopeiensis HB-2. The lengths of the SSC and IR regions of the two Pyrus genotypes were identical, with the only difference present in the LSC region. The GC content was only 0.02% higher in P. hopeiensis HB-1. The structure and size of the chloroplast genome, the gene species, gene number, and GC content of P. hopeiensis were similar to those of the other three Pyrus species. The IR boundary of the two genotypes of P. hopeiensis showed a similar degree of expansion. To determine the evolutionary history of P. hopeiensis within the genus Pyrus and the Rosaceae, 57 common protein-coding genes from 36 Rosaceae species were analyzed. The phylogenetic tree showed a close relationship between the genera Pyrus and Malus, and the relationship between P. hopeiensis HB-1 and P. hopeiensis HB-2 was the closest.

scholarly journals Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Yang He ◽  
Hongtao Xiao ◽  
Cao Deng ◽  
Gang Fan ◽  
Shishang Qin ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Rrna Gene ◽  
Coptis Chinensis ◽  
Medicinal Species ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Next Generation Sequencing Technology ◽  
Complete Sequencing ◽  
Chloroplast Genome Sequence

The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484 bp long with 38.17% GC content. Two 26,758 bp long inverted repeats separated the genome into a typical quadripartite structure. The C. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. C. chinensis diverged from other Ranunculaceae species an estimated 81 million years ago (Mya). The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the C. chinensis ndhG protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in C. chinensis. In summary, the complete sequencing and annotation of the C. chinensis chloroplast genome will facilitate future studies on this important medicinal species.

scholarly journals Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Yingnan Chen ◽  
Nan Hu ◽  
Huaitong Wu
Keyword(s):  
Chloroplast Genome ◽  
Tandem Repeats ◽  
Single Copy ◽  
Rrna Genes ◽  
Whole Genome Sequencing Data ◽  
Trna Genes ◽  
Sequencing Data ◽  
Protein Coding ◽  
Organelle Genomes ◽  
Additional Sequence

Salix wilsonii is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for S. wilsonii based on the chloroplast reads screened from the whole-genome sequencing data generated with the PacBio RSII platform. The obtained pseudomolecule was 155,750 bp long and had a typical quadripartite structure, comprising a large single copy region (LSC, 84,638 bp) and a small single copy region (SSC, 16,282 bp) separated by two inverted repeat regions (IR, 27,415 bp). The S. wilsonii chloroplast genome encoded 115 unique genes, including four rRNA genes, 30 tRNA genes, 78 protein-coding genes, and three pseudogenes. Repetitive sequence analysis identified 32 tandem repeats, 22 forward repeats, two reverse repeats, and five palindromic repeats. Additionally, a total of 118 perfect microsatellites were detected, with mononucleotide repeats being the most common (89.83%). By comparing the S. wilsonii chloroplast genome with those of other rosid plant species, significant contractions or expansions were identified at the IR-LSC/SSC borders. Phylogenetic analysis of 17 willow species confirmed that S. wilsonii was most closely related to S. chaenomeloides and revealed the monophyly of the genus Salix. The complete S. wilsonii chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.

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