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 Characterization of the complete chloroplast genome sequence of Vitis vinifera ‘Guifeimeigui’

2021 ◽  
pp. 001-003
Author(s):  
Liu Li ◽  
Yang Yang ◽  
Li Xiujie ◽  
Li Bo
Keyword(s):  
Vitis Vinifera ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Cp Genome ◽  
Eurasian Species ◽  
Rna Genes

Vitis vinifera ‘Guifeimeigui’ is a diploid table grape, a Eurasian species. This research first reported the complete chloroplast (cp) genome of Vitis vinifera ‘Guifeimeigui’. The size of the complete cp genome is 160,928 bp and its GC content is 37.38%, including a pair of inverted repeats (26,353 bp each) separated by large (89,150 bp) and small (19,072 bp) single-copy regions. It encodes 85 genes, including 40 protein coding genes, 37 transfer RNA genes (tRNA), and 8 ribosomal RNA genes (rRNA). The Maximum Likelihood (ML) phylogenetic tree demonstrated that Vitis vinifera ‘Guifeimeigui’ is close to Vitis vinifera.

scholarly journals The complete chloroplast genome sequence of Korean Neolitsea sericea (Lauraceae)

2021 ◽  
Vol 51 (3) ◽  
pp. 332-336
Author(s):  
Yoo-Jung PARK ◽  
Kyeong-Sik CHEON
Keyword(s):  
Genome Sequence ◽  
Single Copy ◽  
Likelihood Method ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Transfer Rnas ◽  
Chloroplast Genome Sequence ◽  
Cp Genome ◽  
Small Single Copy

The complete chloroplast (cp) genome sequence of Neolitsea sericea was determined by Illumina sequencing. The complete cp genome was 152,446bp in length, containing a large single-copy region of 93,796 bp and a small single-copy region of 18,506bp, which were separated by a pair of 20,072bp inverted repeats. A total of 112 unique genes were annotated, including 78 protein-coding genes (PCGs), 30 transfer RNAs, and four ribosomal RNAs. Among the PCGs, 18 genes contained one or two introns. A very low level of sequence variation between two cp genomes of N. sericea was found with seven insertions or deletions and only one single nucleotide polymorphism. An analysis using the maximum likelihood method showed that N. sericea was closely related to Actinodaphne trichocarpa.

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 Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Forests ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 861
Author(s):  
Huijuan Zhou ◽  
Xiaoxiao Gao ◽  
Keith Woeste ◽  
Peng Zhao ◽  
Shuoxin Zhang
Keyword(s):  
Comparative Analysis ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Species Hybrids ◽  
Rna Genes

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

scholarly journals Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12612
Author(s):  
Tian Zhang ◽  
Sipei Huang ◽  
Simin Song ◽  
Meng Zou ◽  
Tiechui Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Markers ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Medicinal Species ◽  
Protein Coding ◽  
Cp Genome ◽  
Rna Genes ◽  
Unique Genes

The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.

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 The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Wenbin Xu ◽  
Boshun Xia ◽  
Xinwei Li
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
The Other ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Noncoding Sequences ◽  
Chloroplast Genomes ◽  
Rna Genes

AbstractThe six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.

scholarly journals Analyzing and characterization of the chloroplast genome of Salix suchowensis

2016 ◽  
Author(s):  
Congrui Sun ◽  
Jie Li ◽  
Xiaogang Dai ◽  
Yingnan Chen
Keyword(s):  
Tandem Repeats ◽  
Gene Annotation ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Phylogenetic Position ◽  
Shrub Willow ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Rna Genes

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a typical quadripartite structure containing two single copy regions, a large single copy region (LSC 84,385 bp), and a small single copy region (SSC 16,209 bp) separated by inverted repeat regions (IRs 27,457 bp). Gene annotation revealed that the cp genome of S. suchowensis encoded 119 unique genes, including 4 ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes and 3 pseudogenes. Analyzing the repetitive sequences detected 15 tandem repeats, 16 forward repeats and 5 palindromic repeats. In addition, a total of 188 perfect microsatellites were detected, which were characterized as A/T predominance in nucleotide compositions. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with that of other rosids plants. We also built phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae, with 66 orthologous protein-coding genes presented in the cp genomes of 32 species. By sequencing 30 amplicons based on the pseudomolecule, experimental verification achieved accuracy up to 99.84% for the cp genome assembly of S. suchowensis. In conclusion, this study built a high quality pseudomolecule for the cp genome of S. suchowensis, which is a useful resource for facilitating the development of this shrub willow into a more productive bioenergy crop.

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 Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kadriye Kahraman ◽  
Stuart James Lucas
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Single Copy ◽  
Corylus Avellana ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Complete Chloroplast Genome ◽  
A Genome ◽  
Cp Genome

Abstract Background Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar ‘Tombul’ with multiple annotation tools. Results Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales. Conclusion In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.

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