scholarly journals Diploid genome assembly of Kluyveromyces marxianus NRRL Y-50883 (SLP1)

2021 ◽  
Author(s):  
Carolina Gómez-Márquez ◽  
Dania Sandoval-Nuñez ◽  
Anne Gschaedler ◽  
Teresa Romero-Gutiérrez ◽  
Lorena Amaya-Delgado ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Kluyveromyces Marxianus ◽  
Gc Content ◽  
Cellular Component ◽  
Biological Processes ◽  
Growth Inhibitors ◽  
Research Attention ◽  
Diploid Genome ◽  
Biotechnological Processes ◽  
Haplotype A

Abstract The yeast Kluyveromyces marxianus SLP1 has the potential for application in biotechnological processes because it can metabolize several sugars and produce high-value metabolites. K. marxianus SLP1 is a thermotolerant yeast isolated from the mezcal process, and it is tolerant to several cell growth inhibitors such as saponins, furan aldehydes, weak acids, and phenolics compounds. The genomic differences between dairy and non-dairy strains related to K. marxianus variability are a focus of research attention, particularly the pathways leading this species toward polyploidy. We report the diploid genome assembly of K. marxianus SLP1 non-lactide strain into 32 contigs to reach a size of ∼12 Mb (N50 = 1.3Mb) and a ∼39% GC content. Genome size is consistent with the k-mer frequency results. Genome annotation by Funannotate estimated 5000 genes in haplotype A and 4910 in haplotype B. The enriched annotated genes by ontology show differences between alleles in biological processes and cellular component. The analysis of variants related to DMKU3 and between haplotypes shows changes in LAC12 and INU1, which we hypothesize can impact carbon source performance. This report presents the first polyploid K. marxianus strain recovered from non-lactic fermenting medium.

scholarly journals Diploid Genome Assembly of the Wine Grape Carménère

2019 ◽  
Vol 9 (5) ◽  
pp. 1331-1337 ◽  
Author(s):  
Andrea Minio ◽  
Mélanie Massonnet ◽  
Rosa Figueroa-Balderas ◽  
Alvaro Castro ◽  
Dario Cantu
Keyword(s):  
Genome Assembly ◽  
Wine Grape ◽  
Diploid Genome

scholarly journals Proteomic landscape of TGF-β1-induced fibrogenesis in renal fibroblasts

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shujun Zhou ◽  
Xiaoke Yin ◽  
Manuel Mayr ◽  
Mazhar Noor ◽  
Peter J. Hylands ◽  
...  
Keyword(s):  
Transforming Growth Factor ◽  
Rat Kidney ◽  
Cellular Component ◽  
Network Pharmacology ◽  
Spectrometric Analysis ◽  
Biological Processes ◽  
Proteomic Profiling ◽  
Cell Lysate ◽  
Molecular Functions ◽  
Tgf Β1

Abstract Transforming growth factor-β1 (TGF-β1) plays a premier role in fibrosis. To understand the molecular events underpinning TGF-β1-induced fibrogenesis, we examined the proteomic profiling of a TGF-β1-induced in vitro model of fibrosis in NRK-49F normal rat kidney fibroblasts. Mass spectrometric analysis indicated that 628 cell-lysate proteins enriched in 44 cellular component clusters, 24 biological processes and 27 molecular functions were regulated by TGF-β1. Cell-lysate proteins regulated by TGF-β1 were characterised by increased ribosomal proteins and dysregulated proteins involved in multiple metabolic pathways, including reduced Aldh3a1 and induced Enpp1 and Impdh2, which were validated by enzyme-linked immunosorbent assays (ELISA). In conditioned media, 62 proteins enriched in 20 cellular component clusters, 40 biological processes and 7 molecular functions were regulated by TGF-β1. Secretomic analysis and ELISA uncovered dysregulated collagen degradation regulators (induced PAI-1 and reduced Mmp3), collagen crosslinker (induced Plod2), signalling molecules (induced Ccn1, Ccn2 and Tsku, and reduced Ccn3) and chemokines (induced Ccl2 and Ccl7) in the TGF-β1 group. We conclude that TGF-β1-induced fibrogenesis in renal fibroblasts is an intracellular metabolic disorder and is inherently coupled with inflammation mediated by chemokines. Proteomic profiling established in this project may guide development of novel anti-fibrotic therapies in a network pharmacology approach.

scholarly journals A Short-Read Genome Assembly Resource for Leveillula taurica Causing Powdery Mildew Disease of Sweet Pepper (Capsicum annuum)

2020 ◽  
Vol 33 (6) ◽  
pp. 782-786
Author(s):  
Stefan Kusch ◽  
Márk Z. Németh ◽  
Niloofar Vaghefi ◽  
Heba M. M. Ibrahim ◽  
Ralph Panstruga ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Capsicum Annuum ◽  
Genome Assembly ◽  
Reference Genome ◽  
Gc Content ◽  
Sweet Pepper ◽  
Mesophyll Cells ◽  
Short Read ◽  
Leveillula Taurica ◽  
Reference Genome Assembly

