scholarly journals Draft genome of the Brazilian railroad worm Phrixothrix hirtus E.Olivier (Phengodidae: Coleoptera)

2021 ◽  
Author(s):  
Danilo Trabuco Amaral ◽  
Yasuo Mitani ◽  
Isabel Aparecida Silva Bonatelli ◽  
Ricardo Cerri ◽  
Yoshihiro Ohmiya ◽  
...  
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Red Light ◽  
Draft Genome ◽  
Gc Content ◽  
Gene Families ◽  
Neotropical Region ◽  
Comparative Genomic ◽  
List Type ◽  
Draft Genome Assembly

AbstractThe Neotropical region is the richest in bioluminescent Coleoptera species, however, its bioluminescence megadiversity is still underexplored in terms of genomic organization and evolution, mainly within the Phengodidae family. The railroad worm Phrixothrix hirtus is an important biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed the partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing an important source of genomic information and a framework for comparative genomic analyses for the evaluation of the bioluminescent system in Elateroidea. The estimated genome size has ∼3.4Gb, 32% of GC content, and 67% of repetitive elements, being the largest genome described in the Elateroidea superfamily. Several events of gene family expansions associated with anatomical development and morphogenesis, as well as distinct odorant-binding receptors and retrotransposable elements were found in this genome. Similar molecular functions and biological processes are shared with other studied species of Elateriformia. Common genes putatively associated with bioluminescence production and control, including two luciferase genes that displayed 7 exons and 6 introns, and genes that could be involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea. In P. hirtus the conversion of L- to D-luciferin seems to involve additional steps using a Palmitoyl-CoA thioesterase instead of an Acyl-CoA synthetase, which was found in Lampyridae species.HighlightsFirst draft genome assembly of Phengodidae, the largest one described in Coleoptera;Gene family expansions associated with anatomical development and morphogenesis;Bioluminescent control and luciferin biosynthesis genes are common within Elateroidea;Despite similar bioluminescent system, metabolic routes may have evolved independently;

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 Draft Genome Sequence of Branchiibius sp. NY16-3462-2, Isolated from a Mixed Clinical Sample

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Pascal Lapierre ◽  
Tanya A. Halse ◽  
Joseph Shea ◽  
Vincent E. Escuyer ◽  
Kimberlee A. Musser
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Clinical Sample ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Gram Positive ◽  
Draft Genome Assembly ◽  
Gram Positive Cocci

Here, we report the release of a draft genome assembly of a Gram-positive cocci Branchiibius sp. NY16-3462-2 with a high-GC content, sequenced from a mixed clinical sample containing Mycobacterium tuberculosis . This genome is the first publicly available sequence from a representative of the genus Branchiibius .

scholarly journals Comparative Genomic Insights into the Longhorned Tick, Haemaphysalis Longicornis

2020 ◽  
Author(s):  
Rui-Ling Zhang ◽  
Qian Zhang ◽  
Zhong Zhang
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Animal Health ◽  
Gene Families ◽  
High Ratio ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Haemaphysalis Longicornis ◽  
Gene Set ◽  
Terrestrial Vertebrates

Abstract Background: The longhorned tick, Haemaphysalis longicornis Neumann, is widely distributed across temperate regions. It can parasitize terrestrial vertebrates, including birds and a large number of mammals. They are a concern in human and animal health notably for their potential to transmit infectious agents. Methods: Genome survey was investigated using GenomeScope v1.0.0 with a maximum k-mer coverage cutoff of 1,000. Non-redundant assembly was polished with Illumina short reads using two rounds of NextPolish v1.1.0. Genome completeness was assessed using BUSCO v3.0.2 pipeline analyses against arthropod gene set (n = 1, 066). Ab initio predictions were generated using BRAKER v2.1.5. Transcriptomic reads were mapped to the genome with HISAT2 v2.2.0 and assembled with StringTie v2.1.2. Gene functions were assigned against UniProtKB database using Diamond v0.9.24. Orthogroups of 16 Chelicerata species were inferred using OrthoFinder v2.3.8 and gene family evolution was estimated using CAFÉ v4.2.1. Gene families related to digestion and detoxification, i.e. cytochrome P450 (CYP), carboxyl/cholinesterase (CCE), glutathione-S-transferase (GST), ATP-binding cassette (ABC) transporter were annotated by searching in the genome assembly. Results: The final genome assembly has a size of 3.12 Gb, a scaffold N50 of 1.09 Mb, and captured 92.4% of the BUSCO gene set (n=1,066). Genome architecture pattern of the longhorned tick resembles another tick, Ixodes scapularis (Say), particularly in large size, highly repetitive DNA (~65%) and protein-coding genes (21,550). We also identified 5,601 non-coding RNAs with a high ratio of tRNAs (4,271). Gene family evolution revealed 350 rapidly evolving gene families. Combining function enrichment analyses of gene ontology (GO) and KEGG pathway, 255 families experiencing significant expansions mainly involves in cuticle synthesis, digestion and detoxification. Conclusions: The new genome assembly, annotation and comparative genomic analyses provide a valuable resource for insights into parasitic life mode of the longhorned tick.

scholarly journals Draft Genome Assembly of Filamentous Brackish Cyanobacterium Limnoraphis robusta Strain CS-951

