scholarly journals Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8210
Author(s):  
Xueqing Zhao ◽  
Ming Yan ◽  
Yu Ding ◽  
Yan Huo ◽  
Zhaohe Yuan
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Single Copy ◽  
Future Research ◽  
Sequencing Data ◽  
Complete Chloroplast Genome ◽  
Rna Genes

Background Sweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear. Methods In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. Results The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus 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 The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

2019 ◽  
Vol 42 (4) ◽  
pp. 601-611 ◽  
Author(s):  
Yan Li ◽  
Liukun Jia ◽  
Zhihua Wang ◽  
Rui Xing ◽  
Xiaofeng Chi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Single Copy ◽  
Bootstrap Support ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract Saxifraga sinomontana J.-T. Pan & Gornall belongs to Saxifraga sect. Ciliatae subsect. Hirculoideae, a lineage containing ca. 110 species whose phylogenetic relationships are largely unresolved due to recent rapid radiations. Analyses of complete chloroplast genomes have the potential to significantly improve the resolution of phylogenetic relationships in this young plant lineage. The complete chloroplast genome of S. sinomontana was de novo sequenced, assembled and then compared with that of other six Saxifragaceae species. The S. sinomontana chloroplast genome is 147,240 bp in length with a typical quadripartite structure, including a large single-copy region of 79,310 bp and a small single-copy region of 16,874 bp separated by a pair of inverted repeats (IRs) of 25,528 bp each. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs, with 18 duplicates in the IRs. The gene content and organization are similar to other Saxifragaceae chloroplast genomes. Sixty-one simple sequence repeats were identified in the S. sinomontana chloroplast genome, mostly represented by mononucleotide repeats of polyadenine or polythymine. Comparative analysis revealed 12 highly divergent regions in the intergenic spacers, as well as coding genes of matK, ndhK, accD, cemA, rpoA, rps19, ndhF, ccsA, ndhD and ycf1. Phylogenetic reconstruction of seven Saxifragaceae species based on 66 protein-coding genes received high bootstrap support values for nearly all identified nodes, suggesting a promising opportunity to resolve infrasectional relationships of the most species-rich section Ciliatae of Saxifraga.

scholarly journals Multilocus Characterization, Gene Expression Analysis of Putative Immunodominant Protein Coding Regions, and Development of Recombinase Polymerase Amplification Assay for Detection of ‘Candidatus Phytoplasma Pruni’ in Prunus avium

2019 ◽  
Vol 109 (6) ◽  
pp. 983-992 ◽  
Author(s):  
Dan Edward V. Villamor ◽  
Kenneth C. Eastwell
Keyword(s):  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Protein A ◽  
Recombinase Polymerase Amplification ◽  
Sequencing Data ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Reverse Transcription Pcr

Western X (WX) disease, caused by ‘Candidatus Phytoplasma pruni’, is a devastating disease of sweet cherry resulting in the production of small, bitter-flavored fruits that are unmarketable. Escalation of WX disease in Washington State prompted the development of a rapid detection assay based on recombinase polymerase amplification (RPA) to facilitate timely removal and replacement of diseased trees. Here, we report on a reliable RPA assay targeting putative immunodominant protein coding regions that showed comparable sensitivity to polymerase chain reaction (PCR) in detecting ‘Ca. Phytoplasma pruni’ from crude sap of sweet cherry tissues. Apart from the predominant strain of ‘Ca. Phytoplasma pruni’, the RPA assay also detected a novel strain of phytoplasma from several WX-affected trees. Multilocus sequence analyses using the immunodominant protein A (idpA), imp, rpoE, secY, and 16S ribosomal RNA regions from several ‘Ca. Phytoplasma pruni’ isolates from WX-affected trees showed that this novel phytoplasma strain represents a new subgroup within the 16SrIII group. Examination of high-throughput sequencing data from total RNA of WX-affected trees revealed that the imp coding region is highly expressed, and as supported by quantitative reverse transcription PCR data, it showed higher RNA transcript levels than the previously proposed idpA coding region of ‘Ca. Phytoplasma pruni’.

scholarly journals A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9114 ◽  
Author(s):  
Jiawei Wang ◽  
Weizhen Liu ◽  
Dongzi Zhu ◽  
Xiang Zhou ◽  
Po Hong ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Reference Genome ◽  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
High Quality ◽  
Eukaryotic Genes

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

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 Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

2021 ◽  
Vol 12 ◽  
Author(s):  
Jin Xu ◽  
Chen Liu ◽  
Yun Song ◽  
Mingfu Li
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Future Research ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Chloroplast Genomes

The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.

scholarly journals Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huu Quan Nguyen ◽  
Thi Ngoc Lan Nguyen ◽  
Thi Nhung Doan ◽  
Thi Thu Nga Nguyen ◽  
Mai Huong Phạm ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Reconstruction ◽  
Single Copy ◽  
Potential Health ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Long Read ◽  
Phylogenetic Resolution ◽  
Rna Genes

AbstractAdrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla.

