scholarly journals Draft genome of a porcupinefish, Diodon Holocanthus

2019 ◽  
Author(s):  
Mengyang Xu ◽  
Xiaoshan Su ◽  
Mengqi Zhang ◽  
Ming Li ◽  
Xiaoyun Huang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Single Copy ◽  
Single Individual ◽  
Protein Coding ◽  
Long Read ◽  
Phylogeny And Evolution ◽  
Downstream Analysis

AbstractThe long-spine porcupinefish, Diodon holocanthus (Diodontidae, Tetraodontiformes, Actinopterygii), also known as the freckled porcupinefish, attracts great interest of ecology and economy. Its distinct characteristics including inflation reaction, spiny skin and tetradotoxin, however, have not been fully studied without a complete genome assembly.In this study, the whole genome of a single individual was sequenced using single tube-Long Fragment Read co-barcode reads, generating 154.3 Gb of paired-end data (219.8× depth). The gap was further filled using small amount of Oxford Nanopore MinION long read dataset (11.4Gb, 15.9× depth). Taking full use of long, medium, short-range of genome assembly information, the final assembled sequences with a total length of 650.02 Mb obtained contig and scaffold N50 sizes of 2.15 Mb and 8.13 Mb, respectively, despite of high repetitive content. Benchmarking Universal Single-Copy Orthologs captured 95.7% (2,474) of core genes to assess the completeness. In addition, 206.5 Mb (32.10%) of repetitive sequences were identified, and 20,840 protein-coding genes were annotated, among which 18,281 (87.72%) proteins were assigned with possible functions.This is the first demonstration of de novo genome of the porcupinefish, which will benefit downstream analysis of ontogeny, phylogeny, and evolution, and improve the exploration of its unique defensive mechanism.

scholarly journals Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

2019 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

ABSTRACTThe Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

scholarly journals Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing

2021 ◽  
Author(s):  
Chi yang ◽  
Lu Ma ◽  
Donglai Xiao ◽  
Xiaoyu Liu ◽  
Xiaoling Jiang ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Draft Genome ◽  
Edible Mushroom ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Genome Features ◽  
Long Read ◽  
Genomic Studies

Sparassis latifolia is a valuable edible mushroom cultivated in China. In 2018, our research group reported an incomplete and low quality genome of S. latifolia was obtained by Illumina HiSeq 2500 sequencing. These limitations in the available genome have constrained genetic and genomic studies in this mushroom resource. Herein, an updated draft genome sequence of S. latifolia was generated by Oxford Nanopore sequencing and the Hi-C technique. A total of 8.24 Gb of Oxford Nanopore long reads representing ~198.08X coverage of the S. latifolia genome were generated. Subsequently, a high-quality genome of 41.41 Mb, with scaffold and contig N50 sizes of 3.31 Mb and 1.51 Mb, respectively, was assembled. Hi-C scaffolding of the genome resulted in 12 pseudochromosomes containing 93.56% of the bases in the assembled genome. Genome annotation further revealed that 17.47% of the genome was composed of repetitive sequences. In addition, 13,103 protein-coding genes were predicted, among which 98.72% were functionally annotated. BUSCO assay results further revealed that there were 92.07% complete BUSCOs. The improved chromosome-scale assembly and genome features described here will aid further molecular elucidation of various traits, breeding of S. latifolia, and evolutionary studies with related taxa.

scholarly journals Chromosome-Level Assembly of Drosophila bifasciata Reveals Important Karyotypic Transition of the X Chromosome

2020 ◽  
Vol 10 (3) ◽  
pp. 891-897 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

The Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193 Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromeres, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

scholarly journals LRSDAY: Long-read Sequencing Data Analysis for Yeasts

2017 ◽  
Author(s):  
Jia-Xing Yue ◽  
Gianni Liti
Keyword(s):  
Genome Assembly ◽  
Model Organism ◽  
Sequencing Data ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Long Read ◽  
Downstream Analysis ◽  
Eukaryotic Organisms ◽  
Genomic Regions

AbstractLong-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here we present LRSDAY, the first one-stop solution to streamline this process. LRSDAY can produce chromosome-level end-to-end genome assembly and comprehensive annotations for various genomic features (including centromeres, protein-coding genes, tRNAs, transposable elements and telomere-associated elements) that are ready for downstream analysis. Although tailored for S. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable for virtually any eukaryotic organisms. Applying LRSDAY to a S. cerevisiae strain takes ∼43 hrs to generate a complete and well-annotated genome from ∼100X Pacific Biosciences (PacBio) reads using four threads.

scholarly journals Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 289
Author(s):  
Xiao Ma ◽  
Jeanine L. Olsen ◽  
Thorsten B.H. Reusch ◽  
Gabriele Procaccini ◽  
Dave Kudrna ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Zostera Marina ◽  
Draft Genome ◽  
High Molecular Weight Dna ◽  
Protein Coding ◽  
New Findings ◽  
Long Read ◽  
Sanger Sequence ◽  
Assembly Pipeline ◽  
Chromosome Level

Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings.   Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding.  Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins.  Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

scholarly journals The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding

2021 ◽  
Author(s):  
Priyanka Sharma ◽  
Valentine Murigneux ◽  
Jasmine Haimovitz ◽  
Catherine J. Nock ◽  
Wei Tian ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Morphological Characteristics ◽  
Single Copy ◽  
Protein Coding ◽  
Core Eudicots ◽  
Wide Range ◽  
Genes Encoding ◽  
Long Read ◽  
In The Wild

SummaryMacadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii, being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.

scholarly journals Long-Read Genome Sequencing and Assembly of Leptopilina boulardi: A Specialist Drosophila Parasitoid

2020 ◽  
Vol 10 (5) ◽  
pp. 1485-1494
Author(s):  
Shagufta Khan ◽  
Divya Tej Sowpati ◽  
Arumugam Srinivasan ◽  
Mamilla Soujanya ◽  
Rakesh K. Mishra
Keyword(s):  
Dna Methyltransferase ◽  
Hox Genes ◽  
De Novo ◽  
Draft Genome ◽  
Suitable Model ◽  
Heterochromatin Protein 1 ◽  
Protein Coding ◽  
Long Read ◽  
Trna Methyltransferase ◽  
Relationship Of

Leptopilinaboulardi (Hymenoptera: Figitidae) is a specialist parasitoid of Drosophila. The Drosophila-Leptopilina system has emerged as a suitable model for understanding several aspects of host-parasitoid biology. However, a good quality genome of the wasp counterpart was lacking. Here, we report a whole-genome assembly of L. boulardi to bring it in the scope of the applied and fundamental research on Drosophila parasitoids with access to epigenomics and genome editing tools. The 375Mb draft genome has an N50 of 275Kb with 6315 scaffolds >500bp and encompasses >95% complete BUSCOs. Using a combination of ab-initio and RNA-Seq based methods, 25259 protein-coding genes were predicted and 90% (22729) of them could be annotated with at least one function. We demonstrate the quality of the assembled genome by recapitulating the phylogenetic relationship of L. boulardi with other Hymenopterans. The key developmental regulators like Hox genes and sex determination genes are well conserved in L. boulardi, and so is the basic toolkit for epigenetic regulation. The search for epigenetic regulators has also revealed that L. boulardi genome possesses DNMT1 (maintenance DNA methyltransferase), DNMT2 (tRNA methyltransferase) but lacks the de novo DNA methyltransferase (DNMT3). Also, the heterochromatin protein 1 family appears to have expanded as compared to other hymenopterans. The draft genome of L. boulardi (Lb17) will expedite the research on Drosophila parasitoids. This genome resource and early indication of epigenetic aspects in its specialization make it an interesting system to address a variety of questions on host-parasitoid biology.

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 Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Xupo Ding ◽  
Wenli Mei ◽  
Qiang Lin ◽  
Hao Wang ◽  
Jun Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gene Annotation ◽  
Draft Genome ◽  
Single Copy ◽  
Aquilaria Sinensis ◽  
Final Size ◽  
Plant Resources ◽  
Protein Coding ◽  
High Level ◽  
Chromosome Level

Abstract Backgroud Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information. Findings We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18–84.37 million years ago. Conclusions Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.

scholarly journals The draft genome sequence of Eucalyptus polybractea based on hybrid assembly with short- and long-reads reads

2021 ◽  
Author(s):  
Teng Li ◽  
David Kainer ◽  
William J Foley ◽  
Allen Rodrigo ◽  
Carsten Kuelheim
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Draft Genome ◽  
Hybrid Assembly ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Genome Coverage ◽  
Protein Coding Genes ◽  
Long Reads ◽  
Long Read

Eucalyptus polybractea is a small, multi-stemmed tree, which is widely cultivated in Australia for the production of Eucalyptus oil. We report the hybrid assembly of the E. polybractea genome utilizing both short- and long-read technology. We generated 44 Gb of Illumina HiSeq short reads and 8 Gb of Nanopore long reads, representing approximately 83 and 15 times genome coverage, respectively. The hybrid-assembled genome, after polishing, contained 24,864 scaffolds with an accumulated length of 523 Mb (N50 = 40.3 kb; BUSCO-calculated genome completeness of 94.3%). The genome contained 35,385 predicted protein-coding genes detected by combining homology-based and de novo approaches. We have provided the first assembled genome based on hybrid sequences from the highly diverse Eucalyptus subgenus Symphyomyrtus, and revealed the value of including long-reads from Nanopore technology for enhancing the contiguity of the assembled genome, as well as for improving its completeness. We anticipate that the E. polybractea genome will be an invaluable resource supporting a range of studies in genetics, population genomics and evolution of related species in Eucalyptus.

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