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Tuesday, April 21, 2020

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes.

African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow…

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Tuesday, April 21, 2020

Genomic Survey of Bordetella pertussis Diversity, United States, 2000-2013.

We characterized 170 complete genome assemblies from clinical Bordetella pertussis isolates representing geographic and temporal diversity in the United States. These data capture genotypic shifts, including increased pertactin deficiency, occurring amid the current pertussis disease resurgence and provide a foundation for needed research to direct future public health control strategies.

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Tuesday, April 21, 2020

The role of genomic structural variation in the genetic improvement of polyploid crops

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences (presence–absence variation) and the presence of genes or sequences in multiple copies (copy-number variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose…

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Tuesday, April 21, 2020

A reference-grade wild soybean genome.

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2?Mb and a contig N50 of 3.3?Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz…

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Monday, March 30, 2020

Webinar: Amplicon sequencing with confidence – High-fidelity, long-read PacBio sequencing solutions

In this webinar, Lori Aro and Cheryl Heiner of PacBio describe how high-throughput amplicon sequencing using Single Molecule, Real-Time (SMRT) Sequencing and the Sequel System allows for the easy and cost-effective generation of high-fidelity, long reads from amplicons ranging in size from several hundred base pairs to 20 kb. Topics covered include the latest advances in SMRT Sequencing performance for detection of all variant types even in difficult to sequence regions of the genome, multiplexing options to increase throughput and improve efficiency, and examples of amplicon sequencing of clinically relevant targets.

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Monday, March 30, 2020

Webinar: An introduction to PacBio’s long-read sequencing & how it has been used to make important scientific discoveries

In this Webinar, we will give an introduction to Pacific Biosciences’ single molecule, real-time (SMRT) sequencing. After showing how the system works, we will discuss the main features of the technology with an emphasis on the difference between systematic error and random error and how SMRT sequencing produces better consensus accuracy than other systems. Following this, we will discuss several ground-breaking discoveries in medical science that were made possible by the longs reads and high accuracy of SMRT Sequencing.

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Wednesday, February 26, 2020

Resolving the ‘dark matter’ in genomes.

Second-generation sequencing has brought about tremendous insights into the genetic underpinnings of biology. However, there are many functionally important and medically relevant regions of genomes that are currently difficult or impossible to sequence, resulting in incomplete and fragmented views of genomes. Two main causes are (i) limitations to read DNA of extreme sequence content (GC-rich or AT-rich regions, low complexity sequence contexts) and (ii) insufficient read lengths which leave various forms of structural variation unresolved and result in mapping ambiguities.

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