scholarly journals A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

2018 ◽  
Author(s):  
Andreas Wallberg ◽  
Ignas Bunikis ◽  
Olga Vinnere Pettersson ◽  
Mai-Britt Mosbech ◽  
Anna K. Childers ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Genome Assembly ◽  
De Novo ◽  
Hybrid Approach ◽  
Chromosome Length ◽  
Chromatin Interaction ◽  
De Novo Genome Assembly ◽  
Functional Genetic Variation ◽  
Linkage Information ◽  
Interaction Map

AbstractBackgroundThe ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.ResultsEach of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor >98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.ConclusionsThe improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.

scholarly journals A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Andreas Wallberg ◽  
Ignas Bunikis ◽  
Olga Vinnere Pettersson ◽  
Mai-Britt Mosbech ◽  
Anna K. Childers ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Genome Assembly ◽  
De Novo ◽  
Chromosome Length ◽  
De Novo Genome Assembly

scholarly journals Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa

2021 ◽  
Author(s):  
Quan-Kuan Shen ◽  
Min-Sheng Peng ◽  
Adeniyi C Adeola ◽  
Ling Kui ◽  
Shengchang Duan ◽  
...  
Keyword(s):  
West Africa ◽  
De Novo ◽  
Guinea Fowl ◽  
Chromatin Interaction ◽  
De Novo Genome Assembly ◽  
Numida Meleagris ◽  
Whole Genomes ◽  
Genomic Analyses ◽  
Related Wild Species ◽  
Wild Progenitors

Abstract Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

scholarly journals Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)

GigaScience ◽  
2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Xuewei Li ◽  
Ling Kui ◽  
Jing Zhang ◽  
Yinpeng Xie ◽  
Liping Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Malus X Domestica ◽  
De Novo Genome Assembly

scholarly journals Meraculous: De Novo Genome Assembly with Short Paired-End Reads

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e23501 ◽  
Author(s):  
Jarrod A. Chapman ◽  
Isaac Ho ◽  
Sirisha Sunkara ◽  
Shujun Luo ◽  
Gary P. Schroth ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly

Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing

2021 ◽  
Author(s):  
Minxuan Zhou ◽  
Lingxi Wu ◽  
Muzhou Li ◽  
Niema Moshiri ◽  
Kevin Skadron ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly

scholarly journals Optimizing de novo genome assembly from PCR-amplified metagenomes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6902 ◽  
Author(s):  
Simon Roux ◽  
Gareth Trubl ◽  
Danielle Goudeau ◽  
Nandita Nath ◽  
Estelle Couradeau ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Pcr Amplification ◽  
Error Rates ◽  
De Novo Genome Assembly ◽  
Low Input ◽  
Assembly Algorithm ◽  
Coverage Bias ◽  
Size Number ◽  
Assembly Pipeline

Background Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

scholarly journals Accurate long-read de novo assembly evaluation with Inspector

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Chen ◽  
Yixin Zhang ◽  
Amy Y. Wang ◽  
Min Gao ◽  
Zechen Chong
Keyword(s):  
Genome Assembly ◽  
De Novo Assembly ◽  
In Silico ◽  
Large Scale ◽  
De Novo ◽  
Small Scale ◽  
De Novo Genome Assembly ◽  
Consensus Sequences ◽  
Assembly Evaluation ◽  
Long Read

AbstractLong-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read assembly results from multiple long-read data and assemblers, we demonstrate that in addition to providing generic metrics, Inspector can accurately identify both large-scale and small-scale assembly errors.

scholarly journals De novo genome assembly and single nucleotide variations for Soybean yellow common mosaic virus using soybean flower bud transcriptome data

2020 ◽  
Vol 63 (3) ◽  
pp. 189-195
Author(s):  
Yeonhwa Jo ◽  
Hoseong Choi ◽  
Sang-Min Kim ◽  
Bong Choon Lee ◽  
Won Kyong Cho
Keyword(s):  
Mosaic Virus ◽  
Genome Assembly ◽  
De Novo ◽  
Transcriptome Data ◽  
Flower Bud ◽  
De Novo Genome Assembly ◽  
Single Nucleotide ◽  
Single Nucleotide Variations

scholarly journals Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1359
Author(s):  
Esther Camacho ◽  
Sandra González-de la Fuente ◽  
Jose C. Solana ◽  
Alberto Rastrojo ◽  
Fernando Carrasco-Ramiro ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Leishmania Major ◽  
De Novo ◽  
Gene Annotation ◽  
Leishmania Species ◽  
De Novo Genome Assembly ◽  
Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

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