Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data

Abstract

BackgroundWhole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling.ResultsNorgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers.ConclusionNorgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1927-y) contains supplementary material, which is available to authorized users.

Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species

“…A plethora of mitochondrial assembly tools are available, but these generally rely on gDNA or Sanger-derived reads, rather than those sourced from RNA-seq experiments. Programs such as Norgal (Al-Nakeeb, Petersen, & Sicheritz-Pontén, 2017), MitoBIM (Hahn, Bachmann, & Chevreux, 2013) and NOVOPlasty (Dierckxsens, Mardulyn, & Smits, 2016) have proven useful at recovering mitogenome assemblies, particularly when the sequence of a closely related species is available for use as a map for assembly. Increasingly sophisticated tools are available for using gDNA for assembly (Schomaker-Bastos & Prosdocimi, 2018).…”

TERAD: Extraction of transposable element composition from RADseq data

“…We performed unsupervised quality trimming on raw reads using UrQt (Modolo & Lerat, ) and removed mitochondrial DNA using Norgal (Al‐Nakeeb, Petersen, & Sicheritz‐Pontén, ). We used dnaPipeTE (Goubert et al, ) to estimate TEs in the LC‐WGS data.…”

SMART: Statistical Mitogenome Assembly with Repeats

“…Mitochondrial DNA can be experimentally separated from the nuclear DNA and sequenced independently but such protocols are laborious [6]. More commonly, the mitogenomes are assembled from Whole Genome Sequencing (WGS) data, which consists of reads generated from both the nuclear and mitochondrial genomes [6].…”

“…Mitochondrial DNA can be experimentally separated from the nuclear DNA and sequenced independently but such protocols are laborious [6]. More commonly, the mitogenomes are assembled from Whole Genome Sequencing (WGS) data, which consists of reads generated from both the nuclear and mitochondrial genomes [6]. Unfortunately, assembling WGS data with standard de novo assemblers often fails to generate high quality mitochondrial genome sequences due to the large difference in copy number (and hence sequencing depth) between the mitochondrial and nuclear genomes [7].…”

“…However, due to their inherently greedy ap-proach, seed-and-extend methods have difficulty handling repetitive regions present in some mitochondrial genomes [5]. Norgal [6] is a recent tool implementing a de novo approach to mitochondrial genome reconstruction from WGS data, without the need for either a reference or a seed sequence. A similar approach is used by plasmidSPAdes [13] for de novo assembly of circular plasmid genomes from WGS data.…”