Draft genome of a biparental beetle species, Lethrus apterus

Abstract Background The lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding about the evolutionary origin of sociality. Lethrus apterus is one of the few insect species that has biparental care. Division of labour can be observed between parents during the reproductive period in order to provide food and protection for their offspring. Results Here, we report the draft genome of L. apterus, the first genome in the family Geotrupidae. The final assembly consisted of 286.93 Mbp in 66,933 scaffolds. Completeness analysis found the assembly contained 93.5% of the Endopterygota core BUSCO gene set. Ab initio gene prediction resulted in 25,385 coding genes, whereas homology-based analyses predicted 22,551 protein coding genes. After merging, 20,734 were found during functional annotation. Compared to other publicly available beetle genomes, 23,528 genes among the predicted genes were assigned to orthogroups of which 1664 were in species-specific groups. Additionally, reproduction related genes were found among the predicted genes based on which a reduction in the number of odorant- and pheromone-binding proteins was detected. Conclusions These genes can be used in further comparative and functional genomic researches which can advance our understanding of the genetic basis and hence the evolution of parental behaviour.

Download Full-text

The Draft Genome Sequence of The Endophytic Streptomyces Strain VITGV156

10.21203/rs.3.rs-791591/v1 ◽

2021 ◽

Author(s):

Veilumuthu P ◽

Nagarajan T ◽

Sasikumar S ◽

Siva R ◽

J Godwin Christopher

Keyword(s):

Secondary Metabolites ◽

Draft Genome ◽

Gc Content ◽

Gene Clusters ◽

Dominant Group ◽

Protein Coding ◽

Peptide Synthetase ◽

The Family ◽

Modified Peptides ◽

Endophytic Streptomyces

Abstract Streptomyces species is one among the dominant group of bacteria in the family Actinobacteria with a rich repertoire of secondary metabolites. Secondary metabolites with antimicrobial activity and plant growth promotor have been isolated from various Streptomyces sp. Here in this investigation, we present the draft genome of a new species, Streptomyces sp. VITGV156 isolated from healthy tomato plant (Lycopersicon esculentum) which has some rare antimicrobial secondary metabolites, like coelichelin, fluostatins, vicenistatin, nystatin, sipanmycin, and informatipeptin. The genome is 8.18 Mb in size with 6,259 protein coding genes. The average GC content of the genome is 72.61 %. Preliminary analysis with antiSMASH 6.0 revealed the presence of 29 biosynthetic gene clusters for the synthesis of potential secondary metabolites. These includes 4 NRPS (non – ribosomal peptide synthetase), 7 PKS (Polyketide Synthases), 2 RiPP (Ribosomally synthesized and post-translationally modified peptides) clusters. When we look into genes associated with secondary metabolites, 406 genes are present which includes 184 genes for cofactor and vitamins, 72 genes for terpenoids and polyketides, 70 genes for xenobiotics and 80 genes for other metabolites are present. Comparative genome analysis of VITGV156 with its closest neighbor Streptomyces luteus strain TRM45540 revealed ANI 91.22% and dDDH value 44.00%.

Download Full-text

Draft Genome of the Macadamia Husk Spot Pathogen, Pseudocercospora macadamiae

Phytopathology ◽

10.1094/phyto-12-19-0460-a ◽

2020 ◽

Vol 110 (9) ◽

pp. 1503-1506

Author(s):

Olufemi A. Akinsanmi ◽

Lilia C. Carvalhais

Keyword(s):

Plant Disease Resistance ◽

Plant Disease ◽

De Novo ◽

Draft Genome ◽

Gc Content ◽

Disease Development ◽

Closely Related Species ◽

Protein Coding ◽

Protein Coding Genes ◽

The Family

Pseudocercospora macadamiae causes husk spot in macadamia in Australia. Lack of genomic resources for this pathogen has restricted acquiring knowledge on the mechanism of disease development, spread, and its role in fruit abscission. To address this gap, we sequenced the genome of P. macadamiae. The sequence was de novo assembled into a draft genome of 40 Mb, which is comparable to closely related species in the family Mycosphaerellaceae. The draft genome comprises 212 scaffolds, of which 99 scaffolds are over 50 kb. The genome has a 49% GC content and is predicted to contain 15,430 protein-coding genes. This draft genome sequence is the first for P. macadamiae and represents a valuable resource for understanding genome evolution and plant disease resistance.

Download Full-text

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

10.1101/2021.03.05.434149 ◽

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.

Download Full-text

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.

Download Full-text

ONT-based draft genome assembly and annotation of Alternaria atra

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-01-21-0016-a ◽

2021 ◽

Author(s):

Bhawna Bonthala ◽

Corinn Sophia Small ◽

Maximilian Anton Lutz ◽

Alexander Graf ◽

Stefan Krebs ◽

...

