Draft genome of starch-degrading actinobacterium, Microbacterium mangrovi MUSC 115T isolated from intertidal sediments

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Wen-Si Tan ◽  
Huey-Jia Cheng ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
...  
Keyword(s):  
Draft Genome ◽  
Intertidal Sediments ◽  
Total Size ◽  
General Physiology ◽  
Genome Features

Microbacterium mangrovi strain MUSC 115T was isolated from intertidal sediments of Kuantan, Malaysia. Here we describe the draft genome of amylolytic strain MUSC 115T with total size of 4.4 Mbp from 55 contigs and G + C content of 70.0%. Total of 4,096 coding genes were observed, with 2 putative amylases genes in the draft genome of MUSC 115T. These genome features of MUSC 115T can improve our understanding of its starch-degrading mechanism and general physiology of the species, which provide opportunities for biotechnological and industrial exploitation.

scholarly journals Draft Genome Sequence of the d-Xylose-Fermenting Yeast Spathaspora xylofermentans UFMG-HMD23.3

2017 ◽  
Vol 5 (33) ◽  
Author(s):  
Daiane D. Lopes ◽  
Samuel P. Cibulski ◽  
Fabiana Q. Mayer ◽  
Franciele M. Siqueira ◽  
Carlos A. Rosa ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Total Size ◽  
Amazonian Forest

ABSTRACT Here, we report the draft genome sequence of the yeast Spathaspora xylofermentans UFMG-HMD23.3 (=CBS 12681), a d-xylose-fermenting yeast isolated from the Amazonian forest. The genome consists of 298 contigs, with a total size of 15.1 Mb, including the mitochondrial genome, and 5,948 predicted genes.

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.

Draft genome sequence of multidrug-resistant Bradyrhizobium sp. BL isolated from a sewage treatment plant in China

2019 ◽  
Author(s):  
Peng Bao ◽  
Guo-Xiang Li ◽  
Yu-Qin He ◽  
Yi Dai
Keyword(s):  
Antibiotic Resistance ◽  
Municipal Wastewater ◽  
Draft Genome ◽  
Sewage Treatment Plant ◽  
Treatment Plant ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Municipal Wastewater Treatment ◽  
Total Size ◽  
Bradyrhizobium Sp

Abstract The genus Bradyrhizobium is considered to be widespread and abundant group of symbiotic bacteria in many plant-soil ecosystems. However, the ecological versatility of this phylogenetic group remains highly understudied in man-made ecosystems, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this genus for human health, we analyzed the high quality draft genome of Bradyrhizobium strain BL, isolated from a municipal wastewater treatment plant in Ningbo, China. The Bradyrhizobium sp. BL draft genome has a total size of 7,718,431 bp with an overall G + C content of 46.43%. From a total of 7236 predicted sequences, 7176 and 60 are protein and RNA coding sequences, respectively. Moreover, 63.51% of the predicted genes were assigned into to Clusters of Orthologous Groups (COG) functional categories. The Bradyrhizobium sp. BL genome contains various defense mechanisms against antibiotics that up to predicted 60 antibiotic resistance coding genes. The Bradyrhizobium sp. BL genome contains 237 termed virulence factors coding genes which show its potential pathogenicity. This study provides important insights into the genomic diversity of the genus Bradyrhizobium and provides a foundation for future comparative genomic studies that will generate a better understanding of the antibiotic resistance process.

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

2020 ◽  
Vol 12 (7) ◽  
pp. 1074-1079 ◽  
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.

scholarly journals Draft Genome Sequence of Xylaria longipes DSM 107183, a Saprotrophic Ascomycete Colonizing Hardwood

2019 ◽  
Vol 8 (12) ◽  
Author(s):  
Enrico Büttner ◽  
Anna Maria Gebauer ◽  
Martin Hofrichter ◽  
Christiane Liers ◽  
Harald Kellner
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Soft Rot ◽  
Draft Genome Sequence ◽  
Acer Pseudoplatanus ◽  
Whole Genome ◽  
Total Size ◽  
Content Type ◽  
Bavarian Forest