scholarly journals The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ueric José Borges de Souza ◽  
Rhewter Nunes ◽  
Cíntia Pelegrineti Targueta ◽  
José Alexandre Felizola Diniz-Filho ◽  
Mariana Pires de Campos Telles
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Reconstruction ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Coding Regions ◽  
Phylogenetic Studies ◽  
Rna Genes ◽  
Small Single Copy

Abstract Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminosae. The chloroplast genome was reconstructed using de novo and referenced-based assembly of paired-end reads generated by shotgun sequencing of total genomic DNA. The size of the S. adstringens chloroplast genome was 162,169 bp. This genome included a large single-copy (LSC) region of 91,045 bp, a small single-copy (SSC) region of 19,014 bp and a pair of inverted repeats (IRa and IRb) of 26,055 bp each. The S. adstringens chloroplast genome contains a total of 111 functional genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. A total of 137 SSRs and 42 repeat structures were identified in S. adstringens chloroplast genome, with the highest proportion in the LSC region. A comparison of the S. adstringens chloroplast genome with those from other mimosoid species indicated that gene content and synteny are highly conserved in the clade. The phylogenetic reconstruction using 73 conserved coding-protein genes from 19 Leguminosae species was supported to be paraphyletic. Furthermore, the noncoding and coding regions with high nucleotide diversity may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels in this group.

scholarly journals Complete Chloroplast Genome of Castanopsis sclerophylla (Lindl.) Schott: Genome Structures, Comparative and Phylogenetic Analysis

2019 ◽  
Author(s):  
Xuemin Ye ◽  
Dongnan Hu ◽  
Yangping Guo ◽  
Rongxi Sun
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Basic Knowledge ◽  
Illumina Hiseq ◽  
Important Species ◽  
Complete Chloroplast Genome ◽  
Coding Regions ◽  
Rna Genes

AbstractCastanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved forest in subtropical area and has important ecological and economic value. However, there are little studies on its chloroplast genome. In this study, the complete chloroplast genome sequences of C. sclerophylla was reported based on the Illumina Hiseq 2500 platform. The complete chloroplast genome of C. sclerophylla was 160,497bp, including a pair of inverted repeated (IRs) regions (25,675bp) that were separated by a large single copy (LSC) region of 90,255bp, and a small single copy (SSC) region of 18,892bp. The overall GC content of chloroplast genome was 36.82%. A total of 131 genes were found, of these 111 genes were unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the relatively smaller chloroplast genome size of C. sclerophylla compared with other three congeneric species. Sequence analysis detected that the LSC and SSC regions were more divergent than the IR regions within the Castanopsis, furthermore, a higher divergence was found in non-coding regions than in coding regions. The maximum likelihood (ML) phylogenetic analysis showed that these four species of the genus Castanopsis formed a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide basic knowledge about characteristics of C. sclerophylla and also enhance our understanding of Castanopsis species evolution within the Fagaceae family. Meanwhile, these findings will contribute to the exploration, utilization and conservation genetics of C. sclerophylla.

scholarly journals Complete Chloroplast Genome Sequence and Comparative and Phylogenetic Analyses of the Cultivated Cyperus esculentus

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 405
Author(s):  
Wei Ren ◽  
Dongquan Guo ◽  
Guojie Xing ◽  
Chunming Yang ◽  
Yuanyu Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Inverted Repeat ◽  
Single Copy ◽  
Cyperus Esculentus ◽  
Crop Species ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Rna Genes ◽  
Small Single Copy

Cyperus esculentus produces large amounts of oil as one of the main oil storage reserves in underground tubers, making this crop species not only a promising resource for edible oil and biofuel in food and chemical industry, but also a model system for studying oil accumulation in non-seed tissues. In this study, we determined the chloroplast genome sequence of the cultivated C. esculentus (var. sativus Boeckeler). The results showed that the complete chloroplast genome of C. esculentus was 186,255 bp in size, and possessed a typical quadripartite structure containing one large single copy (100,940 bp) region, one small single copy (10,439 bp) region, and a pair of inverted repeat regions of 37,438 bp in size. Sequence analyses indicated that the chloroplast genome encodes 141 genes, including 93 protein-coding genes, 40 transfer RNA genes, and 8 ribosomal RNA genes. We also identified 396 simple-sequence repeats and 49 long repeats, including 15 forward repeats and 34 palindromes within the chloroplast genome of C. esculentus. Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with those of the other four Cyperus species indicated that both the large single copy and inverted repeat regions were more divergent than the small single copy region, with the highest variation found in the inverted repeat regions. In the phylogenetic trees based on the complete chloroplast genomes of 13 species, all five Cyperus species within the Cyperaceae formed a clade, and C. esculentus was evolutionarily more related to C. rotundus than to the other three Cyperus species. In summary, the chloroplast genome sequence of the cultivated C. esculentus provides a valuable genomic resource for species identification, evolution, and comparative genomic research on this crop species and other Cyperus species in the Cyperaceae family.

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