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

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.

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

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1116 ◽  
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.

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

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8450 ◽  
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.

scholarly journals Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 410 ◽  
Author(s):  
Xiaolei Yu ◽  
Wei Tan ◽  
Huanyu Zhang ◽  
Han Gao ◽  
Wenxiu Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Z ◽  
Marker Selection ◽  
Chloroplast Genomes ◽  
Potential Marker ◽  
Cp Genome

Ampelopsis humulifolia (A. humulifolia) and Ampelopsis japonica (A. japonica), which belong to the family Vitaceae, are valuably used as medicinal plants. The chloroplast (cp) genomes have been recognized as a convincing data for marker selection and phylogenetic studies. Therefore, in this study we reported the complete cp genome sequences of two Ampelopsis species. Results showed that the cp genomes of A. humulifolia and A. japonica were 161,724 and 161,430 bp in length, respectively, with 37.3% guanine-cytosine (GC) content. A total of 114 unique genes were identified in each cp genome, comprising 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. We determined 95 and 99 small sequence repeats (SSRs) in A. humulifolia and A. japonica, respectively. The location and distribution of long repeats in the two cp genomes were identified. A highly divergent region of psbZ (Photosystem II reaction center protein Z) -trnG (tRNA-Glycine) was found and could be treated as a potential marker for Vitaceae, and then the corresponding primers were designed. Additionally, phylogenetic analysis showed that Vitis was closer to Tetrastigma than Ampelopsis. In general, this study provides valuable genetic resources for DNA barcoding marker identification and phylogenetic analyses of Ampelopsis.

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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3919 ◽  
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.

scholarly journals Title: The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species

2021 ◽  
Author(s):  
Mahtab Moghaddam ◽  
Atsushi Ohta ◽  
Motoki Shimizu ◽  
Ryohei Terauchi ◽  
Shahrokh Kazempour-Osaloo
Keyword(s):  
Comparative Analysis ◽  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Paired End Sequencing

Abstract Plastid genome sequences provide valuable markers for surveying the evolutionary relationships and population genetics of plant species. In the present study, the complete plastid genome of Onobrychis gaubae, endemic to Iran, was sequenced using Illumina paired-end sequencing and was compared with previously known genomes of the IRLC species of legumes. The O. gaubae plastid genome was 123,645 bp in length and included a large single-copy (LSC) region of 81,034 bp, a small single-copy (SSC) region of 13,788 bp and one copy of the inverted repeat (IRb) of 28,823 bp. The genome encoded 110 genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes and possessed 89 simple sequence repeats (SSRs) and 28 repeated structures with the highest proportion in the LSC. Comparative analysis of the chloroplast genomes across IRLC revealed three hotspot genes (ycf1, ycf2, clpP) which could be used as molecular markers for resolving phylogenetic relationships and species identification. IRLC plastid genomes also showed multiple gene losses and inversions. Phylogenetic analyses revealed that O. gaubae is closely related to Hedysarum. The complete O. gaubae genome is a valuable resource for investigating evolution of Onobrychis species and can be used to identify related species.

scholarly journals Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9132
Author(s):  
Shuilian He ◽  
Yang Yang ◽  
Ziwei Li ◽  
Xuejiao Wang ◽  
Yanbing Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Herbaceous Perennials ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Diversity Assessment ◽  
Cp Genome

The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.

scholarly journals Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6386 ◽  
Author(s):  
Dan Zong ◽  
Anpei Zhou ◽  
Yao Zhang ◽  
Xinlian Zou ◽  
Dan Li ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Genetic ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Western Sichuan ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Species of the genus Populus, which is widely distributed in the northern hemisphere from subtropical to boreal forests, are among the most commercially exploited groups of forest trees. In this study, the complete chloroplast genomes of five Populus species (Populus cathayana, P. kangdingensis, P. pseudoglauca, P. schneideri, and P. xiangchengensis) were compared. The chloroplast genomes of the five Populus species are very similar. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,513, and 156,465 bp, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. The GC content was 36.7% for all plastomes. We analyzed nucleotide substitutions, small inversions, simple sequence repeats and long repeats in the chloroplast genomes and found nine divergence hotspots (ccsA+ccsA-ndhD, ndhC-trnV, psbZ-trnfM, trnG-atpA, trnL-ndhJ, trnR-trnN, ycf4-cemA, ycf1, and trnR-trnN), which could be useful molecular genetic markers for future population genetic and phylogenetic studies. We also observed that two genes (rpoC2 and rbcL) were subject to positive selection. Phylogenetic analysis based on whole cp genomes showed that P. schneideri had a close relationship with P. kangdingensis and P. pseudoglauca, while P. xiangchengensis was a sister to P. cathayana.

