scholarly journals The complete plastid genomes of two Fabaceae orphan crops from Africa

2018 ◽  
Author(s):  
Xuezhu Liao ◽  
Yang Liu ◽  
Huan Liu
Keyword(s):  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Bambara Groundnut ◽  
Vigna Subterranea ◽  
Lablab Purpureus ◽  
Crop Species ◽  
Orphan Crops ◽  
Plastid Genomes ◽  
Orphan Crop ◽  
Traditional Crops

AbstractDolichos bean (Lablab purpureus) and Bambara groundnut (Vigna subterranea) are two traditional crops from Africa with important economic values. The study of such neglected or underused crops (orphan crops) should contribute to the resolution of food shortage in Africa. Here we assembled and described the complete plastid genome of the two Fabaceae orphan crop species. The length of the complete plastomes of L. purpureus and V. subterranea are 151,753 bp and 152,015 bp, respectively. Maximum-likelihood (ML) phylogenetic analyses indicated that L. purpureus and Phaseolus vulgaris are closely related, and V. subterranea and other Vigna species are clustered in one clade, which is congruent with former studies.

scholarly journals A single loss of photosynthesis in diatoms

2018 ◽  
Author(s):  
Anastasiia Onyshchenko ◽  
Elizabeth C. Ruck ◽  
Teofil Nakov ◽  
Andrew J. Alverson
Keyword(s):  
Plastid Genome ◽  
Phylogenetic Diversity ◽  
Phylogenetic Analyses ◽  
Rare Event ◽  
Small Subset ◽  
Plastid Genomes ◽  
Photosynthetic Eukaryotes ◽  
Large Numbers ◽  
Group A ◽  
The Common

AbstractLoss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of ‘apochloritic’ diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic diatoms suggests a single loss of photosynthesis in the common ancestor of these species, previous phylogenetic analyses suggested that photosynthesis was lost multiple times. We sequenced additional phylogenetic markers from the nuclear and mitochondrial genomes for a larger set of taxa and found that the best trees for datasets representing all three genetic compartments provided low to moderate support for monophyly of apochloritic Nitzschia, consistent with a single loss of photosynthesis in diatoms. We sequenced the plastid genome of one apochloritic species and found that it was highly similar in all respects to the plastid genome of another apochloritic Nitzschia species, indicating that streamlining of the plastid genome had completed prior to the split of these two species. Finally, it is increasingly clear that some locales host relatively large numbers apochloritic Nitzschia species that span the phylogenetic diversity of the group, indicating that these species co-exist because of resource abundance or resource partitioning in ecologically favorable habitats. A better understanding of the phylogeny and ecology of this group, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group, a rare event in diatoms.

scholarly journals Complete Plastid Genome Sequencing of Eight Species from Hansenia, Haplosphaera and Sinodielsia (Apiaceae): Comparative Analyses and Phylogenetic Implications

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1523
Author(s):  
Wei Gou ◽  
Sheng-Bin Jia ◽  
Megan Price ◽  
Xian-Lin Guo ◽  
Song-Dong Zhou ◽  
...  
Keyword(s):  
Codon Usage ◽  
Plastid Genome ◽  
Nucleotide Diversity ◽  
Phylogenetic Analyses ◽  
Plastid Genomes ◽  
Usage Frequency ◽  
Phylogenetic Implications ◽  
Insight Into ◽  
Simple Sequence ◽  
Genome Dataset

Hansenia Turcz., Haplosphaera Hand.-Mazz. and Sinodielsia H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of Hap. himalayensis and S. microloba. Therefore, we aimed to conduct comparative (simple sequence repeat (SSR) structure, codon usage bias, nucleotide diversity (Pi) and inverted repeat (IR) boundaries) and phylogenetic analyses of Hansenia, Haplosphaera and Sinodielsia (also compared with Chamaesium and Bupleurum) to reduce uncertainties in intergeneric and interspecific relationships. We newly assembled eight plastid genomes from Hansenia, Haplosphaera and Sinodielsia species, and analyzed them with two plastid genomes from GenBank of Hap. phaea,S. yunnanensis. Phylogenetic analyses used these ten genomes and another 22 plastid genome sequences of Apiaceae. We found that the newly assembled eight genomes ranged from 155,435 bp to 157,797 bp in length and all had a typical quadripartite structure. Fifty-five to 75 SSRs were found in Hansenia, Haplosphaera and Sinodielsia species, and the most abundant SSR was mononucleotide, which accounted for 58.47% of Hansenia, 60.21% of Haplosphaera and 48.01% of Sinodielsia. There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. The Pi analysis showed that trnE(UUC)-trnT(GGU), trnH(GUG)-psbA and trnE(UUC)-trnT(GGU) spacer regions had the highest Pi values in the plastid genomes of Hansenia (0.01889), Haplosphaera (0.04333) and Sinodielsia (0.01222), respectively. The ndhG-ndhI spacer regions were found in all three genera to have higher diversity values (Pi values: 0.01028–0.2), and thus may provide potential DNA barcodes in phylogenetic analysis. IR boundary analysis showed that the length of rps19 and ycf1 genes entering IRs were usually stable in the same genus. Our phylogenetic tree demonstrated that Hap. himalayensis is sister to Han. weberbaueriana; meanwhile, Haplosphaera and Hansenia are nested together in the East Asia clade, and S. microloba is nested within individuals of S. yunnanensis in the Acronema clade. This study will enrich the complete plastid genome dataset of the Apiaceae genera and has provided a new insight into phylogeny reconstruction using complete plastid genomes of Hansenia, Haplosphaera and Sinodielsia.

scholarly journals ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8392 ◽  
Author(s):  
Janice Valencia-D ◽  
José Murillo-A ◽  
Clara Inés Orozco ◽  
Carlos Parra-O ◽  
Kurt M. Neubig
Keyword(s):  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Bootstrap Support ◽  
Nucleotide Substitutions ◽  
Plastid Genomes ◽  
The Family ◽  
High Bootstrap ◽  
Single Genus

Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.

