scholarly journals Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Juan Wang ◽  
Yuan Li ◽  
Chunjuan Li ◽  
Caixia Yan ◽  
Xiaobo Zhao ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Phylogenetic Analyses ◽  
Data Set ◽  
Genome Species ◽  
Chloroplast Genomes ◽  
Cultivated Peanut ◽  
Ssr Loci ◽  
Aa Genome ◽  
Cp Genome ◽  
Wild Peanut

Abstract Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.

scholarly journals Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1143 ◽  
Author(s):  
Hang Ran ◽  
Yanyan Liu ◽  
Cui Wu ◽  
Yanan Cao
Keyword(s):  
Genomic Structure ◽  
Phylogenetic Analyses ◽  
Sister Relationship ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Flora Of China ◽  
Phylogenetic Resolution ◽  
Sister Relationships ◽  
Phylogenomic Analyses ◽  
Cp Genome

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

scholarly journals Synchronous dissection of chloroplast and mitochondrial genomes remodels the intra- and inter-genus phylogeny for the agriculturally important genus Brassica

2019 ◽  
Author(s):  
Jiangwei Qiao ◽  
Xiaojun Zhang ◽  
Biyun Chen ◽  
Fei Huang ◽  
Kun Xu ◽  
...  
Keyword(s):  
De Novo ◽  
Phylogenetic Analyses ◽  
Parallel Evolution ◽  
Male Sterile ◽  
Plant Populations ◽  
Data Set ◽  
Brassica Crops ◽  
Chloroplast Genomes ◽  
Ornamental Crops ◽  
Allotetraploid Species

Abstract Background : The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of the allotetraploid crops and the overall phylogeny of Brassica genus are still far from completely resolved, which has greatly hindered the development of novel Brassica crops. Here, we target and integrate the chloroplast DNA and mitochondrial DNA to investigate the genetic diversity and relationships in large plant populations centering on Brassica genus. Results : The phylogenetic analyses based on a data set including 72 de novo assembled whole chloroplast genomes, delineated a comprehensive evolutional atlas inside and around Brassica genus. The maternal origin of both B. juncea and B. carinata are monophyletic from cam-type B. rapa and B. nigra , respectively. Nonetheless, the current B. napus contains three major cytoplasmic haplotypes: the cam -type which directly inherited from B. rapa , polima -type which is close to cam -type as a sister, and the predominant nap -type. Intriguingly, nap -type seems phylogenetically integrated with certain sparse C-genome wild species, thus implying that which may have primarily contributed the cytoplasm and the corresponding C subgenome to B. napus . Human breeding creation of the B. napus cytoplasmic male sterile lines (e.g., mori and nsa ) dramatically disturbed the concurrent inheritance between mtDNA and cpDNA. Strong parallel evolution among genera Raphanus , Sinapis, Eruca , Moricandia with Brassica indicates their uncomplete divergence from each other. Conclusions : The overall variation data and elaborated phylogenetic relationships obtained herein can substantially facilitate the development of novel Brassica crops, e.g. the allotetraploid rapeseed with new cytonuclear integrations and the allohexaploid rapeseed.

scholarly journals Comparative Chloroplast Genome Analysis of Medicinally Important Veratrum (Melanthiaceae) in China: Insights into Genomic Characterization and Phylogenetic Relationships

2020 ◽  
Author(s):  
Ying-min Zhang ◽  
Li-jun Han ◽  
Ying-Ying Liu ◽  
Cong-wei Yang ◽  
Xing Tian ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Blood Stasis ◽  
Genome Comparison ◽  
Phylogenetic Study ◽  
Species Classification ◽  
Chloroplast Genomes ◽  
Genomic Characterization ◽  
Cp Genome

Abstract Background: Veratrum is a genus of perennial herbs that are widely used as traditional Chinese medicine for emetic, resolving blood stasis and relieve pain. However, the species classification and the phylogenetic relationship of the genus Veratrum have long been controversial due to the complexity of morphological variations. Knowledge on the infrageneric relationships of the genus Veratrum can be obtained from their chloroplast genome sequences and increase the taxonomic and phylogenetic resolution.Methods: Total DNA was extracted from ten species of Veratrum and subjected to next-generation sequencing. The cp genome was assembled by NOVOPlasty. Genome annotation was conducted using the online tool DOGMA and subsequently corrected by Geneious Prime. Then, genomic characterization of the Veratrum plastome and genome comparison with closely related species was analyzed by corresponding software. Moreover, phylogenetical trees were reconstructed, based on the 29 plastomes by maximum likelihood (ML) and Bayesian inference (BI) methods.Results: The whole plastomes of Veratrum species possess a typical quadripartite structure, ranging from 151,597 bp to 153,711 bp in size and comprising 135 genes. The gene order, content, and genome structure were nearly identical with a few exceptions across the Veratrum chloroplast genomes. The total number of simple sequence repeats (SSRs) ranged from 31 to 35, and of large sequence repeats (LSRs) ranged from 65 to 71. Seven highly divergent regions (rpoB-trnC, trnT-trnL, trnS-trnG, psbC-psbZ, psbI, ycf1, and ndhF) were identified that can be used for DNA barcoding in the genus of Veratrum. Phylogenetic analyses based on 29 plastomes strongly supported the monophyly of Veratrum. The circumscription and relationships of infrageneric taxa of Veratrum were well evaluated with high resolutions. Conclusions: Our study identified and analyzed the cp genome features of ten Veratrum species, and suggested high effectivity of chloroplast complete genome in resolving generic circumscription in Veratrum. These results will facilitate the identification, taxonomy, and utilization of Veratrum plants as well as the phylogenetic study of Melanthiaceae simultaneously.

