High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing.

Genes
Christian SiadjeuBernd Weisshaar

Abstract

Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9941 non-coding RNA genes were predicted, and functional annotations were assigned.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 11, 2011·Bioinformatics·Oliver KellerStephan Waack
Jan 11, 2011·Bioinformatics·Guillaume Marçais, Carl Kingsford
Sep 7, 2013·Bioinformatics·Eric P Nawrocki, Sean R Eddy
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
Jan 15, 2015·Genome Biology·Haibao TangJianguo Lu
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Mar 2, 2016·Genome Biology·Jonathan F WendelRod A Wing
Jun 9, 2016·Bioinformatics·Leena SalmelaEsko Ukkonen
Nov 20, 2016·The Plant Journal : for Cell and Molecular Biology·Chia-Yi ChengChristopher D Town
Jan 20, 2017·Genome Research·Robert VaserMile Šikić
Apr 4, 2017·Bioinformatics·Gregory W VurtureMichael C Schatz
Nov 8, 2017·Nucleic Acids Research·Ioanna KalvariAnton I Petrov
Feb 9, 2018·Nature Communications·Todd P MichaelJoseph R Ecker
May 12, 2018·Bioinformatics·Heng Li
May 26, 2018·Scientific Reports·Valentino RuggieriJordi Garcia-Mas
Jan 10, 2019·GigaScience·Pirita PaajanenMatthew D Clark
Feb 21, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Fabien CormierGemma Arnau
Nov 16, 2019·Genome Biology·David M Emms, Steven Kelly
Mar 20, 2020·Nature Communications·T Rhyker Ranallo-BenavidezMichael C Schatz

❮ Previous
Next ❯

Citations

May 28, 2020·Journal of Experimental Botany·Kathryn DumschottBjörn Usadel
Sep 20, 2020·Foods·Jude E ObidiegwuCynthia A Chilaka
Sep 23, 2020·Planta·Janina Epping, Natalie Laibach
Dec 22, 2020·Molecular Plant·Chu-Yu Ye, Longjiang Fan
Jan 25, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sandra Ndagire KamenyaDamaris Achieng Odeny
Nov 20, 2020·Plants·Tommaso DanelliRoberto Pilu

❮ Previous
Next ❯

Datasets Mentioned

BETA
ERP118030

Methods Mentioned

BETA
PCR

Software Mentioned

Smudgeplot
MEM
BLASTp
BLAST
GridION
INFERNAL ( cmscan )
RepeatMasker
Canu
BUSCO
GenomeScope

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.