Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution

BMC Evolutionary Biology
Russell J S OrrKamran Shalchian-Tabrizi

Abstract

The class Diphyllatea belongs to a group of enigmatic unicellular eukaryotes that play a key role in reconstructing the morphological innovation and diversification of early eukaryotic evolution. Despite its evolutionary significance, very little is known about the phylogeny and species diversity of Diphyllatea. Only three species have described morphology, being taxonomically divided by flagella number, two or four, and cell size. Currently, one 18S rRNA Diphyllatea sequence is available, with environmental sequencing surveys reporting only a single partial sequence from a Diphyllatea-like organism. Accordingly, geographical distribution of Diphyllatea based on molecular data is limited, despite morphological data suggesting the class has a global distribution. We here present a first attempt to understand species distribution, diversity and higher order structure of Diphyllatea. We cultured 11 new strains, characterised these morphologically and amplified their rRNA for a combined 18S-28S rRNA phylogeny. We sampled environmental DNA from multiple sites and designed new Diphyllatea-specific PCR primers for long-read PacBio RSII technology. Near full-length 18S rRNA sequences from environmental DNA, in addition to supplementary...Continue Reading

References

May 16, 1998·Genome Research·D GordonP Green
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Apr 10, 2004·Bioinformatics·Thomas HuberPhilip Hugenholtz
Nov 13, 2004·Bioinformatics·Michael D GadberryElizabeth A Kellogg
Nov 17, 2004·International Journal of Systematic and Evolutionary Microbiology·David Bass, Thomas Cavalier-Smith
Sep 8, 2006·Applied and Environmental Microbiology·Kevin E AshelfordAndrew J Weightman
Apr 25, 2007·Nucleic Acids Research·Warren A Kibbe
Oct 16, 2007·Bioinformatics·Damien M de VienneOlivier C Martin
Aug 17, 2010·Bioinformatics·Robert C Edgar
Mar 1, 2009·The Journal of Eukaryotic Microbiology·Marianne Potvin, Connie Lovejoy
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Feb 10, 2012·Molecular Biology and Evolution·Sen ZhaoKamran Shalchian-Tabrizi
Jul 4, 2012·Nature Biotechnology·Sergey Koren Adam M Phillippy
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Jul 17, 2013·Ecotoxicology and Environmental Safety·Zakaria A Mohamed, Abdultahman M Al-Shehri
Aug 27, 2013·Molecular Phylogenetics and Evolution·Sen ZhaoDag Klaveness
Aug 30, 2013·Proceedings. Biological Sciences·Matthew W BrownAndrew J Roger
Jan 24, 2014·Microbiome·Erin B Fichot, R Sean Norman
Apr 8, 2014·Current Biology : CB·Ramiro LogaresRamon Massana
Apr 30, 2015·PloS One·Michael A RuggieroPaul M Kirk
May 23, 2015·Science·Colomban de VargasEric Karsenti
Dec 15, 2015·FEMS Microbiology Ecology·Rebecca C MuellerCheryl R Kuske
Feb 18, 2016·Scientific Reports·Thomas W LaverMichael N Weedon
Jul 9, 2016·PloS One·Asma AsemaninejadR Greg Thorn
Feb 6, 2017·Journal of Microbiological Methods·Bethan M Jones, Adam B Kustka
Mar 30, 2017·BMC Microbiology·Ismail M Al-BulushiAbdullah M Al-Sadi

❮ Previous
Next ❯

Citations

Jun 5, 2020·The Journal of Eukaryotic Microbiology·Luciana SantoferraraGeorge B McManus
Mar 23, 2021·Frontiers in Microbiology·Kasia PiwoszKarel Šimek
Oct 13, 2021·Current Biology : CB·Fabien BurkiMahwash Jamy

❮ Previous
Next ❯

Datasets Mentioned

BETA
JF775022

Methods Mentioned

BETA
PCR
PCRs
electron microscopy

Software Mentioned

PacBio RS
MAFFT add
MAFFT
PacBio Sequel confirming
Primaclade
Uchime
CLC main workbench
Phrap
Phred
OligoCalc

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.