A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues.

Molecular Ecology Resources
Jocelyn P. ColellaMatthew MacManes

Abstract

High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked-read or "synthetic long-read" sequencing technologies, such as 10× Genomics, may provide a cost-effective alternative solution to assemble higher quality de novo genomes from degraded tissue samples. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four new deer mouse (Peromyscus spp.) genomes assembled using linked-read technology and four published genomes assembled from a single shotgun library. At a similar price-point, these approaches produce vastly different assemblies, with linked-read assemblies having overall higher contiguity and completeness, measured by larger N50 values and greater number of genes assembled, respectively. As a proof-of-concept, we used annotated genes from the four Peromyscus linked-read assemblies and eight additional rodent taxa to generate a phylogeny, which reconstructed the expected relationships among species with 100% support. A...Continue Reading

References

Feb 26, 1999·Journal of Biological Rhythms·B J Prendergast, D A Freeman
Apr 3, 2004·Genome Research·Paul HavlakRichard A Gibbs
Feb 25, 2005·Molecular Biology and Evolution·Juan C OpazoEnrique P Lessa
May 7, 2005·Proceedings. Biological Sciences·Eske Willerslev, Alan Cooper
Oct 21, 2005·Nature·Peter Andolfatto
Nov 9, 2007·Trends in Ecology & Evolution·Peter WandelerLukas F Keller
Nov 21, 2007·Genome Research·Brandi L CantarelMark Yandell
Mar 15, 2008·Genome Research·Jonathan ButlerDavid B Jaffe
Jun 2, 2009·Briefings in Bioinformatics·Mihai Pop
Sep 17, 2009·Molecular Phylogenetics and Evolution·M J HickersonA D Yoder
Jan 1, 2007·Journal of Mammalogy·Robert D BradleyC William Kilpatrick
May 8, 2010·Science·Richard E GreenSvante Pääbo
Nov 26, 2010·Nature Methods·Can AlkanEvan E Eichler
Jan 5, 2011·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Aaron N BrooksNitin S Baliga
Jul 28, 2011·Molecular Ecology Resources·Kevin C RoweCraig C Moritz
Sep 22, 2011·Heredity·Z A Cheviron, R T Brumfield
Sep 1, 2012·Science·Matthias MeyerSvante Pääbo
Oct 9, 2012·American Journal of Human Genetics·Menachem FromerShaun M Purcell
Jan 30, 2013·Nature Reviews. Genetics·Niranjan Nagarajan, Mihai Pop
Mar 19, 2013·Systematic Biology·Katerina GuschanskiVincent Savolainen
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach
Jul 3, 2013·Molecular Biology and Evolution·Emma C Teeling, S Blair Hedges
Jul 11, 2013·ELife·Ayelet VoskoboynikStephen R Quake
Oct 15, 2013·Molecular Ecology·Ke BiCraig Moritz
Dec 7, 2013·Nature·Matthias MeyerSvante Pääbo
Feb 25, 2014·Nature Biotechnology·Volodymyr KuleshovMichael Snyder
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Mar 19, 2015·Molecular Ecology Resources·Carly F GrahamChristopher M Somers
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Jul 4, 2015·Molecular Ecology·Matthew R Jones, Jeffrey M Good
Nov 12, 2015·Molecular Biology and Evolution·Gillian C GibbFrédéric Delsuc
Jan 13, 2016·Molecular Ecology·Michael W HolmesMichael W Nachman
Feb 2, 2016·Nature Biotechnology·Grace X Y ZhengHanlee P Ji
Mar 19, 2016·Journal of Mammalogy·Bryan S McLeanJoseph A Cook
May 18, 2016·Nature Reviews. Genetics·Sara GoodwinW Richard McCombie
May 27, 2016·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Diana MandelkerBirgit Funke
Nov 1, 2016·Nature Methods·Chen-Shan ChinMichael C Schatz
Dec 5, 2016·Trends in Genetics : TIG·Katya L Mack, Michael W Nachman
Feb 24, 2017·Current Opinion in Plant Biology·Wen-Biao Jiao, Korbinian Schneeberger

❮ Previous
Next ❯

Citations

Dec 17, 2020·Molecular Ecology Resources·Annabel WhibleyShawn R Narum
May 15, 2021·Genome Biology and Evolution·Emmanuel F A ToussaintNadir Alvarez
Aug 31, 2021·Trends in Ecology & Evolution·Christopher J Raxworthy, Brian Tilston Smith

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJEB33530

Methods Mentioned

BETA
for

Software Mentioned

orthofinder
TapeStation
assemblathon
iqtree
r package plotly
Circulomics
busco
maker

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.