The saprotrophic soft-rot fungus Xylaria longipes was isolated from deadwood of Acer pseudoplatanus collected in the Bavarian Forest, Germany. The whole genome of this strain (DSM 107183) was sequenced with a total size of 43.2 Mb and a G+C content of 48.5%.

scholarly journals Draft Genome Sequence ofBacteroidalesStrain 6E, Isolated from a Rice Paddy Field in Japan

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Dieter M. Tourlousse ◽  
Takuya Honda ◽  
Norihisa Matsuura ◽  
Akiko Ohashi ◽  
Akio Tonouchi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Paddy Field ◽  
Draft Genome ◽  
Rice Paddy ◽  
Draft Genome Sequence ◽  
Total Size ◽  
Protein Coding ◽  
Rice Paddy Field ◽  
Paddy Field Soil ◽  
Rna Genes

We generated a high-quality draft genome sequence ofBacteroidalesstrain 6E, a strict anaerobe newly isolated from Japanese rice paddy field soil. The genome consists of 61 contigs, with a total size of 4,436,542 bp and mean G+C content of 45.4%. Annotation predicted 3,620 protein-coding and 54 RNA genes.

scholarly journals Draft Genome Sequences of Rhodosporidium toruloides Strains ATCC 10788 and ATCC 10657 with Compatible Mating Types

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Jie Hu ◽  
Lianghui Ji
Keyword(s):  
Mating Type ◽  
Draft Genome ◽  
Gc Content ◽  
Rhodotorula Glutinis ◽  
Rhodosporidium Toruloides ◽  
Strain Atcc ◽  
Genome Sequences ◽  
Total Size ◽  
Diploid Parent ◽  
Protein Encoding

Rhodosporidium toruloides ATCC 10788 (haploid, A1 mating type) and ATCC 10657 (haploid, A2 mating type) were derived from the same diploid parent strain Rhodotorula glutinis ATCC 90781 and are important strains for metabolic engineering. Draft genome sequences of both strains are reported here. The current assembly of strain ATCC 10788 comprises 61 scaffolds with a total size of 20.75 Mbp and a GC content of 62.01%, while that of strain ATCC 10657 comprises 137 scaffolds with a total size of 21.49 Mbp and a GC content of 61.81%. Genome annotation predicts 7,730 and 7,800 protein encoding genes for strain ATCC 10788 and strain ATCC 10657, respectively.

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 Sequence ofStreptococcus gordoniiType Strain CCUG 33482T

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Francisco Salvà-Serra ◽  
Hedvig E. Jakobsson ◽  
Kaisa Thorell ◽  
Lucia Gonzales-Siles ◽  
Erika T. Hallbäck ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Type Strain ◽  
Draft Genome ◽  
Bacterial Endocarditis ◽  
Draft Genome Sequence ◽  
Streptococcus Gordonii ◽  
Subacute Bacterial Endocarditis ◽  
Streptococcus Mitis ◽  
Total Size ◽  
Coding Sequences

Streptococcus gordoniitype strain CCUG 33482Tis a member of theStreptococcus mitisgroup, isolated from a case of subacute bacterial endocarditis. Here, we report the draft genome sequence ofS. gordoniiCCUG 33482T, composed of 41 contigs of a total size of 2.15 Mb with 2,061 annotated coding sequences.

scholarly journals Draft Genome Assembly of the Bloom-Forming CyanobacteriumNodularia spumigenaStrain CENA596 in Shrimp Production Ponds

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Rafael Vicentini Popin ◽  
Janaina Rigonato ◽  
Vinicius Augusto Carvalho Abreu ◽  
Ana Paula Dini Andreote ◽  
Savênia Bonoto Silveira ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Assembly ◽  
Draft Genome ◽  
Rio Grande ◽  
Gene Clusters ◽  
Rio Grande Do Sul ◽  
Total Size ◽  
Nodularia Spumigena ◽  
Draft Genome Assembly ◽  
Shrimp Production

We report here the draft genome assembly of the brackish cyanobacteriumNodularia spumigenastrain CENA596 isolated from a shrimp production pond in Rio Grande do Sul, Brazil. The draft genome consists of 291 contigs with a total size of 5,189,679 bp. Secondary metabolite annotations resulted in several predicted gene clusters, including those responsible for encoding the hepatotoxin nodularin.

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