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Sunday, October 25, 2020

Seminar: Optimizing eukaryotic de novo genome assembly with long-read sequencing

This seminar features great hands-on information and best practices for analyzing SMRT Sequencing data for eukaryotic genome assembly. Michael Schatz provides an overview of the assembly tools, provides recommendations for when to use each one, and discusses the challenges of short-read assemblies. James Gurtowski gives an in-depth overview of hybrid assemblies methods, where short read data are used used to correct errors in longer reads. Finally, Sergey Koren presents on chromosome-scale assembly, including the MinHash Alignment Process (MHAP) he developed to dramatically reduce the computational processing power required for genome assemblies.

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Tuesday, April 21, 2020

GAPPadder: a sensitive approach for closing gaps on draft genomes with short sequence reads.

Closing gaps in draft genomes is an important post processing step in genome assembly. It leads to more complete genomes, which benefits downstream genome analysis such as annotation and genotyping. Several tools have been developed for gap closing. However, these tools don’t fully utilize the information contained in the sequence data. For example, while it is known that many gaps are caused by genomic repeats, existing tools often ignore many sequence reads that originate from a repeat-related gap.We compare GAPPadder with GapCloser, GapFiller and Sealer on one bacterial genome, human chromosome 14 and the human whole genome with paired-end and…

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Wednesday, February 26, 2020

Draft genome of horseweed illuminates expansion of gene families that might endow herbicide resistance.

Conyza canadensis (horseweed), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n=2X=18) with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic basis of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000 and PacBio RS) using various libraries with different insertion sizes (~350 bp, ~600 bp, ~3…

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Wednesday, February 26, 2020

Genome analysis of a bacterium that causes lameness.

Lameness is a significant problem resulting in millions of dollars in lost revenue annually. In commercial broilers, the most common cause of lameness is bacterial chondronecrosis with osteomyelitis (BCO). We are using a wire flooring model to induce lameness attributable to BCO. We used 16S ribosomal DNA sequencing to determine that Staphylococcus spp. were the main species associated with BCO. Staphylococcus agnetis, which previously had not been isolated from poultry, was the principal species isolated from the majority of the bone lesion samples. Administering S. agnetis in the drinking water to broilers reared on wire flooring increased the incidence of…

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Wednesday, February 26, 2020

Genome sequencing of microbial genomes using Single Molecule Real-time sequencing (SMRT) technology.

In the last year, high-throughput sequencing technologies have progressed from proof-of-concept to production quality. Although each technology is able to produce vast quantities of sequence information, in every case the underlying chemistry limits reads to very short lengths. We present a examining de novo assembly comparison with bacterial genome assembly varying genome size (from 3.1Mb to 7.6Mb) and different G+C contents (from 43% to 71%), respectively. We analyzed Solexa reads, 454 reads and Pacbio RS reads from Streptomyces sp. (Genome size, 7.6 Mb; G+C content, 71%), Psychrobacter sp. (Genome size, 3.5 Mb; G+C content, 43%), Salinibacterium sp. (Genome size, 3.1…

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Wednesday, February 26, 2020

Genome and transcriptome of the refeneration-competent flatworm, Macrostomum lignano

The free-living flatworm, Macrostomum lignano, much like its better known planarian relative, Schmidtea mediterranea, has an impressive regenerative capacity. Following injury, this species has the ability to regenerate almost an entirely new organism. This is attributable to the presence of an abundant somatic stem cell population, the neoblasts. These cells are also essential for the ongoing maintenance of most tissues, as their loss leads to irreversible degeneration of the animal. This set of unique properties makes a subset of flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell fate specification, and regeneration. The use of…

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Wednesday, February 26, 2020

Progress Toward a Low Budget Reference Grade Genome Assembly

Reference quality de novo genome assemblies were once solely the domain of large, well-funded genome projects. While next-generation short read technology removed some of the cost barriers, accurate chromosome-scale assembly remains a real challenge. Here we present efforts to de novo assemble the goat (Capra hircus) genome. Through the combination of single-molecule technologies from Pacific Biosciences (sequencing) and BioNano Genomics (optical mapping) coupled with high-throughput chromosome conformation capture sequencing (Hi-C), an inbred San Clemente goat genome has been sequenced and assembled to a high degree of completeness at a relatively modest cost. Starting with 38 million PacBio reads, we integrated…

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Sunday, September 22, 2019

Transcriptional adaptations during long-term persistence of Staphylococcus aureus in the airways of a cystic fibrosis patient.