Powdery mildew of sweet pepper (Capsicum annuum) is an economically important disease. It is caused by Leveillula taurica, an obligate biotrophic ascomycete with a partly endophytic mycelium and haustoria, i.e., feeding structures formed in the mesophyll cells of infected host plant tissues. The molecular basis of its pathogenesis is largely unknown because genomic resources only exist for epiphytically growing powdery mildew fungi with haustoria formed exclusively in epidermal cells of their plant hosts. Here, we present the first reference genome assembly for an isolate of L. taurica isolated from sweet pepper in Hungary. The short read–based assembly consists of 23,599 contigs with a total length of 187.2 Mbp; the scaffold N50 is 13,899 kbp and N90 is 3,522 kbp; and the average GC content is 39.2%. We detected at least 92,881 transposable elements covering 55.5 Mbp (30.4%). BRAKER predicted 19,751 protein-coding gene models in this assembly. Our reference genome assembly of L. taurica is the first resource to study the molecular pathogenesis and evolution of a powdery mildew fungus with a partly endophytic lifestyle.

scholarly journals A graph-based approach to diploid genome assembly

2018 ◽  
Vol 34 (13) ◽  
pp. i105-i114 ◽  
Author(s):  
Shilpa Garg ◽  
Mikko Rautiainen ◽  
Adam M Novak ◽  
Erik Garrison ◽  
Richard Durbin ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Diploid Genome

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 Chromosome-scale genome sequence of Alternaria alternata causing Alternaria brown spot of citrus

2021 ◽  
Author(s):  
Yunpeng Gai ◽  
Haijie Ma ◽  
Yanan Chen ◽  
Lei Li ◽  
Yingze Cao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Alternaria Alternata ◽  
Draft Genome ◽  
Gc Content ◽  
Brown Spot ◽  
Toxin Gene ◽  
Alternaria Brown Spot ◽  
Alternaria Species ◽  
Chromosome Level

Alternaria brown spot (ABS) caused by Alternaria alternata is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, we have assembled a draft genome of A. alternata tangerine pathotype strain Z7, which comprises 165 contigs. In this study, we report a chromosome-level genome assembly of A. alternata Z7 through the combination of Oxford nanopore sequencing and Illumina sequencing technologies. The assembly of A. alternata Z7 had a total size of 34.28 Mb, with a GC content of 51.01% and contig N50 of Mb. The genome is encompassed 12067 protein-coding genes, 34 rRNAs, and 107 tRNAs. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes (ECs) and 2 conditionally dispensable chromosomes (CDCs), which is consistent with the experimental evidences of pulsed-field gel electrophoresis (PFGE). To our best knowledge, this is the first chromosome-level genome assembly of A. alternata. In addition, a database for citrus-related Alternaria genomes has been established to provide public resources for the sequences, annotation and comparative genomics data of Alternaria species. The improved genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata. The database will be updated regularly whenever the genomes of newly isolated Alternaria species are available. The citrus-related Alternaria genomes database is open accessible through http://www.zjudata.com/alternaria/blast.php.

scholarly journals First draft genome assembly and identification of SNPs from hilsa shad (Tenualosa ilisha) of the Bay of Bengal

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 320 ◽  
Author(s):  
Md. Bazlur Rahman Mollah ◽  
Mohd Golam Quader Khan ◽  
Md Shahidul Islam ◽  
Md Samsul Alam
Keyword(s):  
Genome Assembly ◽  
Bay Of Bengal ◽  
Draft Genome ◽  
Gc Content ◽  
Population Connectivity ◽  
Whole Genome ◽  
Migratory Fish ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Tenualosa Ilisha

Background: Hilsa shad (Tenualosa ilisha), a widely distributed migratory fish, contributes substantially to the economy of Bangladesh. The harvest of hilsa from inland waters has been fluctuating due to anthropological and climate change-induced degradation of the riverine habitats.  The whole genome sequence of this valuable fish could provide genomic tools for sustainable harvest, conservation and productivity cycle maintenance. Here, we report the first draft genome of T. ilisha from the Bay of Bengal, the largest reservoir of the migratory fish. Methods: A live specimen of T. ilisha was collected from the Bay of Bengal. The whole genome sequencing was performed by the Illumina HiSeqX platform (2 × 150 paired end configuration). We assembled the short reads using SOAPdenovo2 genome assembler and predicted protein coding genes by AUGUSTUS. The completeness of the T. ilisha genome assembly was evaluated by BUSCO (Benchmarking Universal Single Copy Orthologs). We identified single nucleotide polymorphisms (SNPs) by calling them directly from unassembled sequence reads using discoSnp++. Results: We assembled the draft genome of 710.28 Mb having an N50 scaffold length of 64157 bp and GC content of 42.95%. A total of 37,450 protein coding genes were predicted of which 29,339 (78.34%) were annotated with other vertebrate genomes. We also identified 792,939 isolated SNPs with transversion:transition ratio of 1:1.8. The BUSCO evaluation showed 78.1% completeness of this genome. Conclusions: The genomic data generated in this study could be used as a reference to identify genes associated with physiological and ecological adaptations, population connectivity, and migration behaviour of this biologically and economically important anadromous fish species of the Clupeidae family.

