scholarly journals Genome sequences of Aegilops species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

2021 ◽  
Author(s):  
Raz Avni ◽  
Thomas Lux ◽  
Anna Minz-Dub ◽  
Eitan Millet ◽  
Hanan Sela ◽  
...  
Keyword(s):  
Haplotype Block ◽  
Close Relative ◽  
Whole Genome ◽  
Aegilops Species ◽  
Wheat Improvement ◽  
Genome Wide ◽  
Triticum Spp ◽  
Species Specific ◽  
Genomic Regions ◽  
Genome Assemblies

Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Ae. longissima and Ae. speltoides. Whole-genome comparative analysis, along with the recently sequenced Ae. sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly simiar and most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides is the closest ancestor of the wheat B subgenome and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding site leucine rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.

scholarly journals Genome-wide microsatellites and species specific markers in genus Phytophthora revealed through whole genome analysis

3 Biotech ◽  
2020 ◽  
Vol 10 (10) ◽  
Author(s):  
Deepu Mathew ◽  
P. S. Anju ◽  
Amala Tom ◽  
Neethu Johnson ◽  
M. Lidia George ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Genome Wide ◽  
Species Specific

scholarly journals Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 524 ◽  
Author(s):  
Sangang He ◽  
Jiang Di ◽  
Bing Han ◽  
Lei Chen ◽  
Mingjun Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Average Length ◽  
Inbreeding Coefficient ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Genotyping Array ◽  
Genome Region ◽  
Genome Wide ◽  
Genomic Regions ◽  
Genome Wide Scan

In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.

scholarly journals Evaluating the use of ABBA-BABA statistics to locate introgressed loci

2013 ◽  
Author(s):  
Simon H. Martin ◽  
John W. Davey ◽  
Chris D. Jiggins
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Ancestral Population ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Data ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson?s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

scholarly journals Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

2021 ◽  
Author(s):  
Manu Kumar Gundappa ◽  
Thu-Hien To ◽  
Lars Grønvold ◽  
Samuel A M Martin ◽  
Sigbjørn Lien ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Meiotic Pairing ◽  
Genome Wide ◽  
A Genome ◽  
Clock Analysis ◽  
Multiple Species ◽  
Genomic Regions ◽  
Genome Assemblies

The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent 'explosion' of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial 'wave' of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained in a tetraploid state. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Finally, using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. Overall, this study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.

scholarly journals Phylogenomics for Chagas Disease Vectors of the Rhodnius Genus (Hemiptera, Triatominae): What We Learn From Mito-Nuclear Conflicts and Recommendations

2022 ◽  
Vol 9 ◽  
Author(s):  
Jonathan Filée ◽  
Marie Merle ◽  
Héloïse Bastide ◽  
Florence Mougel ◽  
Jean-Michel Bérenger ◽  
...  
Keyword(s):  
Molecular Data ◽  
Mitochondrial Genes ◽  
Valid Species ◽  
Close Relative ◽  
Protein Coding ◽  
Genome Wide ◽  
A Genome ◽  
Chagas Disease Vectors ◽  
Tree Topologies ◽  
Species Specific

We provide in this study a very large DNA dataset on Rhodnius species including 36 samples representing 16 valid species of the three Rhodnius groups, pictipes, prolixus and pallescens. Samples were sequenced at low-depth with whole-genome shotgun sequencing (Illumina technology). Using phylogenomics including 15 mitochondrial genes (13.3 kb), partial nuclear rDNA (5.2 kb) and 51 nuclear protein-coding genes (36.3 kb), we resolve sticking points in the Rhodnius phylogeny. At the species level, we confirmed the species-specific status of R. montenegrensis and R. marabaensis and we agree with the synonymy of R. taquarussuensis with R. neglectus. We also invite to revisit the species-specific status of R. milesi that is more likely R. nasutus. We proposed to define a robustus species complex that comprises the four close relative species: R. marabaensis, R. montenegrensis, R. prolixus and R. robustus. As Psammolestes tertius was included in the Rhodnius clade, we strongly recommend reclassifying this species as R. tertius. At the Rhodnius group level, molecular data consistently supports the clustering of the pictipes and pallescens groups, more related to each other than they are to the prolixus group. Moreover, comparing mitochondrial and nuclear tree topologies, our results demonstrated that various introgression events occurred in all the three Rhodnius groups, in laboratory strains but also in wild specimens. We demonstrated that introgressions occurred frequently in the prolixus group, involving the related species of the robustus complex but also the pairwise R. nasutus and R. neglectus. A genome wide analysis highlighted an introgression event in the pictipes group between R. stali and R. brethesi and suggested a complex gene flow between the three species of the pallescens group, R. colombiensis, R. pallescens and R. ecuadoriensis. The molecular data supports also a sylvatic distribution of R. prolixus in Brazil (Pará state) and the monophyly of R. robustus. As we detected extensive introgression events and selective pressure on mitochondrial genes, we strongly recommend performing separate mitochondrial and nuclear phylogenies and to take advantages of mito-nuclear conflicts in order to have a comprehensive evolutionary vision of this genus.

scholarly journals GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Andrew P. Wilkey ◽  
Anne V. Brown ◽  
Steven B. Cannon ◽  
Ethalinda K. S. Cannon
Keyword(s):  
Snp Array ◽  
Whole Genome ◽  
Array Data ◽  
Link Type ◽  
Snp Data ◽  
Genome Wide ◽  
Genome Visualization ◽  
Data Points ◽  
Genomic Regions ◽  
Genome Scale

