Sow Thistle Chloroplast Genomes: Insights into the Plastome Evolution and Relationship of Two Weedy Species, Sonchus asper and Sonchus oleraceus (Asteraceae)

Prickly sow thistle, Sonchus asper (L.) Hill, and common sow thistle, Sonchus oleraceus L., are noxious weeds. Probably originating from the Mediterranean region, they have become widespread species. They share similar morphology and are closely related. However, they differ in their chromosome numbers and the precise relationship between them remains uncertain. Understanding their chloroplast genome structure and evolution is an important initial step toward determining their phylogenetic relationships and analyzing accelerating plant invasion processes on a global scale. We assembled four accessions of chloroplast genomes (two S. asper and two S. oleraceus) by the next generation sequencing approach and conducted comparative genomic analyses. All the chloroplast genomes were highly conserved. Their sizes ranged from 151,808 to 151,849 bp, containing 130 genes including 87 coding genes, 6 rRNA genes, and 37 tRNA genes. Phylogenetic analysis based on the whole chloroplast genome sequences showed that S. asper shares a recent common ancestor with S. oleraceus and suggested its likely involvement in a possible amphidiploid origin of S. oleraceus. In total, 79 simple sequence repeats and highly variable regions were identified as the potential chloroplast markers to determine genetic variation and colonization patterns of Sonchus species.

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Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽

10.7717/peerj.8450 ◽

2020 ◽

Vol 8 ◽

pp. e8450 ◽

Cited By ~ 2

Author(s):

Sunan Huang ◽

Xuejun Ge ◽

Asunción Cano ◽

Betty Gaby Millán Salazar ◽

Yunfei Deng

Keyword(s):

Adaptive Evolution ◽

Phylogenetic Relationships ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Evolutionary Analysis ◽

Protein Coding ◽

Variable Regions ◽

Protein Coding Genes ◽

Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

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Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽

10.3390/plants9010061 ◽

2020 ◽

Vol 9 (1) ◽

pp. 61 ◽

Cited By ~ 5

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.

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

10.1101/2020.01.27.920181 ◽

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.

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Assembly and comparative analysis of chloroplast genome of wheat K-CMS line and maintainer line

10.21203/rs.3.rs-15231/v1 ◽

2020 ◽

Author(s):

Yucui Han ◽

Yujie Gao ◽

Xiaoguang Zhai ◽

Hao Zhou ◽

Qin Ding ◽

...

Keyword(s):

Triticum Aestivum ◽

Chloroplast Genome ◽

Triticum Aestivum L ◽

Practical Significance ◽

Rrna Genes ◽

Trna Genes ◽

Maintainer Line ◽

Synonymous Mutations ◽

Chloroplast Genomes ◽

Cms Line

Abstract The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.), and the cytoplasmic male sterility (CMS) line has more practical significance in the utilization of heterosis. To reveal the sterile mechanism of wheat K-CMS line K519A from the perspective of the chloroplast genome, the chloroplast genomes of the K519A and its same nuclear genotype maintainer line 519B were sequenced using second-generation high-throughput technology and assembled. Then the chloroplast genomic contents, SSR sequences, long repeat fragments, and qPCR were analyzed. The results showed that the total length of K519A and 519B were 136,996 bp and 136,235 bp, respectively. Both chloroplast genomes encode 126 genes, including 89 protein-coding genes, 8 rRNA genes, and 39 tRNA genes. There were 186 and 188 SSRs in K519A and 519B, respectively. And a developed SSR maker, which from atpF, can be used to distinguish the cytoplasmic type of Aegilops kotschyi and Triticum aestivum, respectively. There were 50 and 52 long repeat fragments, which come from the gene sequences, in K519A and 519B, respectively. A total of 107 mutations between K519A and 519B, which from 45 genes, were identified, of which, 16 genes (matK, rps16, rpoB, rpoC2, atpI, ndhK, atpB, rbcL, psbB, psbH, rpl14, ndhH, ndhF, rpl32, ccsA, ndhA) contained non-synonymous mutations. Further, the qPCR analysis was performed, and the gene expression levels of selected six genes for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development, thus, these non-synonymous mutant genes might affect the fertility of K519A.

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Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

Plants ◽

10.3390/plants9091116 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1116 ◽

Cited By ~ 1

Author(s):

