scholarly journals A Hybridde novoAssembly of the Sea Pansy (Renilla muelleri) Genome

2018 ◽  
Author(s):  
Justin Jiang ◽  
Andrea M. Quattrini ◽  
Warren R. Francis ◽  
Joseph F. Ryan ◽  
Estefanía Rodríguez ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Three Dimensional ◽  
Deep Ocean ◽  
Gene Families ◽  
Celera Assembler ◽  
Final Assembly ◽  
Hybrid Genome ◽  
Reporter Assays

AbstractBackgroundOver 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral “forests” which provide unique niches and three-dimensional living space for other organisms. The octocoral genusRenillainhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans.Renillais especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several cnidarian genomes are currently available, the majority are from hexacorals. Here, we present ade novoassembly of theR. muellerigenome, making this the first complete draft genome from an octocoral.FindingsWe generated a hybridde novoassembly using the Maryland Super-Read Celera Assembler v.3.2.6 (MaSuRCA). The final assembly included 4,825 scaffolds and a haploid genome size of 172 Mb. A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustusab initiogene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone,Nematostella vectensis,or to the Uniprot database. Although theR. muellerigenome is smaller (172 Mb) than other publicly available, hexacoral genomes (256-448 Mb), theR. muellerigenome is similar to the hexacoral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.ConclusionsTheR. muellerihybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.

scholarly journals Insights from the first genome assembly of Onion (Allium cepa)

2021 ◽  
Author(s):  
Richard Finkers ◽  
Martijn P.W. van Kaauwen ◽  
Kai Ament ◽  
Karin Burger-Meijer ◽  
Raymond J. Egging ◽  
...  
Keyword(s):  
Ab Initio ◽  
Genetic Linkage ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Linkage Maps ◽  
Vegetable Crop ◽  
Putative Gene ◽  
Final Assembly ◽  
Genetic Linkage Maps

Onion is an important vegetable crop with an estimated genome size of 16GB. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with a N50 of 461 Kb. Of which 2.2 Gb was ordered into 8 pseudomolecules using five genetic linkage maps. The remainder of the genome is available in 89.8 K scaffolds. Analysis of this genome shows that at least 72.4% of the genome is repetitive and consists, to a large extent, of (retro) transposons. Many (retro) transposons were already quite old as they had accumulated many mutations, facilitating their assembly, however, hampering their identification. The draft ab initio gene prediction indicated 540 925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. 86,073 models showed similarity to published proteins (UNIPROT). No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with A. sativum (garlic) showed collinearity but also major rearrangements between both species. Not-withstanding, this assembly is the first high-quality draft genome sequence available for the study of onion and will be a valuable resource for further research.

scholarly journals Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weitao Chen ◽  
Ming Zou ◽  
Yuefei Li ◽  
Shuli Zhu ◽  
Xinhui Li ◽  
...  
Keyword(s):  
De Novo ◽  
Parental Species ◽  
F1 Hybrids ◽  
Pelteobagrus Fulvidraco ◽  
F1 Hybrid ◽  
Short Reads ◽  
Final Assembly ◽  
Genome Complexity ◽  
Hybrid Genome ◽  
Silurus Asotus

AbstractGenome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

scholarly journals De Novo Genome Assembly of the Meadow Brown Butterfly, Maniola jurtina

2020 ◽  
Vol 10 (5) ◽  
pp. 1477-1484
Author(s):  
Kumar Saurabh Singh ◽  
David J. Hosken ◽  
Nina Wedell ◽  
Richard ffrench-Constant ◽  
Chris Bass ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
De Novo Genome Assembly ◽  
Modern Biology ◽  
Final Assembly ◽  
Gene Sets ◽  
Gene Count ◽  
In The Wild ◽  
Maniola Jurtina

