Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing

The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.

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Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

Genome Announcements ◽

10.1128/genomea.00265-18 ◽

2018 ◽

Vol 6 (16) ◽

pp. e00265-18 ◽

Cited By ~ 8

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.

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Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

10.1101/2021.11.11.468259 ◽

2021 ◽

Author(s):

Roger Huerlimann ◽

Jeff A Cowley ◽

Nicholas M Wade ◽

Yinan Wang ◽

Naga Kasinadhuni ◽

...

Keyword(s):

Genome Assembly ◽

Draft Genome ◽

Penaeus Monodon ◽

Penaeid Shrimp ◽

Protein Coding ◽

Black Tiger Shrimp ◽

Draft Genome Assembly ◽

Repeat Content ◽

Tiger Shrimp ◽

Endogenous Viral Elements

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements (EVEs) have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such EVEs and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ~4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of conjoined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.

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

Genome Biology and Evolution ◽

10.1093/gbe/evaa016 ◽

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.

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A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis

Genome Biology and Evolution ◽

10.1093/gbe/evaa112 ◽

2020 ◽

Vol 12 (7) ◽

pp. 1074-1079 ◽

Cited By ~ 1

Author(s):

Ruihao Shu ◽

Jihong Zhang ◽

Qian Meng ◽

Huan Zhang ◽

Guiling Zhou ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Draft Genome ◽

Gene Clusters ◽

Tibet Plateau ◽

Protein Coding ◽

Draft Genome Assembly ◽

Ophiocordyceps Sinensis ◽

Homologous Protein ◽

Genome Features

Abstract Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or “DongChongXiaCao,” is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genome assembly of O. sinensis. The assembly of 23 contigs was ∼110.8 Mb with a N50 length of 18.2 Mb. We used RNA-seq and homologous protein sequences to identify 8,916 protein-coding genes in the IOZ07 assembly. Moreover, 63 secondary metabolite gene clusters were identified in the improved assembly. The improved assembly and genome features described in this study will further inform the evolutionary study and resource utilization of Chinese cordyceps.

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Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

10.1101/546135 ◽

2019 ◽

Cited By ~ 4

Author(s):

Haley Wight ◽

Junhui Zhou ◽

Muzi Li ◽

Sridhar Hannenhalli ◽

Stephen M. Mount ◽

...

Keyword(s):

De Novo ◽

Draft Genome ◽

Rubus Idaeus ◽

Slow Process ◽

Red Raspberry ◽

Protein Coding ◽

Draft Genome Assembly ◽

Protein Coding Genes ◽

A Genome ◽

Exceptional Value

AbstractThe red raspberry, Rubus idaeus, is widely distributed in all temperate regions of Europe, Asia, and North America and is a major commercial fruit valued for its taste, high antioxidant and vitamin content. However, Rubus breeding is a long and slow process hampered by limited genomic and molecular resources. Genomic resources such as a complete genome sequencing and transcriptome will be of exceptional value to improve research and breeding of this high value crop. Using a hybrid sequence assembly approach including data from both long and short sequence reads, we present the first assembly of the Rubus idaeus genome (Joan J. variety). The de novo assembled genome consists of 2,145 scaffolds with a genome completeness of 95.3% and an N50 score of 638 KB. Leveraging a linkage map, we anchored 80.1% of the genome onto seven chromosomes. Using over 1 billion paired-end RNAseq reads, we annotated 35,566 protein coding genes with a transcriptome completeness score of 97.2%. The Rubus idaeus genome provides an important new resource for researchers and breeders.

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A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)

10.1101/2020.03.03.971721 ◽

2020 ◽

Cited By ~ 1

Author(s):

Qiye Li ◽

Qunfei Guo ◽

Yang Zhou ◽

Huishuang Tan ◽

Terry Bertozzi ◽

...

Keyword(s):

Genome Assembly ◽

Draft Genome ◽

Protein Coding ◽

Large Genome ◽

Draft Genome Assembly ◽

Protein Coding Genes ◽

Repeat Content ◽

Australian Continent ◽

Large Genome Size ◽

Reference Genomes

AbstractAmphibian genomes are usually challenging to assemble due to large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.

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A chromosome-level draft genome of the grain aphid Sitobion miscanthi

GigaScience ◽

10.1093/gigascience/giz101 ◽

2019 ◽

Vol 8 (8) ◽

Cited By ~ 4

Author(s):

Xin Jiang ◽

Qian Zhang ◽

Yaoguo Qin ◽

Hang Yin ◽

Siyu Zhang ◽

...

