MeDuSa: a multi-draft based scaffolder
Emanuele Bosi,Beatrice Donati,Marco Galardini,Sara Brunetti,Marie-France Sagot,Pietro Liò,Pierluigi Crescenzi,Renato Fani,Marco Fondi +8 more
TLDR
MeDuSa formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it, which does not require either prior knowledge on the microrganisms dataset under analysis or the availability of paired end read libraries.Abstract:
Completing the genome sequence of an organism is an important task in comparative, functional and structural genomics. However, this remains a challenging issue from both a computational and an experimental viewpoint. Genome scaffolding (i.e. the process of ordering and orientating contigs) of de novo assemblies usually represents the first step in most genome finishing pipelines. In this paper, we present MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combinatorial optimisation formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries. This makes usability and running time two additional important features of our method. Moreover, benchmarks and tests on real bacterial datasets showed that MeDuSa is highly accurate and, in most cases, outperforms traditional scaffolders. The possibility to use MeDuSa on eukaryotic datasets has also been evaluated, leading to interesting results. MeDuSa web server: http://combo.dbe.unifi.it/medusa A stand-alone version of the software can be downloaded from https://github.com/combogenomics/medusa/releases. All results presented in this work have been obtained with MeDuSa v. 1.3. marco.fondi@unifi.it.read more
Citations
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Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira
Alejandro Palomo,Anders Gorm Pedersen,Jane Fowler,Arnaud Dechesne,Thomas Sicheritz-Pontén,Barth F. Smets +5 more
TL;DR: The authors' analyses indicate that several genes belonging to the ammonia oxidation pathway could have been laterally transferred from β-AOB to comammox Nitrospira, and postulate that the absence ofcomammox genes in other sublineage II Nitro Spira genomes is the result of subsequent loss.
Journal ArticleDOI
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology
Sandra Wiegand,Mareike Jogler,Christian Boedeker,Daniela Pinto,John Vollmers,Elena Rivas-Marín,Timo Kohn,Stijn H Peeters,Anja Heuer,Patrick Rast,Sonja Oberbeckmann,Boyke Bunk,Olga Jeske,Anke Meyerdierks,Julia E. Storesund,Nicolai Kallscheuer,Sebastian Lücker,Olga Maria Lage,Thomas Pohl,Broder J. Merkel,Peter Hornburger,Ralph Walter Müller,Franz Brümmer,Matthias Labrenz,Alfred M. Spormann,Huub J. M. Op den Camp,Jörg Overmann,Rudolf Amann,Mike S. M. Jetten,Thorsten Mascher,Marnix H. Medema,Damien P. Devos,Anne-Kristin Kaster,Lise Øvreås,Manfred Rohde,Michael Y. Galperin,Christian Jogler,Christian Jogler +37 more
TL;DR: Diversity-driven cultivation, characterization and genome sequencing of 79 bacterial strains from all major taxonomic clades of the conspicuous bacterial phylum Planctomycetes are reported, identified previously unknown modes of bacterial cell division and illustrated how ‘microbial dark matter’ can be accessed by cultivation techniques, expanding the organismic background for small-molecule research and drug-target detection.
Journal ArticleDOI
The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism
Xiaohan Yang,Xiaohan Yang,Rongbin Hu,Hengfu Yin,Jerry Jenkins,Shengqiang Shu,Haibao Tang,Degao Liu,Deborah Weighill,Deborah Weighill,Won Cheol Yim,Jungmin Ha,Karolina Heyduk,David Goodstein,Hao-Bo Guo,Robert C. Moseley,Robert C. Moseley,Elisabeth Fitzek,Sara S. Jawdy,Zhihao Zhang,Meng Xie,James Hartwell,Jane Grimwood,Paul E. Abraham,Ritesh Mewalal,Juan D. Beltrán,Susanna F. Boxall,Louisa V. Dever,Kaitlin J. Palla,Kaitlin J. Palla,Rebecca L. Albion,Travis M. Garcia,Jesse A. Mayer,Sung Don Lim,Ching Man Wai,Paul Peluso,Robert Van Buren,Henrique Cestari De Paoli,Henrique Cestari De Paoli,Anne M. Borland,Anne M. Borland,Hong Guo,Jin-Gui Chen,Wellington Muchero,Yanbin Yin,Daniel Jacobson,Daniel Jacobson,Timothy J. Tschaplinski,Robert L. Hettich,Ray Ming,Ray Ming,Klaus Winter,Jim Leebens-Mack,J. Andrew C. Smith,John C. Cushman,Jeremy Schmutz,Gerald A. Tuskan +56 more
TL;DR: Evidence is provided for convergent evolution of protein sequence and temporal gene expression underpinning the multiple independent emergences of CAM through genomic analysis of Kalanchoë fedtschenkoi.
Journal ArticleDOI
Insights into the Evolution of Multicellularity from the Sea Lettuce Genome
Olivier De Clerck,Shu-Min Kao,Kenny A. Bogaert,Jonas Blomme,Fatima Foflonker,Michiel Kwantes,Emmelien Vancaester,Lisa Vanderstraeten,Eylem Aydogdu,Jens Boesger,Gianmaria Califano,Bénédicte Charrier,Rachel Clewes,Andrea Del Cortona,Sofie D'hondt,Noe Fernandez-Pozo,Claire M. M. Gachon,Marc Hanikenne,Linda Lattermann,Frederik Leliaert,Xiaojie Liu,Christine A. Maggs,Zoë A. Popper,John A. Raven,Michiel Van Bel,Per K.I. Wilhelmsson,Debashish Bhattacharya,Juliet C. Coates,Stefan A. Rensing,Dominique Van Der Straeten,Assaf Vardi,Lieven Sterck,Klaas Vandepoele,Yves Van de Peer,Thomas Wichard,John H. F. Bothwell +35 more
TL;DR: The sequenced genome of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds, offers new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage.
Journal ArticleDOI
From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules.
TL;DR: The results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomers, and provides the necessary starting point to explore planctomyCetal small molecules for drug development.
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