Meadow brown butterflies (Maniola jurtina) on the Isles of Scilly represent an ideal model in which to dissect the links between genotype, phenotype and long-term patterns of selection in the wild - a largely unfulfilled but fundamental aim of modern biology. To meet this aim, a clear description of genotype is required. Here we present the draft genome sequence of M. jurtina to serve as a founding genetic resource for this species. Seven libraries were constructed using pooled DNA from five wild caught spotted females and sequenced using Illumina, PacBio RSII and MinION technology. A novel hybrid assembly approach was employed to generate a final assembly with an N50 of 214 kb (longest scaffold 2.9 Mb). The sequence assembly described here predicts a gene count of 36,294 and includes variants and gene duplicates from five genotypes. Core BUSCO (Benchmarking Universal Single-Copy Orthologs) gene sets of Arthropoda and Insecta recovered 90.5% and 88.7% complete and single-copy genes respectively. Comparisons with 17 other Lepidopteran species placed 86.5% of the assembled genes in orthogroups. Our results provide the first high-quality draft genome and annotation of the butterfly M. jurtina.

scholarly journals Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

2020 ◽  
Vol 12 (2) ◽  
pp. 3917-3925
Author(s):  
Greer A Dolby ◽  
Matheo Morales ◽  
Timothy H Webster ◽  
Dale F DeNardo ◽  
Melissa A Wilson ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Mojave Desert ◽  
De Novo ◽  
Stop Codon ◽  
Draft Genome ◽  
Gene Families ◽  
Sea Turtle ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Gene Expansion

Abstract Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.

scholarly journals First de novo draft genome sequence of Oryza coarctata, the only halophytic species in the genus Oryza

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1750 ◽  
Author(s):  
Tapan Kumar Mondal ◽  
Hukam Chand Rawal ◽  
Kishor Gaikwad ◽  
Tilak Raj Sharma ◽  
Nagendra Kumar Singh
Keyword(s):  
West Bengal ◽  
De Novo ◽  
Draft Genome ◽  
Nanopore Sequencing ◽  
Sequencing Technology ◽  
Genome Sequences ◽  
Oxford Nanopore ◽  
Hybrid Genome ◽  
Genus Oryza ◽  
First Time

Oryza coarctata plants, collected from Sundarban delta of West Bengal, India, have been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time that more than 85.71 % of the genome coverage and the data have been deposited in NCBI SRA, with BioProject ID PRJNA396417.

scholarly journals Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

2018 ◽  
Vol 6 (16) ◽  
pp. e00265-18 ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Kathryn Bartley ◽  
Edward J. Marr ◽  
Harry W. Wright ◽  
Robert J. Weaver ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Psoroptes Ovis ◽  
Protein Coding ◽  
Content Type ◽  
Sheep Scab ◽  
Draft Genome Assembly ◽  
Intense Pruritus

ABSTRACT Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene prediction of P. ovis based on PacBio de novo sequencing. The ∼63.2-Mb genome encodes 12,041 protein-coding genes.

scholarly journals DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9762
Author(s):  
Andres Benavides ◽  
Friman Sanchez ◽  
Juan F. Alzate ◽  
Felipe Cabarcas
Keyword(s):  
Quality Control ◽  
De Novo Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Computing Model ◽  
Sequencing Quality ◽  
Prime Objective ◽  
Metagenomic Assembly ◽  
Taxonomic Annotation

Background A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read’s quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages. Method DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time. Results We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome. Conclusions DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.

scholarly journals The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes)

2020 ◽  
Vol 12 (6) ◽  
pp. 860-866 ◽  
Author(s):  
Qing-Song Zhou ◽  
Arong Luo ◽  
Feng Zhang ◽  
Ze-Qing Niu ◽  
Qing-Tao Wu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Draft Genome ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Single Copy ◽  
Gene Family Evolution ◽  
Nesting Biology ◽  
Protein Coding ◽  
Final Assembly ◽  
Long Reads

