scholarly journals Genome description and inventory of immune-related genes of the endangered pen shell Pinna nobilis: a giant bivalve experiencing a mass mortality event

2019 ◽  
Author(s):  
Robert Bunet ◽  
Jean-Marc Prévot ◽  
Nardo Vicente ◽  
José Rafa García-March ◽  
Rajko Martinović ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Innate Immune ◽  
Trna Genes ◽  
Ecological Value ◽  
Illumina Hiseq ◽  
Late 20Th Century ◽  
Pinna Nobilis ◽  
Pen Shell

Abstract Background: The noble pen shell Pinna nobilis is a Mediterranean endemic and emblematic giant bivalve. Already registered as an endangered species in the late 20th century, it is facing a dramatic and rapidly expanding epizooty that decimates its populations since mid-2016. The ecological value of P. nobilis has urged important investigations for conservation purposes. In light of this, we report here the first draft genome of this animal. Results: The whole-genome sequencing has been performed on an Illumina HiSeq X platform using a single paired-end library of short fragments (2x150 bp). The de novo contig assembly accounted for a total size of 584 Mb (96,738 contigs, N50 = 7.6 kb, with 0.4% of “N” nucleotides), representing 77.5% of the predicted genome size of 754 Mb. The pen shell genome is very AT-rich, with a GC-content of 35.6 %. Heterozygosity was found to be in the range of other sequenced bivalves (1%). Over one third (36.2 %) of the genome consisted of repeated elements with a surprising larger number of SINEs elements compared to other molluscan genomes. We were also able to reconstruct the full mitochondrial genome (~19 kb, with 12 protein-coding genes, 2 rRNA and 22 tRNA genes). In relation with the outbreak that affects P. nobilis, we paid a special attention on the innate immune and stress-related genes found in the sequence. We revealed that P. nobilis disposes of a complete chemical defensome, and a relatively sophisticated innate immune system. Conclusion: In addition to offering a valuable resource for further research in comparative biology and evolution, access to the draft genome sequence is central to deepen our understanding of the vulnerability of P. nobilis to new diseases, which are likely to occur more often in the current scenario of a rapidly changing environment.

scholarly journals Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India

2021 ◽  
Author(s):  
VISHNU PRASOODANAN P K ◽  
Shruti S. Menon ◽  
Rituja Saxena ◽  
Prashant Waiker ◽  
Vineet K Sharma
Keyword(s):  
Hot Springs ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Central India ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Protein Coding ◽  
Protein Coding Genes

Discovery of novel thermophiles has shown promising applications in the field of biotechnology. Due to their thermal stability, they can survive the harsh processes in the industries, which make them important to be characterized and studied. Members of Anoxybacillus are alkaline tolerant thermophiles and have been extensively isolated from manure, dairy-processed plants, and geothermal hot springs. This article reports the assembled data of an aerobic bacterium Anoxybacillus sp. strain MB8, isolated from the Tattapani hot springs in Central India, where the 16S rRNA gene shares an identity of 97% (99% coverage) with Anoxybacillus kamchatkensis strain G10. The de novo assembly and annotation performed on the genome of Anoxybacillus sp. strain MB8 comprises of 2,898,780 bp (in 190 contigs) with a GC content of 41.8% and includes 2,976 protein-coding genes,1 rRNA operon, 73 tRNAs, 1 tm-RNA and 10 CRISPR arrays. The predicted protein-coding genes have been classified into 21 eggNOG categories. The KEGG Automated Annotation Server (KAAS) analysis indicated the presence of assimilatory sulfate reduction pathway, nitrate reducing pathway, and genes for glycoside hydrolases (GHs) and glycoside transferase (GTs). GHs and GTs hold widespread applications, in the baking and food industry for bread manufacturing, and in the paper, detergent and cosmetic industry. Hence, Anoxybacillus sp. strain MB8 holds the potential to be screened and characterized for such commercially relevant enzymes.

scholarly journals Draft Genome Sequence of Limisphaera ngatamarikiensis NGM72.4T, a Moderately Alkaliphilic Thermophile Belonging to the Class Verrucomicrobiae

2020 ◽  
Vol 9 (18) ◽  
Author(s):  
Carlo R. Carere ◽  
Jason A. Steen ◽  
Philip Hugenholtz ◽  
Matthew B. Stott
Keyword(s):  
New Zealand ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Coding Sequences ◽  
Content Type ◽  
Aotearoa New Zealand

Limisphaera ngatamarikiensis NGM72.4T is a thermophilic representative of the class Verrucomicrobiae. Isolated from geothermally heated subaqueous clay sediments from a Ngatamariki hotspring in Aotearoa New Zealand, the 3,908,748-bp genome was sequenced using the Illumina HiSeq 2500 platform. Annotation revealed 3,083 coding sequences, including 3,031 proteins, 3 rRNA genes, and 46 tRNA genes.

