Dramatic improvement in genome assembly achieved using doubled-haploid genomes

Scientific Reports
Hong ZhangShuichi Asakawa

Abstract

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

References

Dec 11, 1999·Nature·I DunhamK P O'Brien
Jul 27, 2002·Science·Samuel AparicioSydney Brenner
Jul 27, 2004·Science·Jonathan SebatMichael Wigler
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Mar 3, 2009·Genome Research·Jared T Simpsonİnanç Birol
Nov 7, 2009·The Journal of Heredity·Genome 10K Community of Scientists
Dec 17, 2009·Nature·Ruiqiang LiJun Wang
Jan 12, 2010·Annual Review of Medicine·Paweł Stankiewicz, James R Lupski
Nov 26, 2010·Nature Methods·Can AlkanEvan E Eichler
Dec 29, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sante GnerreDavid B Jaffe
Jul 12, 2011·Nature·Potato Genome Sequencing ConsortiumRichard G F Visser
Aug 13, 2011·Nature·Bastiaan StarKjetill S Jakobsen
Sep 20, 2011·Genome Research·Dent EarlBenedict Paten
Dec 8, 2011·Genome Research·Steven L SalzbergJames A Yorke
Feb 9, 2012·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Takeshi TakeuchiNori Satoh
Mar 24, 2012·Current Opinion in Genetics & Development·Pengfei LiuJames R Lupski
Aug 18, 2012·Marine Genomics·Giacomo BernardiByrappa Venkatesh
May 24, 2013·Nature·Björn NystedtStefan Jansson
Oct 24, 2013·Nature Communications·Wenming ZhengZhensheng Kang
Jun 12, 2014·Nature·Alexander A MyburgJeremy Schmutz

Citations

Oct 20, 2015·Gene·Yuki IwasakiMitsuru Ototake
Aug 21, 2015·Scientific Reports·Jilun HouKatsutoshi Arai
Apr 6, 2018·PloS One·Kris A ChristensenRobert H Devlin
Oct 18, 2018·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Motoshige YasuikeAtushi Fujiwara

Related Concepts

Metazoa
Haploid Cell
Genetic Polymorphism
Reproducibility of Results
cDNA Library
Genome
Computational Molecular Biology
Genomics
Takifugu rubripes
High-Throughput Nucleotide Sequencing

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.

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.

Systemic Juvenile Idiopathic Arthritis

Systemic juvenile idiopathic arthritis is a rare rheumatic disease that affects children. Symptoms include joint pain, but also fevers and skin rashes. Here is the latest on this disease.

Chromatin Regulation and Circadian Clocks

The circadian clock plays an important role in regulating transcriptional dynamics through changes in chromatin folding and remodelling. Discover the latest research on Chromatin Regulation and Circadian Clocks here.

Central Pontine Myelinolysis

Central Pontine Myelinolysis is a neurologic disorder caused most frequently by rapid correction of hyponatremia and is characterized by demyelination that affects the central portion of the base of the pons. Here is the latest research on this disease.

Myocardial Stunning

Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.

Pontocerebellar Hypoplasia

Pontocerebellar hypoplasias are a group of neurodegenerative autosomal recessive disorders with prenatal onset, atrophy or hypoplasia of the cerebellum, hypoplasia of the ventral pons, microcephaly, variable neocortical atrophy and severe mental and motor impairments. Here is the latest research on pontocerebellar hypoplasia.

Cell Atlas Along the Gut-Brain Axis

Profiling cells along the gut-brain axis at the single cell level will provide unique information for each cell type, a three-dimensional map of how cell types work together to form tissues, and insights into how changes in the map underlie health and disease of the GI system and its crosstalk with the brain. Disocver the latest research on single cell analysis of the gut-brain axis here.

Chronic Traumatic Encephalopathy

Chronic Traumatic Encephalopathy (CTE) is a progressive degenerative disease that occurs in individuals that suffer repetitive brain trauma. Discover the latest research on traumatic encephalopathy here.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Sante GnerreDavid B Jaffe
DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Takeshi TakeuchiNori Satoh
© 2021 Meta ULC. All rights reserved