scholarly journals The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

2019 ◽  
Author(s):  
James Worth ◽  
Luxian Liu ◽  
Nobuhiro Tomaru
Keyword(s):  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Chloroplast Genome ◽  
Tree Species ◽  
Fagus Crenata ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Genetic Structure And Diversity

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed between them and differing by 311 single nucleotide polymorphisms. The six most variable regions between the two genomes were the psbK-psbI, trnG-psbfM, trnV, rpl32, ndhD-psaC and ndhI-ndh regions. These highly variable chloroplast regions and the identification of 42 variable chloroplast SSRs found to be shared between the two species will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.

scholarly journals The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

2019 ◽  
Author(s):  
James Worth ◽  
Luxian Liu ◽  
Nobuhiro Tomaru
Keyword(s):  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Chloroplast Genome ◽  
Tree Species ◽  
Fagus Crenata ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Genetic Structure And Diversity

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed between them and differing by 311 single nucleotide polymorphisms. The six most variable regions between the two genomes were the psbK-psbI, trnG-psbfM, trnV, rpl32, ndhD-psaC and ndhI-ndh regions. These highly variable chloroplast regions and the identification of 42 variable chloroplast SSRs found to be shared between the two species will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.

scholarly journals The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7026 ◽  
Author(s):  
James R. P. Worth ◽  
Luxian Liu ◽  
Fu-Jin Wei ◽  
Nobuhiro Tomaru
Keyword(s):  
Chloroplast Genome ◽  
Ribosomal Rna ◽  
Fagus Crenata ◽  
Chloroplast Microsatellites ◽  
Trna Genes ◽  
Protein Coding ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Genetic Structure And Diversity ◽  
Rna Genes

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.

scholarly journals The complete chloroplast genome of Limonium tetragonum (Plumbaginaceae) isolated in Korea

2021 ◽  
Vol 51 (3) ◽  
pp. 337-344
Author(s):  
Yongsung KIM ◽  
Hong XI ◽  
Jongsun PARK
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Sister Group ◽  
Single Copy ◽  
Nucleotide Polymorphisms ◽  
Large Single Copy ◽  
Single Nucleotide ◽  
Complete Chloroplast Genome ◽  
Cp Genome

The chloroplast genome of Limonium tetragonum (Thunb.) Bullock, a halophytic species, was sequenced to understand genetic differences based on its geographical distribution. The cp genome of L. tetragonum was 154,689 bp long (GC ratio is 37.0%) and has four subregions: 84,572 bp of large single-copy (35.3%) and 12,813 bp of small singlecopy (31.5%) regions were separated by 28,562 bp of inverted repeat (40.9%) regions. It contained 128 genes (83 proteincoding genes, eight rRNAs, and 37 tRNAs). Thirty-five single-nucleotide polymorphisms and 33 INDEL regions (88 bp in length) were identified. Maximum-likelihood and Bayesian inference phylogenetic trees showed that L. tetragonum formed a sister group with L. aureum, which is incongruent with certain previous studies, including a phylogenetic analysis.

scholarly journals Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya)

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Junling Cao ◽  
Dan Jiang ◽  
Zhenyu Zhao ◽  
Subo Yuan ◽  
Yujun Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complete Chloroplast Genome ◽  
Genomic Resources ◽  
Chinese Yam ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Simple Sequence

Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs). Seventy simple sequence repeats (SSRs) were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

scholarly journals Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding

PLoS ONE ◽  
2019 ◽  
Vol 14 (8) ◽  
pp. e0220981 ◽  
Author(s):  
Hiroto Yamashita ◽  
Hideyuki Katai ◽  
Lina Kawaguchi ◽  
Atsushi J. Nagano ◽  
Yoriyuki Nakamura ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Wing Geometric Morphometrics of Workers and Drones and Single Nucleotide Polymorphisms Provide Similar Genetic Structure in the Iberian Honey Bee (Apis mellifera iberiensis)

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 89 ◽  
Author(s):  
Dora Henriques ◽  
Julio Chávez-Galarza ◽  
Juliana S. G. Teixeira ◽  
Helena Ferreira ◽  
Cátia J. Neves ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Geometric Morphometrics ◽  
Geographical Information ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Processes ◽  
Single Nucleotide ◽  
Genetic Patterns ◽  
Wing Geometric Morphometrics

Wing geometric morphometrics has been applied to honey bees (Apis mellifera) in identification of evolutionary lineages or subspecies and, to a lesser extent, in assessing genetic structure within subspecies. Due to bias in the production of sterile females (workers) in a colony, most studies have used workers leaving the males (drones) as a neglected group. However, considering their importance as reproductive individuals, the use of drones should be incorporated in these analyses in order to better understand diversity patterns and underlying evolutionary processes. Here, we assessed the usefulness of drone wings, as well as the power of wing geometric morphometrics, in capturing the signature of complex evolutionary processes by examining wing shape data, integrated with geographical information, from 711 colonies sampled across the entire distributional range of Apis mellifera iberiensis in Iberia. We compared the genetic patterns reconstructed from spatially-explicit shape variation extracted from wings of both sexes with that previously reported using 383 genome-wide SNPs (single nucleotide polymorphisms). Our results indicate that the spatial structure retrieved from wings of drones and workers was similar (r = 0.93) and congruent with that inferred from SNPs (r = 0.90 for drones; r = 0.87 for workers), corroborating the clinal pattern that has been described for A. m. iberiensis using other genetic markers. In addition to showing that drone wings carry valuable genetic information, this study highlights the capability of wing geometric morphometrics in capturing complex genetic patterns, offering a reliable and low-cost alternative for preliminary estimation of population structure.

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