scholarly journals Genome Sequence of Trichoderma lixii MUT3171, A Promising Strain for Mycoremediation of PAH-Contaminated Sites

2020 ◽  
Vol 8 (9) ◽  
pp. 1258
Author(s):  
Francesco Venice ◽  
Domenico Davolos ◽  
Federica Spina ◽  
Anna Poli ◽  
Valeria Paola Prigione ◽  
...  
Keyword(s):  
Genome Sequence ◽  
High Throughput Sequencing ◽  
Draft Genome ◽  
Genome Mining ◽  
Bioactive Molecules ◽  
Survival Strategies ◽  
Contaminated Sites ◽  
Gene Repertoire ◽  
Wide Range ◽  
Trichoderma Lixii

Mono- and polycyclic aromatic hydrocarbons (PAHs) are widespread and recalcitrant pollutants that threaten both environmental and human health. By exploiting the powerful enzymatic machinery of fungi, mycoremediation in contaminated sites aims at removing a wide range of pollutants in a cost-efficient and environmentally friendly manner. Next-generation sequencing (NGS) techniques are powerful tools for understanding the molecular basis of biotransformation of PAHs by selected fungal strains, allowing genome mining to identify genetic features of biotechnological value. Trichoderma lixii MUT3171, isolated from a historically PAH-contaminated soil in Italy, can grow on phenanthrene, as a sole carbon source. Here, we report the draft genome sequence of T. lixii MUT3171 obtained with high-throughput sequencing method. The genome of T. lixii MUT3171 was compared with other 14 Trichoderma genomes, highlighting both shared and unique features that can shed a light on the biotransformation of PAHs. Moreover, the genes potentially involved in the production of important biosurfactants and bioactive molecules have been investigated. The gene repertoire of T. lixii MUT3171 indicates a high degrading potential and provides hints on putative survival strategies in a polluted environment.

scholarly journals The draft genome sequence of the grove snail Cepaea nemoralis

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Suzanne V Saenko ◽  
Dick S J Groenenberg ◽  
Angus Davison ◽  
Menno Schilthuizen
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Agricultural Pests ◽  
Shell Color ◽  
Protein Coding ◽  
Cepaea Nemoralis ◽  
Edible Species ◽  
Wide Range ◽  
In Captivity ◽  
Long Read

Abstract Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific variation. More recently, Cepaea has been the focus of citizen science projects on shell color evolution in relation to climate change and urbanization. C. nemoralis is particularly useful for studies on the genetics of shell polymorphism and the evolution of “supergenes,” as well as evo-devo studies of shell biomineralization, because it is relatively easily maintained in captivity. However, an absence of genomic resources for C. nemoralis has generally hindered detailed genetic and molecular investigations. We therefore generated ∼23× coverage long-read data for the ∼3.5 Gb genome, and produced a draft assembly composed of 28,537 contigs with the N50 length of 333 kb. Genome completeness, estimated by BUSCO using the metazoa dataset, was 91%. Repetitive regions cover over 77% of the genome. A total of 43,519 protein-coding genes were predicted in the assembled genome, and 97.3% of these were functionally annotated from either sequence homology or protein signature searches. This first assembled and annotated genome sequence for a helicoid snail, a large group that includes edible species, agricultural pests, and parasite hosts, will be a core resource for identifying the loci that determine the shell polymorphism, as well as in a wide range of analyses in evolutionary and developmental biology, and snail biology in general.

scholarly journals Draft Genome Sequences of Fungus Aspergillus calidoustus

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Fabian Horn ◽  
Jörg Linde ◽  
Derek J. Mattern ◽  
Grit Walther ◽  
Reinhard Guthke ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Sequence ◽  
Functional Annotation ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Genome Sequences

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504) . The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

scholarly journals Draft Genome Sequence of a Medium- and Long-Chain n-Alkane-Degrading Bacterium, Tsukamurella tyrosinosolvens Strain PS2, with Two Genetic Systems for Alkane Degradation

2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Valeriya A. Romanova ◽  
Eugenia A. Boulygina ◽  
Maria N. Siniagina ◽  
Maria I. Markelova ◽  
Tatiana V. Grigoryeva ◽  
...  
Keyword(s):  
Organic Synthesis ◽  
Genome Sequence ◽  
Draft Genome ◽  
Carbon Sources ◽  
Draft Genome Sequence ◽  
Alkane Degradation ◽  
Content Type ◽  
Degrading Bacterium ◽  
Wide Range ◽  
Long Chain

Here, we report the genome sequence of Tsukamurella tyrosinosolvens strain PS2, which was isolated from hydrocarbon sludge of an organic synthesis factory. This strain was able to utilize a wide range of n-alkanes, from C16 to C35, as sole carbon sources.

scholarly journals Draft Genome Sequence of Rhodopirellula baltica Strain BR-MGV, a Planctomycete Isolated from Brazilian Mangrove Soil

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Juliana Eschholz de Araújo ◽  
Rodrigo Gouvêa Taketani ◽  
Michele de Cássia Pereira e Silva ◽  
Marcus Venicius de Mello Lourenço ◽  
Fernando Dini Andreote
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Mangrove Soil ◽  
Wide Range

Members of the phylum Planctomycetes, which are capable of surviving in a wide range of environments, are some of the least-explored bacteria. Here, we report the near-complete draft genome sequence and annotation of the planctomycete Rhodopirellula baltica BR-MGV, which was isolated from the soil of a contaminated Brazilian mangrove.