Abstract Background Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such datasets, to assess characteristics such as overall differences between accessions and regional anomalies across the genome. Results We present GCViT (Genotype Comparison Visualization Tool), for visualizing and exploring large genotyping datasets. GCViT can be used to identify introgressions, conserved or divergent genomic regions, pedigrees, and other features for more detailed exploration. The program can be used online or as a local instance for whole genome visualization of resequencing or SNP array data. The program performs comparisons of variants among user-selected accessions to identify allele differences and similarities between accessions and a user-selected reference, providing visualizations through histogram, heatmap, or haplotype views. The resulting analyses and images can be exported in various formats. Conclusions GCViT provides methods for interactively visualizing SNP data on a whole genome scale, and can produce publication-ready figures. It can be used in online or local installations. GCViT enables users to confirm or identify genomics regions of interest associated with particular traits. GCViT is freely available at https://github.com/LegumeFederation/gcvit. The 1.0 version described here is available at 10.5281/zenodo.4008713.

scholarly journals Widespread false gene gains caused by duplication errors in genome assemblies

2021 ◽  
Author(s):  
Byung June Ko ◽  
Chul Lee ◽  
Juwan Kim ◽  
Arang Rhie ◽  
DongAhn Yoo ◽  
...  
Keyword(s):  
Gene Family ◽  
Zebra Finch ◽  
Whole Genome ◽  
Sequencing Errors ◽  
A Minor ◽  
Genomic Regions ◽  
Assembly Algorithms ◽  
Genome Assemblies ◽  
Sequence Errors

AbstractFalse duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in previous genome assemblies and their new counterparts of the same species (platypus, zebra finch, Anna’s hummingbird) generated by the Vertebrate Genomes Project (VGP). Whole genome alignments revealed that 4 to 16% of the sequences were falsely duplicated in the previous assemblies, impacting hundreds to thousands of genes. These led to overestimated gene family expansions. The main source of the false duplications was heterotype duplications, where the haplotype sequences were more divergent than other parts of the genome leading the assembly algorithms to classify them as separate genes or genomic regions. A minor source was sequencing errors. Although present in a smaller proportion, we observed false duplications remaining in the VGP assemblies that can be identified and purged. This study highlights the need for more advanced assembly methods that better separates haplotypes and sequence errors, and the need for cautious analyses on gene gains.

scholarly journals Pathways to polar adaptation in fishes revealed by long-read sequencing

2021 ◽  
Author(s):  
Scott Hotaling ◽  
Thomas Desvignes ◽  
John S. Sproul ◽  
Luana S.F. Lins ◽  
Joanna L Kelley
Keyword(s):  
Genome Wide ◽  
A Genome ◽  
Cebidichthys Violaceus ◽  
Long Read ◽  
Wide Perspective ◽  
Element Activity ◽  
Genomic Regions ◽  
Genome Assemblies ◽  
Response To Environmental Change ◽  
Globally Distributed

Long-read sequencing is driving a new reality for genome science where highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequencing are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we leveraged long-read sequencing to generate a high-quality genome assembly for an Antarctic eelpout, Opthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that from a genome-wide perspective, selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, selection has acted on genes involved in membrane structure and DNA repair. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic regions known to underlie key adaptations to polar seas: hemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the hemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other teleosts. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus), potentially reflecting a lineage-specific loss of this gene cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.

scholarly journals Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota

2021 ◽  
Vol 11 ◽  
Author(s):  
Stephanie van Wyk ◽  
Brenda D. Wingfield ◽  
Lieschen De Vos ◽  
Nicolaas A. van der Merwe ◽  
Emma T. Steenkamp
Keyword(s):  
Defense Mechanism ◽  
Point Mutations ◽  
Gc Content ◽  
Sliding Window ◽  
Genome Defense ◽  
Genome Wide ◽  
Taxonomic Range ◽  
Window Approach ◽  
Genomic Regions ◽  
Genome Assemblies

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach. Using genome-wide RIP data and two sets of control groups, the association between RIP, TEs, and GC content were contrasted in organisms capable and incapable of RIP. Based on these data, we then set out to determine the extent and occurrence of RIP in 58 representatives of the Ascomycota. The findings were summarized by placing each of the fungi investigated in one of six categories based on the extent of genome-wide RIP. In silico RIP analyses, using a sliding-window approach with stringent RIP parameters, implemented simultaneously within the same genetic context, on high quality genome assemblies, yielded superior results in determining the genome-wide RIP among the Ascomycota. Most Ascomycota had RIP and these mutations were particularly widespread among classes of the Pezizomycotina, including the early diverging Orbiliomycetes and the Pezizomycetes. The most extreme cases of RIP were limited to representatives of the Dothideomycetes and Sordariomycetes. By contrast, the genomes of the Taphrinomycotina and Saccharomycotina contained no detectable evidence of RIP. Also, recent losses in RIP combined with controlled TE proliferation in the Pezizomycotina subphyla may promote substantial genome enlargement as well as the formation of sub-genomic compartments. These findings have broadened our understanding of the taxonomic range and extent of RIP in Ascomycota and how this pathway affects the genomes of fungi harboring it.

scholarly journals Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Peter J. Maughan ◽  
Rebekah Lee ◽  
Rachel Walstead ◽  
Robert J. Vickerstaff ◽  
Melissa C. Fogarty ◽  
...  
Keyword(s):  
Diploid Species ◽  
Genetic Maps ◽  
Human Consumption ◽  
Past Century ◽  
Genome Wide ◽  
Species Analysis ◽  
Homoeologous Relationships ◽  
Species Specific ◽  
Nutritional Benefits ◽  
Genome Assemblies

Abstract Background Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat’s adaptive and food quality characteristics. Results The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species—including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. Conclusions The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.

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