dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

Safonova, Yana; Pevzner, Pavel A.

doi:10.1089/cmb.2014.0153

Cited by 72 publications

(53 citation statements)

References 22 publications

(33 reference statements)

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“…We tested the following assemblers: ABySS [53] , MaSuRCA [20] , Meraculous-2D [28] , SOAPdenovo2 [49] , SPAdes [54] / dipSPAdes [55] , and Velvet [56] . The resulting assemblies were evaluated using a number of metrics, including contiguity statistics, REAPR [44] , Feature Response Curves ( FRC bam ) [57] , BUSCO assessments [34,35] , and the scrutiny of individual enhancer sequences.…”

Section: Choosing An Assemblermentioning

confidence: 99%

Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): A resource for testing evolutionary hypotheses

Bronski

Martinez

Weld

2019

Preprint

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Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich Drosophila montium species group, 22 of which are presented here for the first time. The montium group is uniquely positioned for comparative studies. Within the montium clade, evolutionary distances are such that large numbers of sequences can be accurately aligned while also recovering strong signals of divergence; and the distance between the montium group and D. melanogaster is short enough so that orthologous sequence can be readily identified. All genomes were assembled from a single, small-insert library using MaSuRCA, before going through an extensive post-assembly pipeline. Estimated genome sizes within the montium group range from 155 Mb to 223 Mb (mean=196 Mb). The absence of long-distance information during the assembly process resulted in fragmented assemblies, with the scaffold NG50s varying widely based on repeat content and sample heterozygosity (min=18 kb, max=390 kb, mean=74 kb). The total scaffold length for most assemblies is also shorter than the estimated genome size, typically by 5 -15 %. However, subsequent analysis showed that our assemblies are highly complete. Despite large differences in contiguity, all assemblies contain at least 96 % of known single-copy Dipteran genes (BUSCOs, n=2,799). Similarly, by aligning our assemblies to the D. melanogaster genome and remapping coordinates for a large set of transcriptional enhancers (n=3,457), we showed that each montium assembly contains orthologs for at least 91 % of D. melanogaster enhancers. Importantly, the genic and enhancer contents of our assemblies are comparable to that of far more contiguous Drosophila assemblies. The alignment of our own D. serrata assembly to a previously published PacBio D. serrata assembly also showed that our longest scaffolds (up to 1 Mb) are free of large-scale misassemblies. Our genome assemblies are a valuable resource that can be used to further resolve the montium group phylogeny; study the evolution of protein-coding genes and cis -regulatory sequences; and determine the genetic basis of ecological and behavioral adaptations.

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Section: Choosing An Assemblermentioning

confidence: 99%

Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): A resource for testing evolutionary hypotheses

Bronski

Martinez

Weld

2019

Preprint

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“…This is explained by the pooling of individuals that tends to dilute less frequent heterozygous alleles and thus lowers the first peak. The paired-end reads were assembled with DIP-SPADES 3.5 (Safonova, Bankevich, & Pevzner, 2015) using the -diploid option of the program that merges homologous contigs into one single contig. Contigs over 500 bp were selected for scaffolding by integration of the three Nextera libraries using BESST 1.3.7 (Sahlin, Vezzi, Nystedt, Lundeberg, & Arvestad, 2014) with default parameters.…”

Section: Genome Assemblymentioning

confidence: 99%

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

et al. 2017

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In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation and development, including genes coding Lin12-Notch-repeat (LNR) domain proteins. The Oithona biogeography based on 28S sequences and metagenomic reads from the Tara Oceans expedition showed the presence of O. nana mostly in the Mediterranean Sea (MS) and confirmed the amphitropical distribution of Oithona similis. The population genomics analyses of O. nana in the Northern MS, integrating the Tara Oceans metagenomic data and the O. nana genome, led to the identification of genetic structure between populations from the MS basins. Furthermore, 20 loci were found to be under positive selection including four missense and eight synonymous variants, harbouring soft or hard selective sweep patterns. One of the missense variants was localized in the LNR domain of the coding region of a male-specific gene. The variation in the B-allele frequency with respect to the MS circulation pattern showed the presence of genomic clines between O. nana and another undefined Oithona species possibly imported through Atlantic waters. This study provides new approaches and results in zooplankton population genomics through the integration of metagenomic and oceanographic data.

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“…We used an array of k-mer values to aide in merging orthologous contigs resulting from different k-mer sizes. We further assembled contigs using the DIPSPADES (Safonova et al, 2015) function to better assemble exons and orthologous regions by generating a consensus sequence from both orthologous and haplotype regions. The dedupe.sh script (part of BBMap/BBTools; http://sourceforge.net/projects/bbmap/) was used to remove near exact duplicates and pblat (Kent, 2002;Meng, 2018) was used to match samples to targeted reference loci with a tile size set to eight and minimum sequence identity set to 60.…”

Section: Uces Assembly Probe Matching Alignment and Trimmingmentioning

confidence: 99%

Parachute geckos free fall into synonymy:Gekkophylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements

Wood

Guo

Travers

et al. 2019

Preprint

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Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread "generalist" clades. This is especially true in the Australasia, where the monophyly of Gekko proper has been questioned with respect to phenotypically ornate flaplegged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately "derived" parachute geckos of the genus Ptychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyzed multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme was designed to address four persistent systematic questions in this group: (1) Are Luperosaurus and Ptychozoon monophyletic and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesi's L. iskandari as sister to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not related to Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our final, well-supported topologies, we recognize seven newly defined subgenera to accommodate ∼ 60 species within the more broadly defined and maximally-inclusive Australasian genus Gekko. The newly defined subgenera will aide taxonomists and systematists in species descriptions by allowing them to only diagnose putatively new species from the most relevant members of the same subgenus, not necessarily the phenotypically variable genus Gekko as a whole, and we argue that it appropriately recognizes geographically circumscribed units (e.g., a new subgenus for a novel clade, entirely endemic to the Philippines) while simultaneously recognizing several of the most systematically controversial, phenotypically distinct, and phylogenetically unique lineages. An added benefit of recognizing the most inclusive definition of Gekko, containing m...

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dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

Cited by 72 publications

References 22 publications

Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): A resource for testing evolutionary hypotheses

Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): A resource for testing evolutionary hypotheses

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

Parachute geckos free fall into synonymy:Gekkophylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements

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