4.1 Article

A new microsporidian parasite, Ordospora pajunii sp. nov (Ordosporidae), of Daphnia longispina highlights the value of genomic data for delineating species boundaries

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Sensitive protein alignments at tree-of-life scale using DIAMOND

Benjamin Buchfink et al.

Summary: We are at the beginning of a genomic revolution where all known species are planned to be sequenced. The improved version of DIAMOND allows for quick tree-of-life scale protein alignments.

NATURE METHODS (2021)

Article Evolutionary Biology

Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes

Karen L. Haag et al.

GENOME BIOLOGY AND EVOLUTION (2020)

Review Biotechnology & Applied Microbiology

Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences

D. Libkind et al.

FEMS YEAST RESEARCH (2020)

Article Microbiology

Delineating yeast species with genome average nucleotide identity: a calibration of ANI with haplontic, heterothallicMetschnikowiaspecies

Marc-Andre Lachance et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2020)

Article Evolutionary Biology

Species delimitation in the cyanolichen genus Rostania

Alica Kosuthova et al.

BMC EVOLUTIONARY BIOLOGY (2020)

Article Biochemistry & Molecular Biology

A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae

Luca Cornetti et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)

Article Multidisciplinary Sciences

A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus

Claude Lemieux et al.

NATURE COMMUNICATIONS (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Review Microbiology

Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy

Fernando Hayashi Sant'Anna et al.

CRITICAL REVIEWS IN MICROBIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution

Xuhua Xia

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemical Research Methods

MUMmer4: A fast and versatile genome alignment system

Guillaume Marcais et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Identification of microsporidia host-exposed proteins reveals a repertoire of rapidly evolving proteins

Aaron W. Reinke et al.

NATURE COMMUNICATIONS (2017)

Article Microbiology

A large-scale evaluation of algorithms to calculate average nucleotide identity

Seok-Hwan Yoon et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2017)

Article Microbiology

Fungal Diversity Revisited: 2.2 to 3.8 Million Species

David L. Hawksworth et al.

MICROBIOLOGY SPECTRUM (2017)

Review Genetics & Heredity

What Is Speciation?

B. Jesse Shapiro et al.

PLOS GENETICS (2016)

Review Ecology

More than a rabbit's tale - Encephalitozoon spp. in wild mammals and birds

Barbara Hinney et al.

INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE (2016)

Review Microbiology

Then and now: a systematic review of the systematics of prokaryotes in the last 80 years

Aharon Oren et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2014)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Review Microbiology

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

Jongsik Chun et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2014)

Article Microbiology

Taxonomic use of DNA G plus C content and DNA-DNA hybridization in the genomic age

Jan P. Meier-Kolthoff et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2014)

Article Multidisciplinary Sciences

Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites

Karen L. Haag et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemistry & Molecular Biology

Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia

Timothy Y. James et al.

CURRENT BIOLOGY (2013)

Article Evolutionary Biology

Reduction and Expansion in Microsporidian Genome Evolution: New Insights from Comparative Genomics

Sirintra Nakjang et al.

GENOME BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biotechnology & Applied Microbiology

Web Apollo: a web-based genomic annotation editing platform

Eduardo Lee et al.

GENOME BIOLOGY (2013)

Article Microbiology

Prokaryotic systematics in the genomics era

Xiao-Yang Zhi et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2012)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Multidisciplinary Sciences

Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites

Jean-Francois Pombert et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Mycology

Dating the molecular clock in fungi – how close are we?

Mary L. Berbee et al.

Fungal Biology Reviews (2010)

Article Multidisciplinary Sciences

Shifting the genomic gold standard for the prokaryotic species definition

Michael Richter et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Mycology

Microsporidia: a journey through radical taxonomical revisions

Nicolas Corradi et al.

Fungal Biology Reviews (2009)

Review Genetics & Heredity

Speciation in fungi

Tatiana Giraud et al.

FUNGAL GENETICS AND BIOLOGY (2008)

Article Multidisciplinary Sciences

A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi

Anastasios D. Tsaousis et al.

NATURE (2008)

Article Evolutionary Biology

Species concepts and species delimitation

Kevin De Queiroz

SYSTEMATIC BIOLOGY (2007)

Article Ecology

Inference of parasite local adaptation using two different fitness components

D. Refardt et al.

JOURNAL OF EVOLUTIONARY BIOLOGY (2007)

Article Biochemistry & Molecular Biology

RNAmmer:: consistent and rapid annotation of ribosomal RNA genes

Karin Lagesen et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Microbiology

Towards a genome-based taxonomy for prokaryotes

KT Konstantinidis et al.

JOURNAL OF BACTERIOLOGY (2005)