scholarly journals Draft Genome of the Macadamia Husk Spot Pathogen, Pseudocercospora macadamiae

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.

scholarly journals Draft genome of Bugula neritina, a colonial animal packing powerful symbionts and potential medicines

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Mikhail Rayko ◽  
Aleksey Komissarov ◽  
Jason C. Kwan ◽  
Grace Lim-Fong ◽  
Adelaide C. Rhodes ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Transcriptome Data ◽  
Biomedical Sciences ◽  
Bugula Neritina ◽  
Genome Sequences ◽  
Illumina Hiseq ◽  
Draft Assembly ◽  
Metazoan Genome ◽  
Animal Phyla

Abstract Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum Bryozoa). Interest in this species spans ecology and biomedical sciences because B. neritina is the natural source of bioactive compounds called bryostatins. Here we present a draft assembly of the B. neritina genome obtained from PacBio and Illumina HiSeq data, as well as genes and proteins predicted de novo and verified using transcriptome data, along with the functional annotation. These sequences will permit a better understanding of host-symbiont interactions at the genomic level, and also contribute additional phylogenomic markers to evaluate Lophophorate or Lophotrochozoa phylogenetic relationships. The effort also fits well with plans to ultimately sequence all orders of the Metazoa.

scholarly journals Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach

2018 ◽  
Author(s):  
Sébastien Renaut ◽  
Davide Guerra ◽  
Walter R. Hoeh ◽  
Donald T. Stewart ◽  
Arthur E. Bogan ◽  
...  
Keyword(s):  
De Novo ◽  
Freshwater Mussels ◽  
Draft Genome ◽  
Uniparental Inheritance ◽  
Ecological Value ◽  
Doubly Uniparental Inheritance ◽  
Total Size ◽  
High Coverage ◽  
Genome Coverage ◽  
Eukaryotic Genes

AbstractFreshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecological value and unique “doubly uniparental inheritance” mode of mitochondrial DNA transmission of freshwater mussels. The genome described here was obtained by combining high coverage short reads (65X genome coverage of Illumina paired-end and 11X genome coverage of mate-pairs sequences) with low coverage Pacific Biosciences long reads (0.3X genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54Gb (366,926 scaffolds, N50 = 6.5Kb, with 2.3% of “N” nucleotides), representing 86% of the predicted genome size of 1.80Gb, while over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Given the repeated genetic bottlenecks of V. ellipsiformis populations as a result of glaciations events, heterozygosity was also found to be remarkably low (0.6%), in contrast to most other sequenced bivalve species. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.

scholarly journals Draft genome of the Reindeer (Rangifer tarandus)

2017 ◽  
Author(s):  
Zhipeng Li ◽  
Zeshan Lin ◽  
Lei Chen ◽  
Hengxing Ba ◽  
Yongzhi Yang ◽  
...  
Keyword(s):  
Rangifer Tarandus ◽  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Divergence Time ◽  
Capra Hircus ◽  
High Quality ◽  
Illumina Hiseq

AbstractBackgroundReindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovids’ milk. A high quality reference genome of this specie will assist efforts to elucidate these and other important features in the reindeer.FindingsWe obtained 723.2 Gb (Gigabase) of raw reads by an Illumina Hiseq 4000 platform, and a 2.64 Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21,555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1,339 snRNA and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus, and ancestors of Bos taurus and Capra hircus, is estimated to be 29.55 million years ago (Mya).ConclusionsOur results provide the first high-quality reference genome for the reindeer, and a valuable resource for studying evolution, domestication and other unusual characteristics of the reindeer.

scholarly journals Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India

2021 ◽  
Vol 10 (50) ◽  
Author(s):  
Asha Santhi ◽  
Venkatesh Subramanian ◽  
Krishnaveni Muthan
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Marine Sediment Sample

A DNase-producing Bacillus pacificus strain was isolated, and the whole-genome sequence is reported in this paper. The draft genome sequence of Bacillus pacificus KVCMST-8A-12 constitutes 2.4 Gbp of raw reads, with a GC content of 35.24%. In total, 5,661 protein-coding genes, 64 tRNA genes, and 4 rRNA genes were predicted.

scholarly journals Draft Genome Resources of Two Strains of Xylella fastidiosa XYL1732/17 and XYL2055/17 Isolated from Mallorca Vineyards

2019 ◽  
Vol 109 (2) ◽  
pp. 222-224 ◽  
Author(s):  
Margarita Gomila ◽  
Eduardo Moralejo ◽  
Antonio Busquets ◽  
Guillem Segui ◽  
Diego Olmo ◽  
...  
Keyword(s):  
De Novo ◽  
Xylella Fastidiosa ◽  
Draft Genome ◽  
Open Reading Frames ◽  
Pierce's Disease ◽  
Trna Genes ◽  
The European Union ◽  
Disease Symptoms ◽  
Pierce’S Disease ◽  
Reading Frames