scholarly journals Draft Genome Sequence of the Thermotolerant Cyanobacterium Desertifilum sp. IPPAS B-1220

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Kirill S. Mironov ◽  
Maria A. Sinetova ◽  
Kenzhegul Bolatkhan ◽  
Bolatkhan K. Zayadan ◽  
Vera V. Ustinova ◽  
...  
Keyword(s):  
Bioactive Compounds ◽  
Genome Sequence ◽  
Draft Genome ◽  
Genome Mining ◽  
Draft Genome Sequence ◽  
Nonribosomal Peptides ◽  
Filamentous Cyanobacterium ◽  
Medical Importance

Here, we report the draft genome of the filamentous cyanobacterium Desertifilum sp. strain IPPAS B-1220, isolated from Lake Shar-Nuur, Mongolia. The genome of 6.1 Mb codes for 5,113 genes. Genome mining revealed 10 clusters for the synthesis of bioactive compounds (nonribosomal peptides, polyketides, bacteriocins, and lantipeptides) with potential biotechnological or medical importance.

scholarly journals Draft Genome Sequence of Nonomuraea sp. Strain C10, a Producer of Brartemicin, Isolated from a Mud Dauber Wasp Nest in Nepal

2019 ◽  
Vol 8 (45) ◽  
Author(s):  
Niraj Aryal ◽  
Saefuddin Aziz ◽  
Prajwal Rajbhandari ◽  
Harald Gross
Keyword(s):  
Secondary Metabolites ◽  
Natural Product ◽  
Genome Sequence ◽  
Draft Genome ◽  
Genome Mining ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Insight Into

Nonomuraea sp. strain C10 produces the cytotoxic natural product brartemicin. Here, we report its draft genome sequence to get insight into brartemicin biosynthesis and to enable genome mining for novel secondary metabolites.

scholarly journals Complete Genome Sequence of Lactobacillus plantarum Strain JDARSH, Isolated from Sheep Milk

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Abhinandan Patil ◽  
Anamika Dubey ◽  
Muneer Ahmad Malla ◽  
John Disouza ◽  
Shivaji Pawar ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Genome Sequence ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Sheep Milk ◽  
Wide Range ◽  
Range Of Functions

Lactobacillus plantarum strain JDARSH, a potential probiotic with a wide range of functions, was isolated from sheep milk. Here, we report the whole-genome sequence of this bacterium. The draft genome yielded a 3.20-Mb genome and 2,980 protein-coding sequences.

scholarly journals Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

Nature ◽  
2013 ◽  
Vol 496 (7443) ◽  
pp. 91-95 ◽  
Author(s):  
Jizeng Jia ◽  
◽  
Shancen Zhao ◽  
Xiuying Kong ◽  
Yingrui Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Aegilops Tauschii ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Gene Repertoire

scholarly journals Draft Genome Sequence of Rhodococcus sp. Strain M8, Which Can Degrade a Broad Range of Nitriles

2018 ◽  
Vol 6 (6) ◽  
pp. e01526-17 ◽  
Author(s):  
Andrey D. Novikov ◽  
Konstantin V. Lavrov ◽  
Artem S. Kasianov ◽  
Tatyana V. Gerasimova ◽  
Alexander S. Yanenko
Keyword(s):  
Genome Sequence ◽  
Nitrile Hydratase ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Contaminated Sites ◽  
Degrading Bacterium ◽  
Rhodococcus Sp

ABSTRACT Rhodococcus sp. strain M8 is a nitrile-degrading bacterium isolated from acrylonitrile-contaminated sites. This strain produces the enzymes for sequential nitrile degradation, cobalt-type nitrile hydratase, and amidase in large amounts. Its draft genome sequence, announced here, has an estimated size of 6.3 Mbp.

scholarly journals Deep-BGCpred: A unified deep learning genome-mining framework for biosynthetic gene cluster prediction

2021 ◽  
Author(s):  
Ziyi Yang ◽  
Benben Liao ◽  
Changyu Hsieh ◽  
Chao Han ◽  
Liang Fang ◽  
...  
Keyword(s):  
Natural Products ◽  
Deep Learning ◽  
High Throughput Sequencing ◽  
Short Term Memory ◽  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Bioactive Molecules ◽  
Dual Model ◽  
Biosynthetic Gene

Natural products produced by microorganisms constitute an important source of essential pharmaceuticals, including antimicrobial and anti-tumor drugs. These bioactive molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The rapid increase of microbial genomics resources, due to the availability of high-throughput sequencing technologies, has spurred the development of computational methods for microbial genome mining for BGC discovery. Current machine learning methods, however, have limited successes in uncovering novel BGCs due to an excessive number of false positives in their predictions. To this end, we propose Deep-BGCpred, a framework that effectively addresses the aforementioned issue by improving a deep learning model termed DeepBGC. The new model embeds multi-source protein family domains and employs a stacked Bidirectional Long Short-Term Memory model to boost accuracy for BGC identifications. In particular, it integrates two customized strategies, sliding window strategy and dual-model serial screening, to improve the model's performance stability and reduce the number of false positive in BGC predictions. We compare the proposed model against other well-established methods on common benchmarks and achieve new state-of-the-art results with convincing evidences. We expect that researchers working on genome mining for natural products may be greatly benefited from our newly proposed method, Deep-BGCpred.

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