scholarly journals The complete chloroplast genomes of seventeen Aegilops tauschii: Genome characteristic and comparative analysis

2019 ◽  
Author(s):  
Qing Su ◽  
Luxian Liu ◽  
Mengyu Zhao ◽  
Cancan Zhang ◽  
Dale Zhang ◽  
...  
Keyword(s):  
Common Wheat ◽  
Yellow River ◽  
Genomic Structure ◽  
Aegilops Tauschii ◽  
Intergenic Spacer ◽  
Point Of View ◽  
Western China ◽  
Nucleotide Polymorphisms ◽  
Chloroplast Genomes ◽  
River Region

As the diploid progenitor of common wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14) is regarded to be a potential genetic resource for improving common wheat, which is naturally distributed in central Eurasia, spreading from northern Syria and Turkey to western China. In this work, the chloroplast genomes of seventeen Ae. tauschii accessions showed 135 551~ 136 009 bp in length and contained the typical quadripartite structure of angiosperms. Meanwhile, a total of 127 functional genes, including 78 protein-coding genes, 4 rRNAs, 26 tRNAs, and 19 duplicated genes were identified. Overall genomic structure including gene number, gene order were well conserved with identical IR/SC boundary regions, but few variations predominantly were detected in non-coding regions (intergenic spacer regions). IR expansion and contraction with identical structure among 17 Aegilops tauschii accessions were not influence chloroplast genomes in length. Four cpDNA markers including rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20 showed high nucleotide polymorphisms，which may be used to study on inter- and intra-specific genetic structure and diversity of Ae. tauschii. The ndhF gene in AY46 accession appeared the highest ω value, which might be involved in the adaptation to high altitude ecological environment during the evolution of AY46 accession. The phylogenetic relationships constructed by the complete genome sequences strongly support that Ae. tauschii in the Yellow River region might be directly originated from Central Asia rather than Xinjiang. The specific spreading route of Ae. tauschii revealed in this work, reflects the frequent cultural exchange through the silk road from one point of view. We confirmed that Ae. tauschii derived from monophyletic speciation rather than hybrid speciation at the chloroplast genome level.

scholarly journals The complete chloroplast genomes of seventeen Aegilops tauschii: Genome characteristic and comparative analysis

2019 ◽  
Author(s):  
Qing Su ◽  
Luxian Liu ◽  
Mengyu Zhao ◽  
Cancan Zhang ◽  
Dale Zhang ◽  
...  
Keyword(s):  
Common Wheat ◽  
Yellow River ◽  
Genomic Structure ◽  
Aegilops Tauschii ◽  
Intergenic Spacer ◽  
Point Of View ◽  
Western China ◽  
Nucleotide Polymorphisms ◽  
Chloroplast Genomes ◽  
River Region

As the diploid progenitor of common wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14) is regarded to be a potential genetic resource for improving common wheat, which is naturally distributed in central Eurasia, spreading from northern Syria and Turkey to western China. In this work, the chloroplast genomes of seventeen Ae. tauschii accessions showed 135 551~ 136 009 bp in length and contained the typical quadripartite structure of angiosperms. Meanwhile, a total of 127 functional genes, including 78 protein-coding genes, 4 rRNAs, 26 tRNAs, and 19 duplicated genes were identified. Overall genomic structure including gene number, gene order were well conserved with identical IR/SC boundary regions, but few variations predominantly were detected in non-coding regions (intergenic spacer regions). IR expansion and contraction with identical structure among 17 Aegilops tauschii accessions were not influence chloroplast genomes in length. Four cpDNA markers including rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20 showed high nucleotide polymorphisms，which may be used to study on inter- and intra-specific genetic structure and diversity of Ae. tauschii. The ndhF gene in AY46 accession appeared the highest ω value, which might be involved in the adaptation to high altitude ecological environment during the evolution of AY46 accession. The phylogenetic relationships constructed by the complete genome sequences strongly support that Ae. tauschii in the Yellow River region might be directly originated from Central Asia rather than Xinjiang. The specific spreading route of Ae. tauschii revealed in this work, reflects the frequent cultural exchange through the silk road from one point of view. We confirmed that Ae. tauschii derived from monophyletic speciation rather than hybrid speciation at the chloroplast genome level.

scholarly journals The complete chloroplast genomes of seventeen Aegilops tauschii: genome comparative analysis and phylogenetic inference

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8678 ◽  
Author(s):  
Qing Su ◽  
Luxian Liu ◽  
Mengyu Zhao ◽  
Cancan Zhang ◽  
Dale Zhang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Bread Wheat ◽  
Yellow River ◽  
Genomic Structure ◽  
Aegilops Tauschii ◽  
Western China ◽  
Chloroplast Genomes ◽  
River Region ◽  
Cp Genome ◽  
Rna Genes

The D genome progenitor of bread wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14), which is naturally distributed in Central Eurasia, ranging from northern Syria and Turkey to western China, is considered a potential genetic resource for improving bread wheat. In this study, the chloroplast (cp) genomes of 17 Ae. tauschii accessions were reconstructed. The cp genome sizes ranged from 135,551 bp to 136,009 bp and contained a typical quadripartite structure of angiosperms. Within these genomes, we identified a total of 124 functional genes, including 82 protein-coding genes, 34 transfer RNA genes and eight ribosomal RNA genes, with 17 duplicated genes in the IRs. Although the comparative analysis revealed that the genomic structure (gene order, gene number and IR/SC boundary regions) is conserved, a few variant loci were detected, predominantly in the non-coding regions (intergenic spacer regions). The phylogenetic relationships determined based on the complete genome sequences were consistent with the hypothesis that Ae. tauschii populations in the Yellow River region of China originated in South Asia not Xinjiang province or Iran, which could contribute to more effective utilization of wild germplasm resources. Furthermore, we confirmed that Ae. tauschii was derived from monophyletic speciation rather than hybrid speciation at the cp genome level. We also identified four variable genomic regions, rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20, showing high levels of nucleotide polymorphisms, which may accordingly prove useful as cpDNA markers in studying the intraspecific genetic structure and diversity of Ae. tauschii.

