de novo genome assembly of the red silk cotton tree

A whole

Abstract We report that polyploid species have long been thought to be recalcitrant to whole-genome assembly By combining high-throughput sequencing recent developments in parallel computing and genetic mapping we derive de novo a sequence assembly representing 9 1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat Triticum aestivum and assign 7 1 Gb of this assembly

De novo SNP discovery and genetic linkage mapping in

Aug 18 2016Forests cover about 30 % of Earth's land area and are of significant economic and ecological importance [] Although most forest trees are characterized by their large and complex genomes recent advances in DNA sequencing technology with assistances of available physical maps [2–4] have led to several tree genome sequence assemblies which include two poplar species

Genomic insights from the first chromosome

Nov 22 2019Oat (Avena sativa L ) is a nutritionally important crop throughout the world It is ranked 6th in world cereal production [] and while its primary use continues to be as a livestock feed its uses as a human food and for cosmetics continue to increase [] Among the many nutritional benefits of oat are its high levels of calcium β-glucan soluble fiber [3 4 5 6] and high-quality oil and

De novo genome assembly of the red silk cotton tree

May 01 2018De novo genome assembly of the red silk cotton tree (Bombax ceiba) Gao Y(1) Wang H(1) Liu C(1) Chu H(1) Dai D(1) Song S(2) Yu L(1) Han L(1) Fu Y(3) Tian B(3)(4) Tang L(1)(5) Author information: (1)Center for Yunnan Plateau Biological Resources Protection and Utilization College of Biological Resource and Food Engineering Qujing

Sequenced plant genomes

Jan 07 2015The genome sequence of the black cottonwood tree (Populus trichocarpa) was published in 2006 The genome was originally sequenced to a coverage of 7 5x using Sanger sequencing Poplar was the third plant genome to be published and is now one of two published genomes of tree species (the other being papaya)

Genome sequence of the Asian Tiger mosquito Aedes

A total of 17 539 protein-encoding gene models were predicted de novo and supported by evidence-based searches using reference gene sets from mosquito (Ae aegypti An gambiae and Cx quinquefasciatus) and fruit fly (Drosophila melanogaster) genome annotations and this number is larger than those species with the exception of Cx

Genome Annotation and Curation Using MAKER and MAKER‐P

Dec 12 2014Rishi De‐Kayne Stefan Zoller Philine G D Feulner A de novo chromosome‐level genome assembly of Coregonus sp "Balchen": One representative of the Swiss Alpine whitefish radiation Molecular Ecology Resources 10 1111/1755-0998 13187 20 4 (1093-1109) (2020)

De novo assembly

De novo assembly of a chromosome‐level reference genome of Red Spotted Grouper (Epinephelus akaara) using nanopore sequencing and Hi‐C The red spotted grouper Epinephelus akaara ( E akaara ) is one of the most economically important marine fish in China Japan and Southeast Asia and is a threatened species

The genome of flax (Linum usitatissimum) assembled de novo

SOAPdenovo is a de Bruijn graph‐based assembly program designed to use short WGS reads as its input (Li et al 2009) Applying this software to filtered Illumina reads we generated a de novo assembly in which 50% of the assembly (N 50) was contained in 4427 contigs of 20 125 bp or larger () All contigs were further assembled into 88 384 scaffolds (≥100 bp) of which 132 scaffolds

De Novo Genome Assembly of the Red Silk Cotton Tree

De Novo Genome Assembly of the Red Silk Cotton Tree (Bombax ceiba) author: Gao Y Wang H Liu C Chu H Dai D Song S Yu L Han L Fu Y Tian B Tang L Bombax ceiba L (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia and northern Australia It has great economic and ecological

Chromosome

Jul 06 2020To perform de novo assembly of the cultivated mulberry genome we combined three different technologies: the Oxford Nanopore Illumina HiSeq and high-throughput chromosome conformation capture (Hi-C) platforms Using DNA from the leaves of Heyebai (Figure 1A–1C) we generated 154-fold-coverage Nanopore data (51 5 Gb) 82-fold-coverage Illumina paired-end reads