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

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 881 ◽  
Author(s):  
Cho ◽  
Kim ◽  
Kim ◽  
Mejías ◽  
Kim
Keyword(s):  
Chloroplast Genome ◽  
Rrna Genes ◽  
Recent Common Ancestor ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Widespread Species ◽  
Variable Regions ◽  
Sonchus Asper ◽  
Sonchus Oleraceus ◽  
Chloroplast Genomes

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.

scholarly journals New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing

Horticulturae ◽  
2021 ◽  
Vol 7 (9) ◽  
pp. 301
Author(s):  
Guanglong Hu ◽  
Yiheng Wang ◽  
Yan Wang ◽  
Shuqi Zheng ◽  
Wenxuan Dong ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Analyses ◽  
Rrna Genes ◽  
Published Data ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
History Of ◽  
Important Processing ◽  
Phylogenomic Analyses

Hawthorns (Crataegus L.) are one of the most important processing and table fruits in China, due to their medicinal properties and health benefits. However, the interspecific relationships and evolution history of cultivated Crataegus in China remain unclear. Our previously published data showed C. bretschneideri may be derived from the hybridization of C. pinnatifida with C. maximowiczii, and that introgression occurs between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. In the present study, chloroplast sequences were used to further elucidate the phylogenetic relationships of cultivated Crataegus native to China. The chloroplast genomes of three cultivated species and one related species of Crataegus were sequenced for comparative and phylogenetic analyses. The four chloroplast genomes of Crataegus exhibited typical quadripartite structures and ranged from 159,607 bp (C. bretschneideri) to 159,875 bp (C. maximowiczii) in length. The plastomes of the four species contained 113 genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Six hypervariable regions (ndhC-trnV(UAC)-trnM(CAU), ndhA, atpH-atpI, ndhF, trnR(UCU)-atpA, and ndhF-rpl32), 196 repeats, and a total of 386 simple sequence repeats were detected as potential variability makers for species identification and population genetic studies. In the phylogenomic analyses, we also compared the entire chloroplast genomes of three published Crataegus species: C. hupehensis (MW201730.1), C. pinnatifida (MN102356.1), and C. marshallii (MK920293.1). Our phylogenetic analyses grouped the seven Crataegus taxa into two main clusters. One cluster included C. bretschneideri, C. maximowiczii, and C. marshallii, whereas the other included C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. Taken together, our findings indicate that C. maximowiczii is the maternal origin of C. bretschneideri. This work provides further evidence of introgression between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major, and suggests that C. pinnatifida var. major might have been artificially selected and domesticated from hybrid populations, rather than evolved from C. pinnatifida.

scholarly journals Complete Chloroplast Genome Sequence of Sonchus brachyotus Helps to Elucidate Evolutionary Relationships with Related Species of Asteraceae

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Caixiang Wang ◽  
Juanjuan Liu ◽  
Yue Su ◽  
Meili Li ◽  
Xiaoyu Xie ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Variable Regions ◽  
Ssr Frequency ◽  
Cp Genome

Sonchus brachyotus DC. possesses both edible and medicinal properties and is widely distributed throughout China. In this study, the complete cp genome of S. brachyotus was sequenced and assembled. The total length of the complete S. brachyotus cp genome was 151,977 bp, including an LSC region of 84,553 bp, SSC region of 18,138 bp, and IR region of 24,643 bp. Sequence analyses revealed that the cp genome encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content was 37.6%. One hundred mononucleotide microsatellites, 4 dinucleotide microsatellites, 67 trinucleotide microsatellites, 4 tetranucleotide microsatellites, and 1 long repeat were identified. The SSR frequency of the LSC region was significantly greater than that of the IR and SSC regions. In total, 175 SSRs and highly variable regions were recognized as potential cp markers. By analyzing the IR/LSC and IR/SSC boundaries, structural differences between S. brachyotus and 6 other species were detected. According to phylogenetic analyses, S. brachyotus was most closely related to S. arvensis and S. oleraceus. Overall, this study provides complete cp genome resources for S. brachyotus that will be beneficial for identifying potential molecular markers and evolutionary patterns of S. brachyotus and its closely related species.

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