Keyword(s):

Genome Assembly ◽

Plant Pathogens ◽

Biocontrol Agent ◽

Reference Genome ◽

Gene Prediction ◽

Draft Genome ◽

Protein Coding ◽

Draft Genome Assembly ◽

Reference Genome Assembly ◽

Wide Range

Species of Alternaria (phylum Ascomycota, family Pleosporaceae) are known as serious plant pathogens, causing major losses on a wide range of crops. Alternaria atra (Preuss) Woudenb. & Crous (previously known as Ulocladium atrum) can grow as a saprophyte on many hosts and causes Ulocladium blight on potato. It has been reported that it can also be used as a biocontrol agent against a.o. Botrytis cinerea Here we present a scaffold-level reference genome assembly for A. atra. The assembly contains 43 scaffolds with a total length of 39.62 Mbp, with scaffold N50 of 3,893,166 bp , L50 of 4 and the longest 10 scaffolds containing 89.9% of the assembled data. RNA Seq-guided, gene prediction using BRAKER resulted in 12,173 protein-coding genes with their functional annotation. This first high-quality reference genome assembly and annotation for A. Atra can be used as a resource for studying evolution in the highly complicated Alternaria genus and might help understand the mechanisms defining its role as pathogen or biocontrol agent.

Download Full-text

Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii

BMC Genomics ◽

10.1186/s12864-021-08162-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Dawoon Chung ◽

Yong Min Kwon ◽

Youngik Yang

Keyword(s):

Rna Sequencing ◽

Draft Genome ◽

Sequencing Analysis ◽

Sequencing Data ◽

Terrestrial Plants ◽

Protein Coding ◽

Oxford Nanopore ◽

Wide Range ◽

The Family ◽

Encoding Genes

Abstract Background Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii isolated from decaying bark and decorticated wood was newly identified in the Harzianum clade of Trichoderma. Due to a wide range of applications in agriculture and other industries, genomes of at least 12 Trichoderma spp. have been studied. Moreover, antifungal and enzymatic activities have been extensively characterized in Trichoderma spp. However, the genomic information and bioactivities of T. simmonsii from a particular marine-derived isolate remain largely unknown. While we screened for asparaginase-producing fungi, we observed that T. simmonsii GH-Sj1 strain isolated from edible kelp produced asparaginase. In this study, we report a draft genome of T. simmonsii GH-Sj1 using Illumina and Oxford Nanopore technologies. Furthermore, to facilitate biotechnological applications of this species, RNA-sequencing was performed to elucidate the transcriptional profile of T. simmonsii GH-Sj1 in response to asparaginase-rich conditions. Results We generated ~ 14 Gb of sequencing data assembled in a ~ 40 Mb genome. The T. simmonsii GH-Sj1 genome consisted of seven telomere-to-telomere scaffolds with no sequencing gaps, where the N50 length was 6.4 Mb. The total number of protein-coding genes was 13,120, constituting ~ 99% of the genome. The genome harbored 176 tRNAs, which encode a full set of 20 amino acids. In addition, it had an rRNA repeat region consisting of seven repeats of the 18S-ITS1–5.8S-ITS2–26S cluster. The T. simmonsii genome also harbored 7 putative asparaginase-encoding genes with potential medical applications. Using RNA-sequencing analysis, we found that 3 genes among the 7 putative genes were significantly upregulated under asparaginase-rich conditions. Conclusions The genome and transcriptome of T. simmonsii GH-Sj1 established in the current work represent valuable resources for future comparative studies on fungal genomes and asparaginase production.

Download Full-text

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

Genome Biology and Evolution ◽

10.1093/gbe/evaa090 ◽

2020 ◽

Vol 12 (6) ◽

pp. 860-866 ◽

Cited By ~ 1

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.

Download Full-text

The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe

Genes ◽

10.3390/genes10090708 ◽

2019 ◽

Vol 10 (9) ◽

pp. 708 ◽

Cited By ~ 5

Author(s):

Julien Alban Nguinkal ◽

Ronald Marco Brunner ◽

Marieke Verleih ◽

Alexander Rebl ◽

Lidia de los Ríos-Pérez ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Gene Prediction ◽

Draft Genome ◽

Single Copy ◽

Sander Lucioperca ◽

Illumina Platform ◽

Protein Coding ◽

Draft Genome Assembly ◽

And Performance

The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.

Download Full-text

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

10.1101/424614 ◽

2018 ◽

Cited By ~ 3

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.

Download Full-text

Draft Genome Sequence of Paludibacter jiangxiensis NM7T, a Propionate-Producing Fermentative Bacterium

Genome Announcements ◽

10.1128/genomea.00667-17 ◽

2017 ◽

Vol 5 (29) ◽

Cited By ~ 1

Author(s):

Yan-Ling Qiu ◽

Dieter M. Tourlousse ◽

Norihisa Matsuura ◽

Akiko Ohashi ◽

Yuji Sekiguchi

Keyword(s):

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

High Quality ◽

Protein Coding ◽

Coding Sequences ◽

Content Type ◽

The Family

ABSTRACT We report here a high-quality draft genome sequence of Paludibacter jiangxiensis strain NM7T, a mesophilic, anaerobic, propionate-producing fermentative bacterium within the family Porphyromonadaceae of the phylum Bacteroidetes. The genome comprises 3,664,884 bp in four contigs, has a G+C content of 42.92%, and contains 2,949 protein-coding sequences and 62 RNAs.

Download Full-text