Abstract Despite intense interest in bees, no genomes are available for the bee family Colletidae. Colletes gigas, one of the largest species of the genus Colletes in the world, is an ideal candidate to fill this gap. Endemic to China, C. gigas has been the focus of studies on its nesting biology and pollination of the economically important oil tree Camellia oleifera, which is chemically defended. To enable deeper study of its biology, we sequenced the whole genome of C. gigas using single-molecule real-time sequencing on the Pacific Bioscience Sequel platform. In total, 40.58 G (150×) of long reads were generated and the final assembly of 326 scaffolds was 273.06 Mb with a N50 length of 8.11 Mb, which captured 94.4% complete Benchmarking Universal Single-Copy Orthologs. We predicted 11,016 protein-coding genes, of which 98.50% and 84.75% were supported by protein- and transcriptome-based evidence, respectively. In addition, we identified 26.27% of repeats and 870 noncoding RNAs. The bee phylogeny with this newly sequenced colletid genome is consistent with available results, supporting Colletidae as sister to Halictidae when Stenotritidae is not included. Gene family evolution analyses identified 9,069 gene families, of which 70 experienced significant expansions (33 families) or contractions (37 families), and it appears that olfactory receptors and carboxylesterase may be involved in specializing on and detoxifying Ca. oleifera pollen. Our high-quality draft genome for C. gigas lays the foundation for insights on the biology and behavior of this species, including its evolutionary history, nesting biology, and interactions with the plant Ca. oleifera.

scholarly journals The First Draft Genome Assembly of Snow Sheep (Ovis nivicola)

2020 ◽  
Vol 12 (8) ◽  
pp. 1330-1336 ◽  
Author(s):  
Maulik Upadhyay ◽  
Andreas Hauser ◽  
Elisabeth Kunz ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Single Copy ◽  
Climatic Conditions ◽  
Draft Genome Assembly ◽  
Sheep Genome ◽  
Long Reads

Abstract The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was ∼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised of 41% of the total genome. BUSCO analysis revealed that the snow sheep assembly contained full-length or partial fragments of 97% of mammalian universal single-copy orthologs (n = 4,104), illustrating the completeness of the assembly. In addition, a total of 20,045 protein-coding sequences were identified using comprehensive gene prediction pipeline. Of which 19,240 (∼96%) sequences were annotated using protein databases. Moreover, homology-based searches and de novo identification detected 1,484 tRNAs; 243 rRNAs; 1,931 snRNAs; and 782 miRNAs in the snow sheep genome. To conclude, we generated the first de novo genome of the snow sheep using long reads; these data are expected to contribute significantly to our understanding related to evolution and adaptation within the Ovis genus.

scholarly journals Hybrid Genome Assembly of a Neotropical Mutualistic Ant

2019 ◽  
Vol 11 (8) ◽  
pp. 2306-2311
Author(s):  
Juliane Hartke ◽  
Tilman Schell ◽  
Evelien Jongepier ◽  
Hanno Schmidt ◽  
Philipp P Sprenger ◽  
...  
Keyword(s):  
Communication System ◽  
De Novo ◽  
Draft Genome ◽  
Cuticular Hydrocarbon ◽  
Mechanistic Explanation ◽  
High Quality ◽  
Great Opportunity ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Hybrid Genome

Abstract The success of social insects is largely intertwined with their highly advanced chemical communication system that facilitates recognition and discrimination of species and nest-mates, recruitment, and division of labor. Hydrocarbons, which cover the cuticle of insects, not only serve as waterproofing agents but also constitute a major component of this communication system. Two cryptic Crematogaster species, which share their nest with Camponotus ants, show striking diversity in their cuticular hydrocarbon (CHC) profile. This mutualistic system therefore offers a great opportunity to study the genetic basis of CHC divergence between sister species. As a basis for further genome-wide studies high-quality genomes are needed. Here, we present the annotated draft genome for Crematogaster levior A. By combining the three most commonly used sequencing techniques—Illumina, PacBio, and Oxford Nanopore—we constructed a high-quality de novo ant genome. We show that even low coverage of long reads can add significantly to overall genome contiguity. Annotation of desaturase and elongase genes, which play a role in CHC biosynthesis revealed one of the largest repertoires in ants and a higher number of desaturases in general than in other Hymenoptera. This may provide a mechanistic explanation for the high diversity observed in C. levior CHC profiles.

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