The lungs of Cystic fibrosis (CF) patients are often colonized and/or infected by Staphylococcus aureus for years, mostly by one predominant clone. For long-term survival in this environment, S. aureus needs to adapt during its interactions with host factors, antibiotics, and other pathogens. Here, we study long-term transcriptional as well as genomic adaptations of an isogenic pair of S. aureus isolates from a single patient using RNA sequencing (RNA-Seq) and whole genome sequencing (WGS). Mimicking in vivo conditions, we cultivated the S. aureus isolates using artificial sputum medium before harvesting RNA for subsequent analysis. We confirmed our RNA-Seq data using…

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Sunday, September 22, 2019

Improving PacBio long read accuracy by short read alignment.

The recent development of third generation sequencing (TGS) generates much longer reads than second generation sequencing (SGS) and thus provides a chance to solve problems that are difficult to study through SGS alone. However, higher raw read error rates are an intrinsic drawback in most TGS technologies. Here we present a computational method, LSC, to perform error correction of TGS long reads (LR) by SGS short reads (SR). Aiming to reduce the error rate in homopolymer runs in the main TGS platform, the PacBio® RS, LSC applies a homopolymer compression (HC) transformation strategy to increase the sensitivity of SR-LR alignment…

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Sunday, September 22, 2019

Draft genome sequence of Sulfurospirillum sp. strain MES, reconstructed from the metagenome of a microbial electrosynthesis system.

A draft genome of Sulfurospirillum sp. strain MES was isolated through taxonomic binning of a metagenome sequenced from a microbial electrosynthesis system (MES) actively producing acetate and hydrogen. The genome contains the nosZDFLY genes, which are involved in nitrous oxide reduction, suggesting the potential role of this strain in denitrification. Copyright © 2015 Ross et al.

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Sunday, September 22, 2019

Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis.

Ichthyophthirius multifiliis is the etiologic agent of “white spot”, a commercially important disease of freshwater fish. As a parasitic ciliate, I. multifiliis infects numerous host species across a broad geographic range. Although Ichthyophthirius outbreaks are difficult to control, recent sequencing of the I. multifiliis genome has revealed a number of potential metabolic pathways for therapeutic intervention, along with likely vaccine targets for disease prevention. Nonetheless, major gaps exist in our understanding of both the life cycle and population structure of I. multifiliis in the wild. For example, conjugation has never been described in this species, and it is unclear whether…

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Sunday, September 22, 2019

Candidatus Dactylopiibacterium carminicum, a nitrogen-fixing symbiont of Dactylopius cochineal insects (Hemiptera: Coccoidea: Dactylopiidae)

The domesticated carmine cochineal Dactylopius coccus (scale insect) has commercial value and has been used for more than 500?years for natural red pigment production. Besides the domesticated cochineal, other wild Dactylopius species such as Dactylopius opuntiae are found in the Americas, all feeding on nutrient poor sap from native cacti. To compensate nutritional deficiencies, many insects harbor symbiotic bacteria which provide essential amino acids or vitamins to their hosts. Here, we characterized a symbiont from the carmine cochineal insects, Candidatus Dactylopiibacterium carminicum (betaproteobacterium, Rhodocyclaceae family) and found it in D. coccus and in D. opuntiae ovaries by fluorescent in situ…

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Sunday, September 22, 2019

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides.

Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in different ordered sequences. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability, and resilience and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical…

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Sunday, September 22, 2019

Lentinula edodes genome survey and postharvest transcriptome analysis.

Lentinula edodes is a popular, cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems, such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction for Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and by using long reads by PacBio, resulting in a contig number of 1,951 and an N50 of 1 Mb. Furthermore, we predicted genes by Augustus using transcriptome sequencing (RNA-seq) data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes.…

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