scholarly journals Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242591
Author(s):  
Jie Li ◽  
Guang-ying Ye ◽  
Hai-lin Liu ◽  
Zai-hua Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Intergenic Spacer ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Protein Coding ◽  
Important Species ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Mutational Hotspots

Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.

scholarly journals Genomic structure and diversity of oak populations in British Parklands

2021 ◽  
Author(s):  
Gabriele Nocchi ◽  
Nathan Brown ◽  
Tim Coker ◽  
William Plumb ◽  
Jonathan Stocks ◽  
...  
Keyword(s):  
Genomic Structure ◽  
Phylogenetic Network ◽  
Pedunculate Oak ◽  
Nucleotide Polymorphisms ◽  
Clustering Methods ◽  
Effective Population ◽  
Seed Sources ◽  
Chloroplast Genomes ◽  
Nuclear Genomes ◽  
Clear Differentiation

AbstractThe two predominant oak species in Britain are Quercus robur (English or pedunculate oak) and Q. petraea (sessile oak). We sequenced the whole genomes of 386 oak trees from four British parkland sites and found over 50 million nuclear single nucleotide polymorphisms (SNPs), allowing us to identify 360 Q. robur, ten Q. petraea and 16 hybrid individuals using clustering methods. Comparing Q. robur and Q. petraea trees from Attingham Park, we found that the nuclear genomes of the two species are largely undifferentiated but identified 81 coding regions exhibiting strong interspecific differentiation. The nuclear genomes of our 360 Q. robur individuals showed no clear differentiation among the four parkland sites. Scans for selective sweeps in Q. robur highlighted regions containing genes with putative involvement in stress tolerance, one of which was moderately differentiated from Q. petraea. Reconstructions of past effective population sizes suggested a long population size decline in both Q. robur and Q. petraea over the Pleistocene, but population growth after the last glacial maximum. We assembled the whole chloroplast genomes of 287 Q. robur, 8 Q. petraea and 14 hybrid trees. In a phylogenetic network, these fell into five major haplotypes, which were shared among species but differed in frequency among parkland sites. We matched our chloroplast genome haplotypes to restriction enzyme fragment haplotypes identified in older studies that had surveyed ancient woodlands in Britain and much of Europe. This suggested that the parkland populations in our study derive from local seed sources.

scholarly journals Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

2021 ◽  
Vol 22 (4) ◽  
pp. 1832
Author(s):  
Eugene Metakovsky ◽  
Laura Pascual ◽  
Patrizia Vaccino ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Group Iv ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

Natural Dust and Pneumoconiosis in High Asia

2003 ◽  
Author(s):  
Edward Derbyshire
Keyword(s):  
Loess Plateau ◽  
Yellow River ◽  
Western China ◽  
Human Populations ◽  
The Loess Plateau ◽  
The North ◽  
High Asia ◽  
Uplift Rates ◽  
Few Data ◽  
Tian Shan

High Asia, defined here as that great tract of land from the Himalaya- Karakoram in the south to the Tian Shan in the north and the Pamir in the west to the Qinling Mountains in the east, is a very dusty place. Whole communities of people in this region are exposed to the adverse effects of natural (aerosolic) dusts at exposure levels reaching those encountered in some high-risk industries. Outdooor workers are at particular risk. However, few data are available on the magnitude of the dust impact on human health. The effect of such far-travelled particles on the health of the human population in the Loess Plateau, and including major Chinese cities, has received relatively little attention to date. A combination of the highest known uplift rates, rapid river incision (up to 12 mm/yr: Burbank et al. 1996), unstable slopes, glaciation and widespread rock breakup by crystal growth during freezing (frost action), and by hydration of salts (salt weathering) makes the High Asia region the world’s most efficient producer of silty (defined as between 2 and 63 μm) debris. The earliest written records of the dust hazard come from China, most notably in the “Yu Gong” by Gu Ban (ca 200 BC) (Wang and Song 1983). Here, deposits of wind-blown silt (known as ‘loess’) cover the landscape in a drape that is locally 500 m thick. In North China, the loess covers an area of over 600,000 km², most of it in the Loess Plateau, situated in the middle reaches of the Huang He (Yellow River). The characteristic properties of loess include high porosity and collapsibility on wetting (Derbyshire et al. 1995, Derbyshire and Meng 2000).Thus, it is readily reworked and redistributed by water. This process concentrates silts in large alluvial fans (up to 50 x 50 km) in the piedmont zones of 6,000 m high glacier- and snow-covered mountain ranges of western China, including the Altai Shan (‘shan’ = mountains), Tian Shan, Kunlun Shan, Qilian Shan, and Karakoram. These zones are loci for human populations, and also a major source of wind-blown dust.

Genetic Mapping of an Aegilops tauschii -derived Hessian Fly Resistance Gene in Common Wheat

Crop Science ◽  
2010 ◽  
Vol 50 (2) ◽  
pp. 612-616 ◽  
Author(s):  
L. M. Miranda ◽  
D. E. Bland ◽  
S. E. Cambron ◽  
J. H. Lyerly ◽  
J. Johnson ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Resistance Gene ◽  
Common Wheat ◽  
Aegilops Tauschii ◽  
Hessian Fly ◽  
Hessian Fly Resistance

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.

Sign in / Sign up

Export Citation Format

Share Document