Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex

BMC Evolutionary Biology
Nicole L GarrisonJ E Bond

Abstract

Mygalomorph spiders represent a diverse, yet understudied lineage for which genomic level data has only recently become accessible through high-throughput genomic and transcriptomic sequencing methods. The Aptostichus atomarius species complex (family Euctenizidae) includes two coastal dune endemic members, each with inland sister species - affording exploration of dune adaptation associated patterns at the transcriptomic level. We apply an RNAseq approach to examine gene family conservation across the species complex and test for patterns of positive selection along branches leading to dune endemic species. An average of ~ 44,000 contigs were assembled for eight spiders representing dune (n = 2), inland (n = 4), and atomarius species complex outgroup taxa (n = 2). Transcriptomes were estimated to be 64% complete on average with 77 spider reference orthologs missing from all taxa. Over 18,000 orthologous gene clusters were identified within the atomarius complex members, > 5000 were detected in all species, and ~ 4700 were shared between species complex members and outgroup Aptostichus species. Gene family analysis with the FUSTr pipeline identified 47 gene families appearing to be under selection in the atomarius ingroup; four...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
Jun 18, 2002·Science·Niall G HowlettAlan D D'Andrea
Aug 16, 2003·The Journal of Heredity·T R Gregory, D P Shorthouse
May 7, 2005·Evolution & Development·Austin L Hughes, Robert Friedman
Jun 21, 2006·DNA Repair·Allan M Gurtan, Alan D D'Andrea
Apr 25, 2007·Nucleic Acids Research·Karin LagesenDavid W Ussery
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Apr 21, 2009·Molecular Biology and Evolution·Morgan N PriceAdam P Arkin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Apr 26, 2011·BMC Bioinformatics·Vincent MieleLaurent Duret
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
May 20, 2011·Nucleic Acids Research·Robert D FinnSean R Eddy
Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
Nov 10, 2011·Toxins·Natalie J SaezGlenn F King
Nov 15, 2011·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Dec 1, 2011·Nucleic Acids Research·Marco PuntaRobert D Finn
Aug 23, 2012·Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology·Leanda D MasonBarbara Y Main
Oct 2, 2012·Annual Review of Entomology·Glenn F King, Margaret C Hardy
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Oct 12, 2013·Bioinformatics·Ole Kristian EksethVladimir Mironov
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
May 8, 2014·Nature Communications·Kristian W SanggaardJun Wang
Jan 17, 2015·Cell·Anderson T Wang, Agata Smogorzewska
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Mar 1, 2016·PeerJ·Nicole L GarrisonJason E Bond
Jun 3, 2016·Genome Research·Richard Smith-UnnaSteven Kelly
Jun 10, 2016·Evolutionary Bioinformatics Online·Edward C StanleySteven Q Irvine
Jul 21, 2016·Current Opinion in Insect Science·David K YeatesAndreas Zwick
Mar 7, 2017·Nature Methods·Rob PatroCarl Kingsford
Jun 13, 2017·Current Biology : CB·Martin SchwentnerGonzalo Giribet

❮ Previous
Next ❯

Methods Mentioned

BETA
458
RNAseq
electrophoresis

Software Mentioned

OrthoFinder
SNAP ( Scalable Nucleotide Alignment Program )
Trimmomatic
Trinotate
SiLix
Aliscore
HMMER
CyVerse Discovery Platform
COATS
mafft

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.