A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence

Prasad, Arjun B.; Mullikin, James C.; Program, Nisc Comparative Sequencing; Green, Eric D.

doi:10.1016/j.ympev.2012.11.023

Cited by 3 publications

(4 citation statements)

References 65 publications

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“…SNPs are becoming increasingly important in establishing source identity of introgressions (Paraskevis et al, 2005;Huang et al, 2009;Anderson et al, 2011;Austin et al, 2011;Prasad et al, 2013;V ıquez-Zamora et al, 2013;Chen et al, 2014). Plant genomes, also those of crop species, contain massive amounts of SNPs in their gene pools.…”

Section: Discussionmentioning

confidence: 99%

“…Any General Feature Format (GFF) file containing segmentation information can be used, such as coordinates of CDSs, genes, exons or QTLs. If no particular segmentation pattern is specified, the reference genome FASTA file may be used to create a GFF file containing a userdefined, evenly spaced, segmentation pattern (Huang et al, 2009;Anderson et al, 2011;Prasad et al, 2013;Chen et al, 2014;, Liu et al, 2014. The resulting GFF is then used to split the VCF files into the desired segments, as consecutive windows, sliding windows, or any arbitrary filtering from the annotation file of the reference genome such as CDS, genes, exons, introns, etc.…”

Section: The Back-endmentioning

confidence: 99%

“…Several methods to visualize such whole-genome SNP (wgSNP) data have been presented (Posada, 2002;Martin et al, 2011;Lechat et al, 2013;Kim et al, 2014) including software packages such as VISRD (Strimmer et al, 2003), SHOREMAP (Schneeberger et al, 2009), RECOMBINE (Anderson et al, 2011), NGM (Austin et al, 2011), PARTFINDER (Prasad et al, 2013) and PHYLONET-HMM . SHOREMAP and NGM focus on identifying causal SNPs for phenotypes in segregating populations.…”

Section: Introductionmentioning

confidence: 99%

“…The examination of Genome-wide Single Nucleotide Polymorphisms (SNPs) is an alternative strategy that becomes increasingly attractive for disclosing genome organization and topological context of target genes underlying agronomically important traits. Several methods to visualize such whole-genome SNP (wgSNP) data have been presented (Posada, 2002;Martin et al, 2011;Lechat et al, 2013; including software packages such as VISRD (Strimmer et al, 2003), SHOREMAP (Schneeberger et al, 2009), RECOMBINE (Anderson et al, 2011), NGM (Austin et al, 2011), PARTFINDER (Prasad et al, 2013) and PHYLONET-HMM (Liu et al, 2014). SHOREMAP and NGM focus on identifying causal SNPs for phenotypes in segregating populations.…”

Section: Introductionmentioning

confidence: 99%

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Introgression browser: high‐throughput whole‐genome SNP visualization

et al. 2015

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SUMMARYBreeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (IBROWSER), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, multi-nucleotide polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the IBROWSER in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of IBROWSER makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes IBROWSER a valuable breeding tool.

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Section: Discussionmentioning

confidence: 99%

Section: The Back-endmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Introgression browser: high‐throughput whole‐genome SNP visualization

et al. 2015

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Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory

Cutter

2013

Molecular Phylogenetics and Evolution

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Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae)

Ilves

Torti

López‐Fernández

2018

Molecular Phylogenetics and Evolution

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The phenotypic, geographic, and species diversity of cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia (Oreochromis niloticus) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome.

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A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence

Cited by 3 publications

References 65 publications

Introgression browser: high‐throughput whole‐genome SNP visualization

Introgression browser: high‐throughput whole‐genome SNP visualization

Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory

Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae)

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