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Anusuya Willis ◽  
Matthew Parks ◽  
Michele A. Burford
Keyword(s):  
Genome Assembly ◽  
Brackish Water ◽  
Draft Genome ◽  
Gc Content ◽  
Lyngbya Majuscula ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Putative Protein ◽  
Protein Coding Genes ◽  
A Genome

Limnoraphis robusta CS-951 is a sheathed, filamentous benthic, nonheterocystous cyanobacterium. It was isolated from brackish water and identified morphologically as Lyngbya majuscula . We report the draft genome of L. robusta CS-951, with a genome size of 7,314,117 bp, a 41.6% GC content, and 6,791 putative protein-coding genes assembled into 361contigs.

scholarly journals Draft Genome Sequence of the Fungus Paraphoma sp. B47-9, a Producer of a Biodegradable Plastic–Degrading Enzyme

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yuka Sameshima-Yamashita ◽  
Hideaki Koike ◽  
Motoo Koitabashi ◽  
Azusa Saika ◽  
Tomotake Morita ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gc Content ◽  
Biodegradable Plastic ◽  
Draft Genome Sequence ◽  
Degrading Enzyme ◽  
Draft Genome Assembly

Paraphoma sp. B47-9 is a producer of a biodegradable plastic–degrading enzyme. Here, we report the draft genome sequence of this strain. The draft genome assembly has a size of 39.3 Mb with a GC content of 52.4% and consists of 185 scaffolds.

scholarly journals Genome Sequence of a California Isolate of Fusarium oxysporum f. sp. lycopersici Race 3, a Fungus Causing Wilt Disease on Tomato

2019 ◽  
Vol 8 (15) ◽  
Author(s):  
Peter M. Henry ◽  
Michelle Stueven ◽  
Sampson Li ◽  
Eugene M. Miyao ◽  
Thomas R. Gordon ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gc Content ◽  
Wilt Disease ◽  
Read Coverage ◽  
High Quality ◽  
Content Type ◽  
Draft Genome Assembly ◽  
Important Disease

Fusarium wilt of tomato, caused by the soilborne fungus Fusarium oxysporum f. sp. lycopersici, is an increasingly important disease of tomato. This paper reports the high-quality draft genome assembly of F. oxysporum f. sp. lycopersici isolate D11 (race 3), which consists of 39 scaffolds with 57,281,978 bp (GC content, 47.5%), an N 50 of 4,408,267 bp, a mean read coverage of 99.8×, and 17,682 predicted genes.

scholarly journals Draft Genome Assembly of Floccularia luteovirens, an Edible and Symbiotic Mushroom on Qinghai-Tibet Plateau

2020 ◽  
Vol 10 (4) ◽  
pp. 1167-1173
Author(s):  
Xiaolong Gan ◽  
Dong Cao ◽  
Zhenyu Zhang ◽  
Shu Cheng ◽  
Le Wei ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Gene Families ◽  
Ectomycorrhizal Fungus ◽  
Tibet Plateau ◽  
Specific Gene ◽  
Illumina Hiseq ◽  
Draft Genome Assembly ◽  
Protection And Utilization ◽  
Qinghai Tibet Plateau

Floccularia luteovirens, also known as “Yellow mushroom”, is an edible ectomycorrhizal fungus widely distributed in the Qinghai-Tibet Plateau alpine meadow. So far, little genomic information is known about F. luteovirens, which is not conductive to the protection and utilization of it. In this manuscript, we present a first draft genome assembly and annotation of F. luteovirens. The fruiting body of F. luteovirens was sequenced with PacBio Sequel and Illumina Hiseq 2500 system. The assembled genome size was 28.8 Mb, and comprising 183 contigs with a N50 contig size of 571 kb. A total of 8,333 protein-coding genes were predicted and 7,999 genes were further assigned to different public protein databases. Besides, 400 CAZymes were identified in F. luteovirens. Phylogenetic analysis suggested that F. luteovirens should belong to the Agaricaceae family. Time tree result showed that the speciation of F. luteovirens happened approximately 170 Million years ago. Furthermore, 357 species-specific gene families were annotated against KEGG and GO database. This genome assembly and annotation should be an essential genomic foundation for understanding the phylogenetic, metabolic and symbiotic traits of F. luteovirens.

scholarly journals Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Bhavani Manivannan ◽  
Niranjana Mahalingam ◽  
Sudhir Jadhao ◽  
Amrita Mishra ◽  
Pravin Nilawe ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Genome Assembly ◽  
Biofilm Formation ◽  
Draft Genome ◽  
Drug Resistant ◽  
Draft Genome Assembly ◽  
Extensively Drug Resistant ◽  
History Of ◽  
Urinary Tuberculosis

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

2012 ◽  
Vol 71 (6) ◽  
pp. 895-906 ◽  
Author(s):  
Luming Yang ◽  
Dal-Hoe Koo ◽  
Yuhong Li ◽  
Xuejiao Zhang ◽  
Feishi Luan ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Genome Assembly ◽  
Draft Genome ◽  
High Density ◽  
Chromosome Rearrangements ◽  
Draft Genome Assembly

scholarly journals The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

2019 ◽  
Author(s):  
Mosè Manni ◽  
Felipe A. Simao ◽  
Hugh M. Robertson ◽  
Marco A. Gabaglio ◽  
Robert M. Waterhouse ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gene Families ◽  
Sister Group ◽  
Sensu Stricto ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Animal Group ◽  
Origin And Evolution ◽  
Genomic Analyses ◽  
Metabolism Gene

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

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