A Near Chromosome Assembly of the Dromedary Camel Genome

Frontiers in Genetics
Daniil RuvinskiyMarta Farré

Abstract

The dromedary camel is an economically and socially important species of livestock in many parts of the world, being used for transport and the production of milk and meat. Much like cattle and horses, the camel may be found in industrial farming conditions as well as used in sporting. Camel racing is a multi-million dollar industry, with some specimens being valued at upward of 9.5 million USD. Despite its apparent value to humans, the dromedary camel is a neglected species in genomics. While cattle and other domesticated species have had much attention in terms of genome assembly, the camel has only been assembled to scaffold level, which does not give a clear indication of the order or chromosomal location of sequenced fragments. In this study, the Reference Assistant Chromosome Assembly (RACA) algorithm was implemented to use read-pair information of camel scaffolds, aligned with the cattle and human genomes in order to organize and orient these scaffolds in a near-chromosome level assembly. This method generated 72 large size fragments (N50 54.36 Mb). These predicted chromosome fragments (PCFs) were then compared with comparative maps of camel and cytogenetic map of alpaca chromosomes, allowing us to further upgrade the as...Continue Reading

References

Jun 7, 2000·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·A S GraphodatskyM A Ferguson-Smith
Sep 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·W James KentDavid Haussler
Feb 19, 2004·Nature Reviews. Genetics·Leif Andersson, Michel Georges
Aug 3, 2007·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Gabriel BalmusMalcolm A Ferguson-Smith
Apr 25, 2009·Science·UNKNOWN Bovine Genome Sequencing and Analysis ConsortiumFeng-Qi Zhao
Jul 15, 2009·Genome Research·Harris A LewinStephen J O'Brien
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Sep 18, 2010·Nature Reviews. Genetics·Matthew MeyersonGad Getz
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
Jan 6, 2011·Biopolymers·Robert K NeelyJohan Hofkens
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 26, 2012·Nucleic Acids Research·Andreas UntergasserSteven G Rozen
Jan 12, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jaebum KimJian Ma
May 29, 2013·Genome Biology·Martin HuntThomas D Otto
Jun 17, 2014·Bioinformatics·Mikhail KolmogorovSon Pham
Oct 22, 2014·Nature Communications·Huiguang WuJun Wang
Feb 11, 2015·Cytogenetic and Genome Research·Felipe AvilaTerje Raudsepp
Jun 4, 2015·Molecular Biology and Evolution·Peter D HeintzmanBeth Shapiro
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Jul 17, 2015·Molecular Ecology Resources·Robert R FitakPamela A Burger
Nov 7, 2015·Genomics, Proteomics & Bioinformatics·Anthony Rhoads, Kin Fai Au
Mar 5, 2016·Genome Medicine·Rachel L GoldfederEuan A Ashley
Jul 13, 2016·Genome Biology and Evolution·Marta FarréDenis M Larkin
Feb 13, 2018·Nature Biotechnology·Miten JainMatthew Loose
Mar 10, 2018·G3 : Genes - Genomes - Genetics·Carson HoltMichael D Shapiro

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRR1693817

Methods Mentioned

BETA
PCR
electrophoresis
Hi-C
HiC

Software Mentioned

Kent
HiC
Bowtie2
FastQC
Lastz
SRA
BLAT
UCSC Genome Browser
Primer3
Chromosome Assembly

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.