Xylella fastidiosa is a plant-pathogenic bacterium that causes serious diseases in many crops of economic importance and is a quarantine organism in the European Union. This study reports a de novo-assembled draft genome sequence of the first isolates causing Pierce’s disease in Europe: X. fastidiosa subsp. fastidiosa strains XYL1732/17 and XYL2055/17. Both strains were isolated from grapevines (Vitis vinifera) showing Pierce’s disease symptoms at two different locations in Mallorca, Spain. The XYL1732/17 genome is 2,444,109 bp long, with a G+C content of 51.5%; it contains 2,359 open reading frames and 48 tRNA genes. The XYL2055/17 genome is 2,456,780 bp long, with a G+C content of 51.5%; it contains 2,384 open reading frames and 48 tRNA genes.

scholarly journals Draft genome of Meyerozyma guilliermondii strain vka1: a yeast strain with composting potential

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Ravisankar Valsalan ◽  
Deepu Mathew
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Hybrid Approach ◽  
Sequence Annotation ◽  
Illumina Hiseq ◽  
Meyerozyma Guilliermondii ◽  
Genome Wide ◽  
Number Of Genes ◽  
Proteome Profile ◽  
Organic Compost

Abstract Background Meyerozyma guilliermondii is a yeast which could be isolated from a variety of environments. The vka1 strain isolated and purified from the organic compost was found to have composting potential. To better understand the genes assisting the composting potential in this yeast, whole genome sequencing and sequence annotation were performed. Results The genome of M. guilliermondii vka1 strain was sequenced using a hybrid approach, on Illumina Hiseq-2500 platform at 100× coverage followed by Nanopore platform at 20× coverage. The de novo assembly using dual-fold approach had given draft genome of 10.8 Mb size. The genome was found to contain 5385 genes. The annotation of the genes was performed, and the enzymes identified to have roles in the degradation of macromolecules are discussed in relation to its composting potential. Annotation of the genome assembly of the related strains had revealed the unique biodegradation related genes in this strain. Phylogenetic analysis using the rDNA region has confirmed the position of this strain in the Ascomycota family. Raw reads are made public, and the genome wide proteome profile is presented to facilitate further studies on this organism. Conclusions Meyerozyma guilliermondii vka1 strain was sequenced through hybrid approach and the reads were de novo assembled. Draft genome size and the number of genes in the strain were assessed and discussed in relation to the related strains. Scientific insights into the composting potential of this strain are also presented in relation to the unique genes identified in this strain.

scholarly journals Characterization of genomic, physiological, and probiotic features of Lactiplantibacillus plantarum DY46 strain isolated from Turkish fermented turnip juice (Shalgam)

2021 ◽  
Author(s):  
Ahmet E. Yetiman ◽  
Abdullah KESKİN ◽  
Busra Nur DARENDELI ◽  
Seyfullah Enes KOTIL ◽  
Fatih ORTAKCI ◽  
...  
Keyword(s):  
Alcoholic Beverage ◽  
Draft Genome ◽  
Gc Content ◽  
Illumina Miseq ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Acid And Bile Tolerance ◽  
Miseq Platform ◽  
Pass Through

Abstract A new Lb. plantarum strain DY46 was isolated from a traditionally fermented non-alcoholic beverage called shalgam from the Southern region of Anatolia following incubation on MRS agar at 30°C for 5 days. DY46 is gram-positive, short rod and catalase-negative. This bacterium fermented 22 of the 49 substrates tested on API CH50 fermentation panels. Whole-genome sequencing was performed using the Illumina Miseq platform to learn more about the metabolic capabilities of DY46. The sequences were assembled into a 3.32 Mb draft genome using PATRIC 3.6.8. consisting of 153 contigs, and preliminary genome annotation was performed using the RAST algorithm. The DY46 genome consists of a single circular chromosome of 3,332,827 bp that is predicted to carry 3219 genes, including 61 tRNA genes, 2 rRNA operons. The genome has a GC content of 44.3% includes 98 predicted pseudogenes, 25 complete or partial transposases and 3 intact prophages. DY46 genome also predicted to carry genes of Plantaricin-E, Plantaricin-F and Plantaricin-K showing the antimicrobial potential of this bacterium which can be linked-to in vitro antagonism tests that DY46 can inhibit Salmonella Typimirium ATCC14028, Klebsiella pneumonie ATCC13883, and Proteus vulgaris ATCC8427. The acid and bile tolerance of DY46 revealed this strain could potentially pass through the stomach and reach into the gut to provide probiotic therapeutic affects on health.

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