Chromosome

A high-quality chromosome-level genome of the domesticated mulberry (Morus alba) was presented in this study and analysis of genomic data confirmed that M alba is a diploid with 28 chromosomes (2n = 2x = 28) Population genomic analysis based on resequencing of 134 mulberry accessions classified domesticated mulberry into three geographical groups which all belong to one species

De novo assembly

De novo assembly of a chromosome‐level reference genome of Red Spotted Grouper (Epinephelus akaara) using nanopore sequencing and Hi‐C The red spotted grouper Epinephelus akaara ( E akaara ) is one of the most economically important marine fish in China Japan and Southeast Asia and is a threatened species

Silk genes and silk gene expression in the spider Tengella

Sep 20 2018Most spiders spin multiple types of silk including silks for reproduction prey capture and draglines Spiders are a megadiverse group and the majority of spider silks remain uncharacterized For example nothing is known about the silk molecules of Tengella perfuga a spider that spins sheet webs lined with cribellar silk Cribellar silk is a type of adhesive capture thread composed of

De novo transcriptome sequencing in Bixa orellana to

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs SSRs and candidate genes journal January 2012 Ashrafi Hamid Hill Theresa Stoffel Kevin BMC Genomics Vol 13 Issue 1 DOI: 10 1186/1471-2164-13-571

The genome of flax (Linum usitatissimum) assembled de novo

SOAPdenovo is a de Bruijn graph‐based assembly program designed to use short WGS reads as its input (Li et al 2009) Applying this software to filtered Illumina reads we generated a de novo assembly in which 50% of the assembly (N 50) was contained in 4427 contigs of 20 125 bp or larger () All contigs were further assembled into 88 384 scaffolds (≥100 bp) of which 132 scaffolds

De novo assembly

De novo assembly of a chromosome‐level reference genome of Red Spotted Grouper (Epinephelus akaara) using nanopore sequencing and Hi‐C The red spotted grouper Epinephelus akaara ( E akaara ) is one of the most economically important marine fish in China Japan and Southeast Asia and is a threatened species

Long Reads

Sep 04 2015Using MinION nanopore sequencing to generate a de novo eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga Galdieria sulphuraria strain SAG 107 79 Reported here is the de novo assembly of a eukaryotic genome using only MinION nanopore DNA sequence data by examining a novel Galdieria

Draft genome of the mountain pine beetle Dendroctonus

Mar 27 2013The mountain pine beetle Dendroctonus ponderosae Hopkins is the most serious insect pest of western North American pine forests A recent outbreak destroyed more than 15 million hectares of pine forests with major environmental effects on forest health and economic effects on the forest industry The outbreak has in part been driven by climate change and will contribute to increased

Nature Genetics: doi:10 1038/ng

the durian lineage underwent a whole genome duplication (WGD) event ~60 MYA (from our analysis) leading to large duplicated syntenic regions in the genome the genome has since undergone extensive shuffling and diploidization 2 Our assembly process used Falcon-Unzip to merge haplotigs into a single locus in the assembly

Draft genome sequences of Chrysoporthe austroafricana

Jun 01 2015Draft genome sequence of Leptographium lundbergii Leptographium lundbergii described in 1927 as a cause of blue stain in spruce in Sweden (Lagerberg et al 1927) is the type species of Leptographium s lat This is an ascomycete genus residing in Ophiostomatales that currently accommodates more than 100 species (de Beer Wingfield 2013) Most species of Leptographium s

Chromosome

A high-quality chromosome-level genome of the domesticated mulberry (Morus alba) was presented in this study and analysis of genomic data confirmed that M alba is a diploid with 28 chromosomes (2n = 2x = 28) Population genomic analysis based on resequencing of 134 mulberry accessions classified domesticated mulberry into three geographical groups which all belong to one species

Genome Report: Whole Genome Sequence and Annotation of the

Aug 01 2020The genome assembly strategy of N giraulti includes the constructions of three draft de novo assemblies using different assemblers and a final step to reconcile three draft assemblies into a final high-quality assembly The first de novo assembly of N giraulti genome was performed with the Supernova 2 0 assembler (Weisenfeld et al 2017