Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

Genome Biology
Lakshmipuram Seshadri SwapnaJohn Parkinson

Abstract

In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations. In this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic functional annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that the TRAF gene family has been greatly expanded in planarians. We further provide a single-cell RNA sequencing analysis of 2000 cells, revealing both known and novel cell types defined by unique signatures of gene expression. Among these are a novel mesenchymal cel...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Feb 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·A F Smit, A D Riggs
Oct 3, 1998·Trends in Biochemical Sciences·A H ChishtiK B Hoover
Apr 16, 1999·The Journal of Nutrition·L B Bailey, J F Gregory
Mar 20, 2001·Nature Reviews. Molecular Cell Biology·U TepassM Peifer
Oct 19, 2001·Oncogene·J R Bradley, J S Pober
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Jul 18, 2002·American Journal of Physiology. Gastrointestinal and Liver Physiology·Guillaume van Niel, Martine Heyman
Aug 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Phillip A NewmarkAlejandro Sánchez Alvarado
Nov 7, 2003·Nucleic Acids Research·Clotilde Claudel-RenardDaniel Kahn
Oct 12, 2004·Annual Review of Cell and Developmental Biology·Peter W Reddien, Alejandro Sánchez Alvarado
Dec 2, 2004·BMC Bioinformatics·James D Wasmuth, Mark L Blaxter
Jan 28, 2006·Cell·Alejandro Sánchez Alvarado
Dec 15, 2006·BMC Genomics·Adrian K ArakakiJeffrey Skolnick
May 29, 2007·Nucleic Acids Research·Yuki MoriyaMinoru Kanehisa
Nov 7, 2007·Nature Reviews. Genetics·Thomas WickerAlan H Schulman
Dec 13, 2007·Nucleic Acids Research·Derek WilsonSarah A Teichmann
Dec 14, 2007·Annual Review of Genetics·Cédric Feschotte, Ellen J Pritham
Apr 3, 2008·Proceedings of the National Academy of Sciences of the United States of America·Daisuke D IkedaYuichi Iino
May 15, 2008·Nucleic Acids Research·Shujiro OkudaMinoru Kanehisa
Nov 22, 2008·Cold Spring Harbor Symposia on Quantitative Biology·P A NewmarkT Chong
Jan 24, 2009·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Bret J PearsonAlejandro Sánchez Alvarado
Apr 21, 2009·Methods in Molecular Biology·Stéphane GuindonOlivier Gascuel
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Salvador Capella-GutiérrezToni Gabaldón
Nov 7, 2009·Nucleic Acids Research·Gabriel OstlundErik L L Sonnhammer
Feb 17, 2010·Journal of Biology·Marco Gallo, Donald L Riddle
Dec 15, 2010·Trends in Parasitology·Stacy S Hung, John Parkinson
Jan 5, 2011·BMC Genomics·Josep F AbrilEmili Saló
May 10, 2011·Experimental Gerontology·Stijn MoutonBart P Braeckman
Aug 19, 2011·Genome Biology·Thomas SandmannKerstin Bartscherer
Nov 15, 2011·Nature Biotechnology·Piero DalerbaStephen R Quake
Oct 13, 2012·Bioinformatics·Limin FuWeizhong Li
Nov 10, 2012·Development Genes and Evolution·Jochen C Rink
Nov 14, 2012·Annual Review of Genetics·Cheng Ran Lisa HuangJef D Boeke
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner

❮ Previous
Next ❯

Citations

Apr 3, 2020·ELife·David J ForsthoefelPhillip A Newmark
Apr 2, 2020·Biological Chemistry·Iana V KimClaus-D Kuhn
Apr 10, 2019·Nature Communications·Lauren E CotePeter W Reddien
Feb 6, 2020·International Journal of Molecular Sciences·Paul G BarghouthNéstor J Oviedo
Apr 17, 2021·Proceedings of the National Academy of Sciences of the United States of America·Andy ChanDanny Chan
Dec 24, 2020·Molecular Biology and Evolution·Jules DuruzSimon G Sprecher
Oct 17, 2020·The FEBS Journal·Mallory Wiggans, Bret J Pearson
Jun 4, 2021·Frontiers in Molecular Biosciences·Susanne HoltzeArne Sahm
Sep 10, 2021·Glycobiology·Sabarinath Peruvemba SubramanianRamaswamy Subramanian

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA215411
GSE115280

Methods Mentioned

BETA
scRNAseq
amputation
RNAseq
single-cell sequencing
RNA-seq
fluorescence-activated cell sorting
Drop-seq

Software Mentioned

ESTScan
Ensembl
Pathway and
European Molecular Biology Open Software Suite ( EMBOSS )
R
ProDom
R package Seurat
PhyML
KEGG
BLASTP

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.