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Tuesday, April 21, 2020

Complete Genome Sequence of Leptospira kmetyi LS 001/16, Isolated from a Soil Sample Associated with a Leptospirosis Patient in Kelantan, Malaysia.

The Gram-negative pathogenic spirochetal bacteria Leptospira spp. cause leptospirosis in humans and livestock animals. Leptospira kmetyi strain LS 001/16 was isolated from a soil sample associated with a leptospirosis patient in Kelantan, which is among the states in Malaysia with a high reported number of disease cases. Here, we report the complete genome sequence of Leptospira kmetyi strain LS 001/16. Copyright © 2019 Yusof et al.

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Tuesday, April 21, 2020

The conservation of polyol transporter proteins and their involvement in lichenized Ascomycota.

In lichen symbiosis, polyol transfer from green algae is important for acquiring the fungal carbon source. However, the existence of polyol transporter genes and their correlation with lichenization remain unclear. Here, we report candidate polyol transporter genes selected from the genome of the lichen-forming fungus (LFF) Ramalina conduplicans. A phylogenetic analysis using characterized polyol and monosaccharide transporter proteins and hypothetical polyol transporter proteins of R. conduplicans and various ascomycetous fungi suggested that the characterized yeast’ polyol transporters form multiple clades with the polyol transporter-like proteins selected from the diverse ascomycetous taxa. Thus, polyol transporter genes are widely conserved among Ascomycota, regardless…

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Tuesday, April 21, 2020

Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant.

Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in plant research. T-DNA integration in plants is complex and still largely unknown. In this work, we reported that multiple T-DNA fragments caused chromosomal translocation and deletion in a birch (Betula platyphylla × B. pendula) T-DNA mutant yl.We performed PacBio genome resequencing for yl and the result revealed that two ends of a T-DNA can be integrated into plant genome independently because the two ends can be linked to different chromosomes and…

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Tuesday, April 21, 2020

Retrotranspositional landscape of Asian rice revealed by 3000 genomes.

The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations…

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Monday, March 30, 2020

PAG Conference: Reference-quality drosophila genome assemblies for evolutionary analysis of previously inaccessible genomic regions

In this presentation, Andrew Clark from Cornell University describes work from a collaboration with Manyuan Long of the University of Chicago and Rod Wing of the University of Arizona to look at heterochromatic regions with long simple satellite repeats in drosophila genomes. The group used PacBio sequencing to create new genome assemblies of 10 drosophila species, including de novo assemblies of two individual flies using as little as 26 ng of gDNA.

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Wednesday, February 26, 2020

Best practices for whole-genome de novo sequencing with long-read SMRT Sequencing.

With the introduction of P6-C4 chemistry, PacBio has made significant strides with Single Molecule, Real-Time (SMRT) Sequencing . Read lengths averaging between 10 and 15 kb can be now be achieved with extreme reads in the distribution of > 60 kb. The chemistry attains a consensus accuracy of 99.999% (QV50) at 30x coverage which coupled with an increased throughput from the PacBio RS II platform (500 Mb – 1 Gb per SMRT Cell) makes larger genome projects more tractable. These combined advancements in technology deliver results that rival the quality of Sanger “clone-by-clone” sequencing efforts; resulting in closed microbial genomes…

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Wednesday, February 26, 2020

The resurgence of reference quality genome sequence.

Since the advent of Next-Generation Sequencing (NGS), the cost of de novo genome sequencing and assembly have dropped precipitately, which has spurred interest in genome sequencing overall. Unfortunately the contiguity of the NGS assembled sequences, as well as the accuracy of these assemblies have suffered. Additionally, most NGS de novo assemblies leave large portions of genomes unresolved, and repetitive regions are often collapsed. When compared to the reference quality genome sequences produced before the NGS era, the new sequences are highly fragmented and often prove to be difficult to properly annotate. In some cases the contiguous portions are smaller than…

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