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Tuesday, April 21, 2020

The Chinese chestnut genome: a reference for species restoration

Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally. While sources of resistance may be available in related species, or among surviving trees, introgression of resistance genes into threatened tree species in reasonable time frames requires genome-wide breeding tools. Asian species of chestnut (Castanea spp.) are being employed as donors of disease resistance genes to restore native chestnut species in North America and Europe. To aid in the restoration of threatened chestnut species, we present the assembly of…

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Tuesday, April 21, 2020

A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

Background A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens…

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Tuesday, April 21, 2020

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies.

Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the…

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Tuesday, April 21, 2020

Potential of TLR-gene diversity in Czech indigenous cattle for resistance breeding as revealed by hybrid sequencing

A production herd of Czech Simmental cattle (Czech Red Pied, CRP), the conserved subpopulation of this breed, and the ancient local breed Czech Red cattle (CR) were screened for diversity in the antibacterial toll-like receptors (TLRs), which are members of the innate immune system. Polymerase chain reaction (PCR) amplicons of TLR1, TLR2, TLR4, TLR5, and TLR6 from pooled DNA samples were sequenced with PacBio technology, with 3–5×?coverage per gene per animal. To increase the reliability of variant detection, the gDNA pools were sequenced in parallel with the Illumina X-ten platform at low coverage (60× per gene). The diversity in conserved…

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Tuesday, April 21, 2020

Chloroplast genome of Dalbergia cochinchinensis (Fabaceae), a rare and Endangered rosewood species in Southeast Asia

Dalbergia cochinchinensis is an tree species in Southeast Asia, its wood and wood products are incred- ibly valuable and are also of important medicinal value. In this study, its chloroplast genome was char- acterized using next generation Illumina pair-end and Pacbio sequencing dataset. The whole genome was 156,576bp in length and contains a pair of 25,682bp inverted repeat regions, which were sepa- rated by a large single copy region and a small single copy region of 85,886 and 19,326bp in length, respectively. The cp genome contained 111 genes, including 77 protein-coding genes, 30 tRNAs and 4 rRNAs. A neighbor-joining phylogenetic…

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Tuesday, April 21, 2020

Genome analysis of the rice coral Montipora capitata.

Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation. Here we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and transcriptome data from the dominant rice coral, Montipora capitata from Hawai’i. Our work provides insights into the architecture of coral genomes and shows how they differ in size and gene inventory, putatively due to population size variation. We describe a recent…

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Monday, March 30, 2020

PAG Conference: Endless forms: Genomes from the Darwin Tree of Life Project

Mark Blaxter, project lead of the Sanger Institute’s Darwin Tree of Life, shared an update of the ambitious effort to sequence all 60,000 species believed to be on the British Isles over the next 12 years in this presentation at the PAG 2020 Conference. The Sanger team has already generated data for 94 species, including 44 new moth and butterfly (Lepidoptera) PacBio assemblies, which Blaxter describes in this presentation.

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Monday, March 30, 2020

PAG PacBio Workshop: Conservation genomics of a critically endangered Hawaiian bird: A high quality genome assembly of the ‘alala will assist in population management and reintroduction

Oliver Ryder speaks about efforts to rescue the Hawaiian crow, a bird that has been extinct in the wild since 2002, and reintroduce it to its native habitat. Critical to this work is a new SMRT Sequencing reference genome assembly, which Ryder says is already one of the best avian assemblies out there. The resource may help deal with challenges like inbreeding and disease susceptibility.

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Monday, March 30, 2020

AGBT Conference: Long-read sequence of the gorilla genome

Christopher Hill presents data from efforts to produce reference-grade assemblies for the great ape species. Using SMRT Sequencing, Hill and his colleagues are generating assemblies with much higher contiguity to resolve repetitive and other particularly complex regions. In this talk, he focuses on data from their new high-quality gorilla assembly.

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Monday, March 30, 2020

PAG PacBio Workshop: De novo sequencing of the koala genome

Rebecca Johnson, director of the Australian Museum Research Institute presents finding from de novo sequencing of the koala genome. Using PacBio sequencing the Koala Genome Consortium obtained an assembly with an N50 of 11.5 Mbp and have undertaken functional genomic analysis highlighting the unique genes associated with lactation and immune function of koalas. Johnson goes on to describe efforts to obtain a chromosome level assembly and current work using ‘super scaffolding’ to compare shared synteny across diverse lineages to generate chromosome scaffold maps.

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Monday, March 30, 2020

PAG PacBio Workshop: Comparative analyses of next generation technologies for generating chromosome-level reference genome assemblies

At PAG 2017, Rockefeller University’s Erich Jarvis offered an in-depth comparison of methods for generating highly contiguous genome assemblies, using hummingbird as the basis to evaluate a number of sequencing and scaffolding technologies. Analyses include gene content, error rate, chromosome metrics, and more. Plus: a long-read look at four genes associated with vocal learning.

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Monday, March 30, 2020

Webinar: Assembling high-quality genomes to solve nature’s mysteries

In this webinar, Barbara Block of Stanford University and Paul Peluso of PacBio describe how plant and animal whole genome sequencing remains a challenging endeavor, particularly due to genome size, high density of repetitive elements, and heterozygosity. Because of this, often only a single, fragmented reference genome is available for a species, genus, or even family, limiting the ability to answer important biological questions. Looking at the trends in genome assembly and annotation over the past year, such as pan-genomes and phasing, this webinar explores how Single Molecule, Real-Time (SMRT) Sequencing is utilized to develop long-lasting genomic resources, supporting research…

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Monday, March 30, 2020

PAG Conference: Domestication: through the canines of a dingo

In this PAG 2018 presentation, Bill Ballard of University of New South Wales, presents research into the origins and potential domestication of the Australian dingo, winner of the 2017 SMRT Grant Program. Ballard used PacBio long-read whole genome sequencing to sequence and assemble the dingo genome. Ongoing work focuses on identifying common and unique genomic regions with a domestic dog genome to better understand shared ancestry and ultimately to aid in dingo conservation efforts.

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