Keyword(s):

Genome Assembly ◽

Acyrthosiphon Pisum ◽

Draft Genome ◽

Chromosome Length ◽

Trophic Levels ◽

Final Size ◽

Entire Genome ◽

Protein Coding ◽

Draft Genome Assembly ◽

Environmentally Safe

AbstractBackgroundSitobion miscanthi is an ideal model for studying host plant specificity, parthenogenesis-based phenotypic plasticity, and interactions between insects and other species of various trophic levels, such as viruses, bacteria, plants, and natural enemies. However, the genome information for this species has not yet to be sequenced and published. Here, we analyzed the entire genome of a parthenogenetic female aphid colony using Pacific Biosciences long-read sequencing and Hi-C data to generate chromosome-length scaffolds and a highly contiguous genome assembly.ResultsThe final draft genome assembly from 33.88 Gb of raw data was ∼397.90 Mb in size, with a 2.05 Mb contig N50. Nine chromosomes were further assembled based on Hi-C data to a 377.19 Mb final size with a 36.26 Mb scaffold N50. The identified repeat sequences accounted for 26.41% of the genome, and 16,006 protein-coding genes were annotated. According to the phylogenetic analysis, S. miscanthi is closely related to Acyrthosiphon pisum, with S. miscanthi diverging from their common ancestor ∼25.0–44.9 million years ago.ConclusionsWe generated a high-quality draft of the S. miscanthi genome. This genome assembly should help promote research on the lifestyle and feeding specificity of aphids and their interactions with each other and species at other trophic levels. It can serve as a resource for accelerating genome-assisted improvements in insecticide-resistant management and environmentally safe aphid management.

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Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

GigaScience ◽

10.1093/gigascience/giz112 ◽

2019 ◽

Vol 8 (9) ◽

Cited By ~ 11

Author(s):

Yu Xing ◽

Yang Liu ◽

Qing Zhang ◽

Xinghua Nie ◽

Yamin Sun ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Genetic Improvement ◽

De Novo ◽

Draft Genome ◽

Whole Genome Sequence ◽

Whole Genome ◽

High Quality ◽

Chinese Chestnut ◽

Castanea Mollissima

AbstractBackgroundThe Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima.FindingsWe produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago.ConclusionsThe high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

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Whole Genome Sequence of Wilsonomyces Carpophilus, the Causal Agent of Shot Hole of Stone Fruits: Insights Into Secreted Proteins of a Necrotrophic Fungal Repository

10.21203/rs.3.rs-541535/v1 ◽

2021 ◽

Author(s):

Mahiya Farooq ◽

Mehraj D. Shah ◽

Bilal A. Padder ◽

T.A. Sofi ◽

Khalid k. Masoodi ◽

...

Keyword(s):

Genome Assembly ◽

Proteolytic Enzymes ◽

Pathogenic Fungus ◽

Draft Genome ◽

Secreted Proteins ◽

Whole Genome Sequence ◽

Secretory Proteins ◽

Stone Fruits ◽

Illumina Hiseq ◽

Draft Genome Assembly

Abstract Wilsonomyces carpophilus is a necrotrophic plant pathogenic fungus with a wide host range infecting all stone fruits such as peach, plum, apricot and cherry, and almonds among the nut crops. Necrotrophs are more devastating with a complex pathogenicity mechanism and least known effector repositories. Here, we report a 29.9 megabase draft genome assembly of W. carpophilus. We explored the hybrid technology of Illumina HiSeq and PacBio sequencing technologies to get the unbiased results of sequence reads. We aligned short Illumina reads against the long PacBio reads. A total of 10,901 protein-coding genes were predicted that includes varied set of genes such as HET genes, cytochrome-p450 genes, kinases etc. We mined 2851 simple sequence repeats (SSRs) in the genome assembly. We also predicted the diverse inventory of secretory proteins, transporters, primary and secondary metabolic enzymes. A total of 225 secreted proteins, hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic and proteolytic enzymes were the most significant proteins reflecting the necrotrophic lifestyle of the W. carpophilus. We also identified 146 tRNAs and 52 rRNAs in the pathogen genome.

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Chromosomal-level genome assembly of the bioluminescent cardinalfish Siphamia tubifer, an emerging model for symbiosis research

10.1101/2021.09.03.458932 ◽

2021 ◽

Author(s):

Alison L Gould ◽

James B Henderson ◽

Athena W Lam

Keyword(s):

Genome Assembly ◽

Muscle Development ◽

Draft Genome ◽

Protein Coding ◽

Draft Genome Assembly ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Microbial Symbiosis ◽

Symbiosis Research ◽

Siphamia Tubifer

The bioluminescent symbiosis between the sea urchin cardinalfish Siphamia tubifer (Kurtiformes: Apogonidae) and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate-bacteria model for the study of microbial symbiosis. However, there is little genetic data available for the host fish, limiting the scope of potential research that can be carried out with this association. In this study, we present a chromosomal-level genome assembly of S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final genome assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO completeness score of 99%. A comparison of the S. tubifer genome to that of another non-luminous cardinalfish revealed a high degree of synteny, whereas a similar comparison to a more distant relative in the Gobiiformes order revealed a fusion of two chromosomes in the cardinalfish genomes. An additional comparison of orthologous clusters among these three genomes revealed a set of 710 clusters that were unique to S. tubifer in which 23 GO pathways were significantly enriched, including several relating to host-microbe interactions and one involved in visceral muscle development, which could be related to the musculature involved in the gut-associated light organ of S. tubifer. We also assembled the complete mitogenome of S. tubifer and discovered both an inversion in the WANCY tRNA gene region resulting in a WACNY gene order as well as heteroplasmy in the length of the control region for this individual. A phylogenetic analysis based on the whole mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, bringing up questions of the involvement of the bioluminescent symbiosis in the initial divergence of the ancestral Siphamia species. This draft genome assembly of S. tubifer will enable future studies investigating the evolution of bioluminescence in fishes as well as candidate genes involved in the symbiosis and will provide novel opportunities to use this system as a vertebrate-bacteria model for symbiosis research.

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