Split-alignment of genomes finds orthologies more accurately

Frith, Martin C.; Kawaguchi, Risa Karakida

doi:10.1186/s13059-015-0670-9

Cited by 110 publications

(105 citation statements)

References 45 publications

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Section: Resultsmentioning

confidence: 99%

“…Left (red): chicken chromosomes from the GRCg6a assembly; right (blue): guinea fowl chromosomes from the NumMel1.0 assembly. Alignment was done with the last software as described inFrith and Kawaguchi (2015) [Colour figure can be viewed at wileyonlinelibrary.com] per pool). However, Figures 4 and 5 indicate that these three populations are relatively homogeneous, so we considered them as a single group for this analysis, as well as the selection scans described below.First, this tree showed several hierarchical levels that were consistent with the PCA.…”

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confidence: 99%

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A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes

Vignal

Boitard

Thébault

et al. 2019

Molecular Ecology Resources

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The helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub‐Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2,000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Today, it is still farmed in Africa, mainly as a traditional village poultry, and is also bred more intensively in other countries, mainly France and Italy. The lack of available molecular genetic markers has limited the genetic studies conducted to date on guinea fowl. We present here a first‐generation whole‐genome sequence draft assembly used as a reference for a study by a Pool‐seq approach of wild and domestic populations from Europe and Africa. We show that the domestic populations share a higher genetic similarity between each other than they do to wild populations living in the same geographical area. Several genomic regions showing selection signatures putatively related to domestication or importation to Europe were detected, containing candidate genes, most notably EDNRB 2 , possibly explaining losses in plumage coloration phenotypes in domesticated populations.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes

Vignal

Boitard

Thébault

et al. 2019

Molecular Ecology Resources

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“…We test, to the best of our knowledge, all known approaches to quantify expression in polyploids with four approaches: 1. A standard genome alignment based RNA-seq analysis on the full allopolyploid reference genome with two different alignment tools STAR [20] and LAST [21,22]. [23] on the full allopolyploid transcriptome.…”

Section: Introductionmentioning

confidence: 99%

Homeolog expression quantification methods for allopolyploids

Kuo¹,

Hatakeyama

Tameshige

et al. 2018

Preprint

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Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi, and plants, and is especially common in crop plants. There is increasing interest in the study of allopolyploids due to advances in polyploid genome assembly, however the high level of sequence similarity in duplicated gene copies (homeologs) pose many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (> 10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (< 1% using EAGLE-RC, < 2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method. In general, disagreement in low expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision.

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“…The core algorithm MetaG uses LAST (Kiełbasa et al 2011) to compare the user's query reads to a database. Optionally, ambiguous alignments are filtered using LAST-SPLIT (Frith and Kawaguchi 2015 filtered based on user-given settings (see Figure 1). After removing alignments with too high e-values, the alignment scores per query read are analyzed (see Figure 1).…”

Section: Resultsmentioning

confidence: 99%

MetaGenomic analysis of short and long reads

Manske¹,

Grundmann²,

Makałowski³

2020

Preprint

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Identifying single organisms in environmental samples is one of the key tasks of metagenomics.During the last few years, third generation sequencing technologies have enabled researchers to sequence much longer molecules, but at the expense of sequencing accuracy. Thus, new algorithms needed to be developed to cope with this new type of data. With this in mind, we developed a tool called MetaG. An intuitive web interface makes the software accessible to a vast range of users, including those without extensive bioinformatic expertise. Evaluation of MetaG's performance showed that it makes nearly perfect classifications of viral isolates using simulated short and long reads.MetaG also outperformed current state-of-the-art algorithms on data from targeted sequencing of the 16S and 28S rRNA genes. Since MetaG's output is also supplemented with information about hosts and antibiotic resistances of pathogens, we expect it to be especially useful to the healthcare sector.Moreover, the outstanding accuracy of the taxonomic assignments will make MetaG a serious alternative for anyone working with metagenomic sequences. MetaG can be accessed at

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Split-alignment of genomes finds orthologies more accurately

Cited by 110 publications

References 45 publications

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes

Homeolog expression quantification methods for allopolyploids

MetaGenomic analysis of short and long reads

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