scholarly journals Genome‐wide sequence information reveals recurrent hybridization among diploid wheat wild relatives

2020 ◽  
Vol 102 (3) ◽  
pp. 493-506 ◽  
Author(s):  
Nadine Bernhardt ◽  
Jonathan Brassac ◽  
Xue Dong ◽  
Eva‐Maria Willing ◽  
C. Hart Poskar ◽  
...  
Keyword(s):  
Wild Relatives ◽  
Diploid Wheat ◽  
Sequence Information ◽  
Genome Wide ◽  
Wheat Wild Relatives

scholarly journals Genome-wide sequence information reveals recurrent hybridization among diploid wheat wild relatives

2019 ◽  
Author(s):  
Nadine Bernhardt ◽  
Jonathan Brassac ◽  
Xue Dong ◽  
Eva-Maria Willing ◽  
C. Hart Poskar ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Diploid Species ◽  
Wild Relatives ◽  
Testable Hypothesis ◽  
Sequence Information ◽  
Genome Wide ◽  
Wheat Group ◽  
Polyploid Formation ◽  
Extant Species ◽  
Wheat Wild Relatives

AbstractMany conflicting hypotheses regarding the relationships among crops and wild species closely related to wheat (the genera Aegilops, Amblyopyrum, and Triticum) have been postulated. The contribution of hybridization to the evolution of these taxa is intensely discussed. To determine possible causes for this, and provide a phylogeny of the diploid taxa based on genome-wide sequence information, independent data was obtained from genotyping-by-sequencing and a target-enrichment experiment that returned 244 low-copy nuclear loci. The data were analyzed with Bayesian, likelihood and coalescent-based methods. D statistics were used to test if incomplete lineage sorting alone or together with hybridization is the source for incongruent gene trees. Here we present the phylogeny of all diploid species of the wheat wild relatives. We hypothesize that most of the wheat-group species were shaped by a primordial homoploid hybrid speciation event involving the ancestral Triticum and Am. muticum lineages to form all other species but Ae. speltoides. This hybridization event was followed by multiple introgressions affecting all taxa but Triticum. Mostly progenitors of the extant species were involved in these processes, while recent interspecific gene flow seems insignificant. The composite nature of many genomes of wheat group taxa results in complicated patterns of diploid contributions when these lineages are involved in polyploid formation, which is, for example, the case in the tetra-and hexaploid wheats. Our analysis provides phylogenetic relationships and a testable hypothesis for the genome compositions in the basic evolutionary units within the wheat group of Triticeae.

Bacterial origin of thymidylate and folate metabolism in Asgard Archaea

2021 ◽  
Author(s):  
Jonathan Filee ◽  
Hubert J. Becker ◽  
Lucille Mellottee ◽  
Zhihui LI ◽  
Jean-Christophe Lambry ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Phylogenetic Trees ◽  
De Novo ◽  
Horizontal Transmission ◽  
Folate Metabolism ◽  
Ecological Niches ◽  
Sequence Information ◽  
Amino Acid Utilization ◽  
Genome Wide

Little is known about the evolution and biosynthetic function of DNA precursor and the folate metabolism in the Asgard group of archaea. As Asgard occupy a key position in the archaeal and eukaryotic phylogenetic trees, we have exploited very recently emerged genome and metagenome sequence information to investigate these central metabolic pathways. Our genome-wide analyses revealed that the recently cultured Asgard archaeon Candidatus Prometheoarchaeum syntrophicum strain MK-D1 (Psyn) contains a complete folate-dependent network for the biosynthesis of DNA/RNA precursors, amino acids and syntrophic amino acid utilization. Altogether our experimental and computational data suggest that phylogenetic incongruences of functional folate-dependent enzymes from Asgard archaea reflect their persistent horizontal transmission from various bacterial groups, which has rewired the key metabolic reactions in an important and recently identified archaeal phylogenetic group. We also experimentally validated the functionality of the lateral gene transfer of Psyn thymidylate synthase ThyX. This enzyme uses bacterial-like folates efficiently and is inhibited by mycobacterial ThyX inhibitors. Our data raise the possibility that the thymidylate metabolism, required for de novo DNA synthesis, originated in bacteria and has been independently transferred to archaea and eukaryotes. In conclusion, our study has revealed that recent prevalent lateral gene transfer has markedly shaped the evolution of Asgard archaea by allowing them to adapt to specific ecological niches.

scholarly journals Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples

Viruses ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 749 ◽  
Author(s):  
Melanie Hiltbrunner ◽  
Gerald Heckel
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Common Vole ◽  
Natural Host ◽  
Sequence Information ◽  
Coding Region ◽  
Sequence Capture ◽  
Genome Wide ◽  
The Impact

Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average >99%) and sequencing depth (average >247×). A comparison with partial Sanger sequences indicated an accuracy of >99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.

scholarly journals Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0151424 ◽  
Author(s):  
Hua Yang ◽  
Chao-Ling Wei ◽  
Hong-Wei Liu ◽  
Jun-Lan Wu ◽  
Zheng-Guo Li ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Genetic Divergence ◽  
Wild Relatives ◽  
Rad Sequencing ◽  
Genome Wide

scholarly journals Drought-adaptive traits derived from wheat wild relatives and landraces

2006 ◽  
Vol 58 (2) ◽  
pp. 177-186 ◽  
Author(s):  
M. Reynolds ◽  
F. Dreccer ◽  
R. Trethowan
Keyword(s):  
Wild Relatives ◽  
Adaptive Traits ◽  
Wheat Wild Relatives

Evaluation of Wheat Wild Relatives for Resistance to Septoria Tritici Blotch

Crop Science ◽  
1994 ◽  
Vol 34 (4) ◽  
pp. 1080-1084 ◽  
Author(s):  
A. L. McKendry ◽  
G. E. Henke
Keyword(s):  
Wild Relatives ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Wheat Wild Relatives

scholarly journals Variation in key leaf photosynthetic traits across wheat wild relatives is accession dependent not species dependent

2020 ◽  
Vol 228 (6) ◽  
pp. 1767-1780
Author(s):  
Lorna McAusland ◽  
Silvere Vialet‐Chabrand ◽  
Iván Jauregui ◽  
Amanda Burridge ◽  
Stella Hubbart‐Edwards ◽  
...  
Keyword(s):  
Wild Relatives ◽  
Wheat Wild Relatives ◽  
Photosynthetic Traits

41 Using Sequence Data to Increase Accuracy of Genomic Predictions in Livestock: Are We There Yet?

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 22-23
Author(s):  
Daniela Lourenco ◽  
Shogo Tsuruta ◽  
Sungbong Jang ◽  
Breno O Fragomeni ◽  
Ignacy Misztal
Keyword(s):  
Functional Data ◽  
Large Scale ◽  
Sequence Data ◽  
Single Step ◽  
Sequence Information ◽  
Genome Wide ◽  
Snp Panel ◽  
Increase In Accuracy ◽  
Genomic Predictions ◽  
Variance Explained

Abstract As sequence data is becoming available for many livestock species, there is a question on whether this information can help to boost the accuracy of genomic predictions beyond what has already been achieved with SNP chips. Several studies have been conducted by our group using simulated and real livestock populations that included from 1,000 to 100,000 animals with full or imputed sequence information. For the real datasets, the potential causative variants were identified based on genome-wide association (GWA) and were added to the current SNP chips. Additional scenarios included the use of only causative variants and the use of all sequence SNP. Genomic predictions were obtained based on single-step GBLUP (ssGBLUP), and in some cases, Bayesian regressions. Overall, in real datasets, we observed no significant increase in accuracy by using all sequence SNP, causative variants alone, or combined with SNP currently used for genomic prediction. However, an increase in accuracy of almost 100% was observed in simulated datasets when the causative variants were added to a 60k SNP panel and their simulated variances were accounted for by the prediction model. Our results show that if true causative variants are identified, together with their position and the variance explained, a boost in accuracy can be observed. This raises a question on the effectiveness of the methods and size of the datasets used to select causative variants in real livestock populations. We observed distinct GWA methods work differently depending on the data structure, and the number of genotyped animals with phenotypes. The combination of large-scale sequence and other layers of omics data (e.g., functional data) can help to identify some of the true causative variants. This could possibly promote an increase in the accuracy of genomic predictions in real populations.

CLONNING OF DREB1 GENE IN WHEAT WILD RELATIVES AND DEVELOPMENT OF A DNA MARKER FOR ITS MONITORING IN WHEAT BACKGROUND

2018 ◽  
Vol 53 (3) ◽  
pp. 499-510
Author(s):  
A.A. Pochtovyy ◽  
◽  
P.Yu. Kroupin ◽  
M.G. Divashuk ◽  
A.A. Kocheshkova ◽  
...  
Keyword(s):  
Dna Marker ◽  
Wild Relatives ◽  
Wheat Wild Relatives

Heteromorphic seeds of wheat wild relatives show germination niche differentiation

Plant Biology ◽  
2019 ◽  
Vol 22 (2) ◽  
pp. 191-202 ◽  
Author(s):  
M. Gianella ◽  
A. Balestrazzi ◽  
A. Pagano ◽  
J. V. Müller ◽  
A. C. Kyratzis ◽  
...  
Keyword(s):  
Niche Differentiation ◽  
Wild Relatives ◽  
Wheat Wild Relatives ◽  
Germination Niche
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