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 Synchronous dissection of chloroplast and mitochondrial genomes clarifies the intra- and inter-genus phylogeny for the agriculturally important genus Brassica

2020 ◽  
Author(s):  
Jiangwei Qiao ◽  
Xiaojun Zhang ◽  
Biyun Chen ◽  
Fei Huang ◽  
Kun Xu ◽  
...  
Keyword(s):  
De Novo ◽  
Phylogenetic Analyses ◽  
Parallel Evolution ◽  
Brassica Species ◽  
Type B ◽  
Male Sterile ◽  
Data Set ◽  
Chloroplast Genomes ◽  
Ornamental Crops ◽  
Allotetraploid Species

Abstract Background : The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of B. napus and the detailed interspecific relationships within Brassica genus remains unresolved and somewhere confused. By synchronous sequencing of both the chloroplast DNA and mitochondrial DNA, the whole Brassica phylogeny and the origination of the predominant nap -type B. napus have been clarified based on a large plant population, which maximally integrated the known Brassica species. Results : The phylogenetic analyses based on a data set including 72 de novo assembled whole chloroplast genomes, delineated a comprehensive evolutional atlas inside and around Brassica genus. Different from the monophyletical maternal origin of B. juncea and B. carinata from cam-type B. rapa and B. nigra , respectively, the natural B. napus has multiplex maternal origins. It contains three major cytoplasmic haplotypes: the cam -type which directly inherited from B. rapa , polima -type which is close to cam -type as a sister, and the predominant nap -type. Intriguingly, nap -type seems phylogenetically integrated with certain sparse C-genome wild species , thus implying that which may have primarily contributed the cytoplasm and the corresponding C subgenome to B. napus . Human breeding creation of the B. napus cytoplasmic male sterile lines (e.g., mori and nsa ) have dramatically disturbed the concurrent inheritance between mtDNA and cpDNA. Strong parallel evolution among genera Raphanus , Sinapis, Eruca , Moricandia with Brassica indicates their uncomplete divergence from each other. Conclusions : The elaborated phylogenetic relationships and overall variation data obtained herein can substantially facilitate to develop novel Brassica germplasms and to improve the Brassica crops.

scholarly journals Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 157 ◽  
Author(s):  
Inkyu Park ◽  
Jun-Ho Song ◽  
Sungyu Yang ◽  
Byeong Cheol Moon
Keyword(s):  
Herbal Medicine ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Comparative Sequence Analysis ◽  
Indel Marker ◽  
Sequence Information ◽  
Genome Sequences ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Rna Genes

Actaea (Ranunculaceae; syn. Cimicifuga) is a controversial and complex genus. Dried rhizomes of Actaea species are used as Korean traditional herbal medicine. Although Actaea species are valuable, given their taxonomic classification and medicinal properties, sequence information of Actaea species is limited. In this study, we determined the complete chloroplast (cp) genome sequences of three Actaea species, including A. simplex, A. dahurica, and A. biternata. The cp genomes of these species varied in length from 159,523 to 159,789 bp and contained 112 unique functional genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, orientation, and content were well conserved in the three cp genomes. Comparative sequence analysis revealed the presence of hotspots, including ndhC-trnV-UAC, in Actaea cp genomes. High-resolution phylogenetic relationships were established among Actaea species based on cp genome sequences. Actaea species were clustered into each Actaea section, consistent with the Angiosperm Phylogeny Group (APG) IV system of classification. We also developed a novel indel marker, based on copy number variation of tandem repeats, to facilitate the authentication of the herbal medicine Cimicifugae Rhizoma. The availability Actaea cp genomes will provide abundant information for the taxonomic and phylogenetic analyses of Actaea species, and the Actaea (ACT) indel marker will be useful for the authentication of the herbal medicine.

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 Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Yang Yu ◽  
Yuwei Han ◽  
Yingmei Peng ◽  
Zunzhe Tian ◽  
Peng Zeng ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
New Taxon ◽  
Genomic Features ◽  
Chloroplast Genomes ◽  
Potential Marker ◽  
Cp Genome ◽  
Timber Market ◽  
High Degree ◽  
Contraction And Expansion

Abstract Background In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as “Bingpian” in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency. Methods In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci. Results The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae. Conclusions Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.

scholarly journals Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qian Xiong ◽  
Yuxin Hu ◽  
Wenqi Lv ◽  
Qinghua Wang ◽  
Guoxiang Liu ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Small Variation ◽  
Molecular Data ◽  
Evolutionary Relationships ◽  
Single Family ◽  
Chloroplast Genomes ◽  
Morphological Criteria ◽  
Cp Genome

Abstract Background The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales. Results The five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats. Conclusions Our results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

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.

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