scholarly journals Whole Genome Sequencing Assembly and Annotation of Halobacillus Trueperi S61 Isolated From the Qarhan Salt Lake

2022 ◽  
Author(s):  
Wei Li ◽  
Shuo Shen ◽  
Jian Wang
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Protein Function ◽  
Salt Lake ◽  
Gc Content ◽  
Whole Genome ◽  
Biological Processes ◽  
Circular Chromosome ◽  
Advanced Analysis ◽  
Qarhan Salt Lake

Abstract Background: Halophilic microbial as prospective resources of biotechnology due to the advantages of flexible survivability. Qarhan Salt Lake is the second largest Salt Lake in the world which contains rich-unique extremophiles and deserved in-depth exploration. Results: Present study first time isolated novel strain Halobacillus trueperi S61 from Qarhan Salt Lake and performed whole-genome sequencing through combined third-generation PacBio and second-generation Illumina technology. The whole genome of Halobacillus trueperi S61 identified 57549 total reads and consists a complete circular chromosome of 4047887 bp with 43.86% GC content without gaps. Total number of 139 non-coding RNA (included 86 tRNA, 30 rRNA and 23 sRNA), 16 gene islands with 260275 bp and two prophages (with 82682 length) were predicted. In addition, the whole genome of Halobacillus trueperi S61 summarized basic annotation for 3982 protein-coding genes, 3980, 3667, 2998 and 2303 unigenes were annotated with Nr, Swissport, KOG and KEGG database. Combined with advanced analysis, 561 carbohydrate enzymes and 4416 pathogen host interactions related genes were identified. The protein function of Halobacillus trueperi S61 was mainly focus on biological processes, and the protein function was mainly distributed in gene transcription and amino acids, and carbohydrates metabolism. Conclusions: The complete whole genome sequence assembly and annotation of novel strain Halobacillus trueperi S61 isolated from Qarhan Salt Lake mainly focus on protein biological processes and antibiotic resistance, provides a potential resource for biotechnology.

scholarly journals Draft Genome Sequence of a Sporulating and Motile Strain of Lachnotalea glycerini Isolated from Water in Québec City, Canada

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
Andrée F. Maheux ◽  
Dominique K. Boudreau ◽  
Ève Bérubé ◽  
Maurice Boissinot ◽  
Frédéric Raymond ◽  
...  
Keyword(s):  
Water Sample ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Quebec City ◽  
Content Type

ABSTRACT Lachnotalea glycerini CCRI-19302 belongs to the genus Lachnotalea. The strain was isolated from a water sample harvested in Québec City, Canada. The genome assembly comprised 4,694,231 bp, with 34.6% GC content. This is the first documentation to report the genome sequence of a sporulating and motile strain of L. glycerini.

scholarly journals Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nadège Guiglielmoni ◽  
Antoine Houtain ◽  
Alessandro Derzelle ◽  
Karine Van Doninck ◽  
Jean-François Flot
Keyword(s):  
Genome Assembly ◽  
Model Organism ◽  
Model Organisms ◽  
Post Processing ◽  
Diploid Genome ◽  
Long Reads ◽  
Long Read ◽  
Eukaryote Genome ◽  
Chromosome Level

Abstract Background Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are usually error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Failure to properly collapse haplotypes results in fragmented and structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, yet this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking. Results We tested different assembly strategies on the genome of the rotifer Adineta vaga, a non-model organism for which high coverages of both PacBio and Nanopore reads were available. The assemblers we tested (Canu, Flye, NextDenovo, Ra, Raven, Shasta and wtdbg2) exhibited strikingly different behaviors when dealing with highly heterozygous regions, resulting in variable amounts of uncollapsed haplotypes. Filtering reads generally improved haploid assemblies, and we also benchmarked three post-processing tools aimed at detecting and purging uncollapsed haplotypes in long-read assemblies: HaploMerger2, purge_haplotigs and purge_dups. Conclusions We provide a thorough evaluation of popular assemblers on a non-model eukaryote genome with variable levels of heterozygosity. Our study highlights several strategies using pre and post-processing approaches to generate haploid assemblies with high continuity and completeness. This benchmark will help users to improve haploid assemblies of non-model organisms, and evaluate the quality of their own assemblies.

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