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 Complete plastid genome of Angelica, Ostericum and related species (Apiaceae): genomic evolution and phylogenetic implications

2021 ◽  
Author(s):  
Qiu-Ping Jiang ◽  
Megan Price ◽  
Xian-Lin Guo ◽  
Wei Gou ◽  
Song-Dong Zhou ◽  
...  
Keyword(s):  
Related Species ◽  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Protein Coding ◽  
Next Generation Sequencing Technology ◽  
Plastid Genomes ◽  
Phylogenetic Implications ◽  
Usage Patterns ◽  
Intergenic Regions

Abstract Background Subtribe Angelicinae is a large and taxonomically complex group of Apiaceae, encompassing Angelica, Archangelica, Coelopleurum, Conioselinum, Czernaevia, Glehnia, Levisticum and Ostericum that are distributed in the Northern Hemisphere, and whether this taxa is natural is debatable, especially between Angelica and Ostericum. To determine genommic evolution and phylogenetic relationships between Angelica, Ostericum, and related species, we newly assembled the complete plastid genome sequences of eight subtribe Angelicinae species and Melanosciadium pimpinelloideum using next-generation sequencing technology. Results The nine plastid genomes we sequenced were conserved, and their size ranged from 146765 bp to 164329 bp, showing the typical quadripartite circular structure with an overall GC content of 37.5–37.8%. IR boundary analyses showed that the genes in the LSC region transfer into the IR regions and the SSC region was relatively stable. Codon usage patterns were similar among these species and we identified 66–86 SSRs, with the most abundant SSR being mononucleotide. The Pi analyses showed that petA-psbJ(0.02778), atpI-atpH(0.17333) and petA-psbJ(0.04726) intergenic regions had the highest Pi values in Angelica, Ostericum, and ten species, respectively. Conclusions Ostericum exhibited significant differences in size of genomes, content of genes and tRNAs, GC content, some type of SSRs, and IR boundaries to Angelica, and phylogenetic analyses found the relatedness between Angelica and Ostericum is more distant in protein-coding genes of the plastid genomes trees and nrITS trees.

GENETIC DIVERSITY IN BAMBARA GROUNDNUT (Vigna subterranean) AS REVEALED BY MOLECULAR WEIGHTS OF THE SEEDS’ PROTEINS

2018 ◽  
Vol 30 (2) ◽  
pp. 19-28
Author(s):  
A. J. Oludare ◽  
J. I. Kioko ◽  
A. A. Akeem ◽  
A. T. Olumide ◽  
K. R. Justina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Seed Proteins ◽  
Electrophoretic Analysis ◽  
Protein Characterization ◽  
Bambara Groundnut ◽  
Vigna Subterranea ◽  
Phylogenetic Relatedness ◽  
Molecular Weights ◽  
National Centre ◽  
Standard Marker

Nine accessions of Bambara groundnut (Vigna subterranea (L.) Verdc.,syn. Voandzeia subterranea (L.) Thouars ex DC.)  obtained from National Centre for Genetic Resources and Biotechnology (NACGRAB), Ibadan, Oyo state, were assessed for their genetic and phylogenetic relatedness through electrophoretic analysis of the seed proteins. 0.2g of the seeds were weighed and macerated with mortar and pestle in 0.2M phosphate buffer containing 0.133M of acid (NaH2PO4) and 0.067 of base (Na2HPO4) at pH 6.5. Protein characterization with standard marker revealed that the seeds of the nine accessions contained proteins (B.S.A, Oval Albumin, Pepsinogen, Trypsinogen and Lysozyme) with molecular weights ranging from 66kda and above, 45 – 65 kDa, 44 – 33 kda, 32-24 kDa and 23-14 kDa, respectively. The student T-test revealed that accessions B, C, E, F, H and I have molecular weights not significantly different from one another (P<0.05) while samples A, D and G showed significantly different values (P>0.05). All the accessions had at least two proteins and two major bands in common. The study revealed intra-specific similarities and genetic diversity in protein contents among the nine accessions of Bambara groundnut (Vigna subterraranea (L.) Verdc.syn

Genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 995-999 ◽  
Author(s):  
H I Amadou ◽  
P J Bebeli ◽  
P J Kaltsikes
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Bambara Groundnut ◽  
International Institute ◽  
Tropical Agriculture ◽  
Vigna Subterranea ◽  
Ibadan Nigeria

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop.Key words: germplasm, PCR, RAPD, Vigna subterranea.

scholarly journals Utilization of bambara groundnut (Vigna subterranea (L.) Verdc.) for sustainable food and nutrition security in semi-arid regions of Zimbabwe

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0204817 ◽  
Author(s):  
Juliet Mubaiwa ◽  
Vincenzo Fogliano ◽  
Cathrine Chidewe ◽  
Evert Jan Bakker ◽  
Anita R. Linnemann
Keyword(s):  
Arid Regions ◽  
Bambara Groundnut ◽  
Vigna Subterranea ◽  
Sustainable Food ◽  
Food And Nutrition Security ◽  
Nutrition Security ◽  
Food And Nutrition ◽  
Semi Arid
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