2
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.

          Related collections

          Most cited references92

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Fast and accurate short read alignment with Burrows–Wheeler transform

          Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

              Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
                Bookmark

                Author and article information

                Journal
                Microb Genom
                Microb Genom
                mgen
                mgen
                Microbial Genomics
                Microbiology Society
                2057-5858
                2021
                24 December 2021
                24 December 2021
                : 7
                : 12
                Affiliations
                [ 1] departmentDepartment of Parasitology , Faculty of Science, Charles University, BIOCEV, Průmyslová 595 , 252 42 Vestec, Czech Republic
                [ 2] departmentInstitute of Evolutionary Biology , Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw , Warsaw, Poland
                Author notes
                *Correspondence: Sebastian Cristian Treitli, sebastian.treitli@ 123456yahoo.com
                *Correspondence: Vladimír Hampl, vlada@ 123456natur.cuni.cz
                Article
                000745
                10.1099/mgen.0.000745
                8767320
                34951395
                c68fbb93-55b8-4c2e-ae37-e3b9b2af53a8
                © 2021 The Authors

                This is an open-access article distributed under the terms of the Creative Commons Attribution License.

                Product
                Funding
                Funded by: European Molecular Biology Organization
                Award Recipient : AnnaKarnkowska
                Funded by: H2020 European Research Council
                Award ID: 771592
                Award Recipient : VladimirHampl
                Categories
                Research Articles
                Genomic Methodologies
                Custom metadata
                0

                monocercomonoides,amitochondriate,genome,nanopore
                monocercomonoides, amitochondriate, genome, nanopore

                Comments

                Comment on this article