Xue-Li Zhao ◽

Zhang-Ming Zhu

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Process ◽

Rrna Genes ◽

Trna Genes ◽

Sister Relationship ◽

Protein Coding ◽

Variable Regions ◽

Chloroplast Genomes ◽

Distinct Genus ◽

Relationship Of

Taxonomic and phylogenetic relationships of Christia, Urariopsis, Uraria and related genera within the tribe Desmodieae (Fabaceae: Papilionoideae) have long been controversial. Here, we report the complete chloroplast (cp) genomes of Christia vespertilionis and Urariopsis brevissima and perform comparative and phylogenetic analyses with Uraria lagopodioides and other relatives in the Desmodieae. The cp genomes of C. vespertilionis and U. brevissima are 149,656 and 149,930 bp long, with 128 unique genes (83 protein-coding genes, 37 tRNA genes and 8 rRNA genes), respectively. Comparative analyses revealed 95-129 simple sequence repeats (SSRs) and eleven highly variable regions (trnK-rbcL, rbcL-atpB, ndhJ-trnF, trnL-trnT, psbD-rpoB, accD-cemA, petA-psbL, psbE-petL, rps11-rps19, ndhF-ccsA, and rps15-ycf1) among six Desmodieae species. Phylogenetic analyses clearly resolved two subtribes (Desmodiinae and Lespedezinae) of Desmodieae as monophyletic, and the newly reported C. vespertilionis and U. brevissima clustered in subtribe Desmodiinae. A sister relationship of C. vespertilionis to U. lagopodioides was supported. Evidence was presented to support the treatment of Urariopsis as a distinct genus rather than in synonymy with Uraria. The results provide valuable information for further studies on species delimitation, phylogenetics, population genetics, and the evolutionary process of speciation in the Desmodieae.

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Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis

Molecules ◽

10.3390/molecules24030474 ◽

2019 ◽

Vol 24 (3) ◽

pp. 474 ◽

Cited By ~ 13

Author(s):

Dong-Mei Li ◽

Chao-Yi Zhao ◽

Xiao-Fei Liu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Species Identification ◽

Single Copy ◽

Rrna Genes ◽

Genome Sequences ◽

Variable Regions ◽

Complete Chloroplast Genome ◽

Kaempferia Galanga ◽

Chloroplast Genomes

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

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Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Forests ◽

10.3390/f12050608 ◽

2021 ◽

Vol 12 (5) ◽

pp. 608

Author(s):

Sang-Chul Kim ◽

Jei-Wan Lee ◽

Byoung-Ki Choi

Keyword(s):

Chloroplast Genome ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Coding Regions ◽

Chloroplast Genomes ◽

Ion Torrent Sequencing ◽

Species Specific ◽

Taxonomic Characterization

In the present study, chloroplast genome sequences of four species of Symplocos (S. chinensis for. pilosa, S. prunifolia, S. coreana, and S. tanakana) from South Korea were obtained by Ion Torrent sequencing and compared with the sequences of three previously reported Symplocos chloroplast genomes from different species. The length of the Symplocos chloroplast genome ranged from 156,961 to 157,365 bp. Overall, 132 genes including 87 functional genes, 37 tRNA genes, and eight rRNA genes were identified in all Symplocos chloroplast genomes. The gene order and contents were highly similar across the seven species. The coding regions were more conserved than the non-coding regions, and the large single-copy and small single-copy regions were less conserved than the inverted repeat regions. We identified five new hotspot regions (rbcL, ycf4, psaJ, rpl22, and ycf1) that can be used as barcodes or species-specific Symplocos molecular markers. These four novel chloroplast genomes provide basic information on the plastid genome of Symplocos and enable better taxonomic characterization of this genus.

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Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae

Scientific Reports ◽

10.1038/s41598-021-94137-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Liwei Wu ◽

Liping Nie ◽

Qing Wang ◽

Zhichao Xu ◽

Yu Wang ◽

...

Keyword(s):

Codon Usage ◽

Phylogenetic Analyses ◽

Ornamental Plants ◽

Network Evolution ◽

Rrna Genes ◽

Trna Genes ◽

Species Relationship ◽

Variable Regions ◽

Chloroplast Genomes ◽

Usage Analysis

AbstractPlants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia.

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

Frontiers in Genetics ◽

10.3389/fgene.2021.687844 ◽

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.

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The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae

PeerJ ◽

10.7717/peerj.3919 ◽

2017 ◽

Vol 5 ◽

pp. e3919 ◽

Cited By ~ 27

Author(s):

Hui Cheng ◽

Jinfeng Li ◽

Hong Zhang ◽

Binhua Cai ◽

Zhihong Gao ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Rrna Genes ◽

Trna Genes ◽

Illumina Hiseq ◽

Complete Chloroplast Genome ◽

Coding Regions ◽

Chloroplast Genomes

Compared with other members of the family Rosaceae, the chloroplast genomes ofFragariaspecies exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing ofFragariaspecies is needed. In this study, we sequenced the complete chloroplast genome ofF. × ananassa‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination ofde novoassembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of theF. × ananassa‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallestFragariachloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content inFragaria, particularly among three octoploid strawberries which wereF. × ananassa‘Benihoppe’,F.chiloensis(GP33) andF.virginiana(O477). However, when the sequences of the coding and non-coding regions ofF. × ananassa‘Benihoppe’ were compared in detail with those ofF.chiloensis(GP33) andF.virginiana(O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK,trnS-trnG,atpF-atpH,trnC-petN,trnT-psbDandtrnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genusFragaria.

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