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Wednesday, November 15, 2017

Investigating Splicing of Transcripts in Cancer Cells: SMRT Grant Winner Announced

We’re pleased to announce the winner of this year’s ‘Open Your Eyes to Isoform Diversity’ SMRT Grant, which was launched during the American Association for Cancer Research annual meeting. The grant program, co-sponsored by PacBio and GENEWIZ, received many compelling entries, and it was a challenge choosing just one winner. Congratulations to Andrew Ludlow, a new faculty member at the University of Michigan, who impressed reviewers with his proposal to investigate the splicing of transcripts regulated by the oncogene NOVA1. Ludlow notes that in lung cancer cells, NOVA1 acts as a splicing enhancer to produce full-length hTERT and promote telomerase…

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Tuesday, November 14, 2017

Fungal Genome Study Sheds Light on Pathogenicity in Plants

Photo of Armillaria gallica by Roberto Petruzzo They are colonizers and killers, growing as large as 2,400 acres, leaving devastation in their wake. Armillaria fungi are the cause of root rot disease in forests, fields, parks, and vineyards in more than 500 host plant species across the world. But despite this huge impact on agriculture, the pathogenicity of Armillaria species has been poorly understood. A new international study led by Hungarian researchers, published in Nature Ecology & Evolution, reveals novel insights into how the fungus spreads and kills. Lead author György Sipos of the University of Sopron, senior author László Nagy of the Hungarian…

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Tuesday, November 7, 2017

Medicinal Plants: Investigating Biosynthesis with SMRT Sequencing

Photo of Panax ginseng by Eugene Kim Three recent publications report results from transcriptome studies of plants often used for medicinal purposes, all powered by SMRT Sequencing and the Iso-Seq method. The papers on ginseng, Huangqi, and tea collectively show the importance of sequencing full-length isoforms for the most accurate and comprehensive gene expression analysis; they also demonstrate the usefulness of characterizing gene models for complex species in the absence of a reference genome assembly. In “Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome,” scientists from the National Institute of Horticultural and Herbal Science, Chungbuk National University, and…

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Monday, November 6, 2017

Sanger Celebrates 25 Years by Generating 25 High-Quality Genomes of UK Species

We’re pleased to be teaming up with the Wellcome Trust Sanger Institute on a project to celebrate their twenty-fifth anniversary: generating high-quality genome assemblies for 25 species that are integral to the ecosystems found in the United Kingdom. For this work, Sanger scientists will use the Sequel System and complementary technologies to produce reference-grade assemblies. Twenty organisms have already been selected, and the last five will be chosen by a public vote reminiscent of our own SMRT Grant program, which earlier this year saw dingo beat out bombardier beetle, sea slug, temple pitviper, and pink pigeon for the coveted sequencing…

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Thursday, November 2, 2017

With Chromosome-Scale Resolution, Draft Durian Genome Explains Smelly Fruit

Photo by مانفی Scientists in Singapore, Hong Kong, and Malaysia recently reported the high-quality draft genome assembly of Durio zibethinus, a type of durian fruit commonly eaten in southeast Asia. The team used SMRT Sequencing and chromosome mapping techniques to produce the assembly, which will be an important tool for agricultural monitoring. “The draft genome of tropical fruit durian (Durio zibethinus)” was published in Nature Genetics from lead authors Bin Tean Teh, Kevin Lim, Chern Han Yong, Cedric Chuan Young Ng, senior author Patrick Tan, and collaborators at the Duke-NUS Medical School and other institutions. They chose to study durian…

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Wednesday, November 1, 2017

Iso-Seq Analysis of Polyploid Cotton Yields Important Discoveries for Fiber Breeding

Photo by Forest & Kim Starr Scientists at Huazhong Agricultural University in China and collaborating institutions recently published results of an Iso-Seq analysis of allotetraploid cotton. The team’s findings are expected to be particularly useful for functional genomics, driving advances for cotton breeders as well as research biologists. “A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation” was published in New Phytologist by lead authors Maojun Wang and Pengcheng Wang, senior author Xianlong Zhang, and collaborators. Existing genome assemblies for polyploidy cotton were not “released with a well-annotated transcript isoform set,” the scientists write, “and so…

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