Monday, July 11, 2016 4:45:42 PM
Monday, July 11, 2016
A paper from scientists at Colorado State University and the National Center for Genome Resources provides an in-depth view of the transcriptome of sorghum, a crop that’s important for human and animal food and also shows potential as a biofuel. Through this project, the team produced a new isoform analysis pipeline for community use and identified novel genes, as well as far more alternative splicing than had been expected for this plant.
The publication, “A survey of the sorghum transcriptome using single-molecule long reads,” comes from lead author Salah Abdel-Ghany, senior author Anireddy Reddy, and collaborators. The researchers were particularly interested in alternative splicing and alternative polyadenylation, two mechanisms that increase transcript diversity and may help plants adapt to stress. “Despite the fact that several large-scale RNA-seq studies have been performed in plants to analyse [alternative splicing], currently it is not known how many distinct splice isoforms are produced,” the team writes. “This is primarily due to challenges associated with short-read sequencing in accurately reconstructing full-length splice variants.”
To directly observe full-length splice isoforms, they turned to long-read SMRT Sequencing to characterize the transcriptome of sorghum seedlings. The scientists also developed the Transcriptome Analysis Pipeline for Isoform Sequencing, or TAPIS, to identify alternative splicing events and evidence of alternative polyadenylation. “The analysis of sorghum Iso-Seq data uncovered over 7,000 novel [alternative splicing] events, ~11,000 novel splice isoforms, over 2,100 novel genes and several thousand transcripts that differ in 3' untranslated regions due to [alternative polyadenylation],” the team reports, noting that many of the novel genes are putative long non-coding transcripts. The total number of unique transcripts was nearly 28,000, covering more than 14,000 genes.
The scientists discovered a significantly higher rate of alternative splicing than had been expected for sorghum. “Previously, it was reported that pre-mRNAs of ~1,500 genes undergo [alternative splicing] in sorghum,” they note. “In this work, we demonstrate that this number is much higher.” Indeed, they found more than 10,000 alternative splicing events, compared with fewer than 3,000 included in existing gene models. The scientists performed a number of validation studies to confirm these and other novel findings and have made their TAPIS tool available for use in other organisms.
“Pacific Biosciences single-molecule long reads obtained using the Iso-Seq protocol offer a considerable advantage in transcriptome-wide identification of full-length splice isoforms and other forms of post-transcriptional regulatory events such as [alternative polyadenylation],” the team writes.--http://www.pacb.com/blog/first-comprehensive-view-alternative-splicing-sorghum-powered-smrt-sequencing/?platform=hootsuite
Recent PACB News
- PacBio Announces the HiFi Solves Sub-fertility Consortium in Asia Pacific • GlobeNewswire Inc. • 09/11/2024 01:05:00 PM
- Revio to Power Research in Male Infertility and Rare Disease at Münster University Hospital • GlobeNewswire Inc. • 09/04/2024 01:05:00 PM
- PacBio to Present at the Morgan Stanley 22nd Annual Global Healthcare Conference • GlobeNewswire Inc. • 08/26/2024 08:03:00 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 08/20/2024 09:27:01 PM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 08/20/2024 09:25:47 PM
- Form 144 - Report of proposed sale of securities • Edgar (US Regulatory) • 08/19/2024 08:24:44 PM
- Form 144 - Report of proposed sale of securities • Edgar (US Regulatory) • 08/16/2024 08:29:03 PM
- Form 10-Q - Quarterly report [Sections 13 or 15(d)] • Edgar (US Regulatory) • 08/09/2024 12:46:25 AM
- Form 8-K/A - Current report: [Amend] • Edgar (US Regulatory) • 08/07/2024 08:09:35 PM
- Form 8-K - Current report • Edgar (US Regulatory) • 08/07/2024 08:08:10 PM
- PacBio Announces Second Quarter 2024 Financial Results • GlobeNewswire Inc. • 08/07/2024 08:05:00 PM
- Singapore’s National Precision Medicine (NPM) programme will partner with PacBio to propel HiFi Sequencing in Southeast Asia • GlobeNewswire Inc. • 08/05/2024 08:05:00 PM
- Novogene to Power Cancer, Rare Disease, and Environmental Research with PacBio Sequencing • GlobeNewswire Inc. • 07/23/2024 01:05:00 PM
- PacBio to Report Second Quarter 2024 Financial Results on August 7, 2024 • GlobeNewswire Inc. • 07/15/2024 08:03:00 PM
- PacBio and International Research Consortium CoLoRS Announce Release of First-Ever HiFi Long-Read Variant Database • PR Newswire (US) • 06/10/2024 01:05:00 PM
- Form DEFA14A - Additional definitive proxy soliciting materials and Rule 14(a)(12) material • Edgar (US Regulatory) • 05/30/2024 01:52:04 AM
- Form 4 - Statement of changes in beneficial ownership of securities • Edgar (US Regulatory) • 05/22/2024 09:25:43 PM
- Ambry Genetics and PacBio Announce Collaboration to Sequence Up to 7,000 Human Genomes Aimed at Providing Answers for Families Battling Rare Diseases • PR Newswire (US) • 05/15/2024 01:45:00 PM
- Form S-3ASR - Automatic shelf registration statement of securities of well-known seasoned issuers • Edgar (US Regulatory) • 05/09/2024 08:33:12 PM
- Form 10-Q - Quarterly report [Sections 13 or 15(d)] • Edgar (US Regulatory) • 05/09/2024 08:21:46 PM
- Form 8-K - Current report • Edgar (US Regulatory) • 05/09/2024 08:12:15 PM
- PacBio Announces First Quarter 2024 Financial Results • PR Newswire (US) • 05/09/2024 08:05:00 PM
- PacBio Announces Preliminary First Quarter 2024 Revenue and Updates 2024 Revenue Guidance • PR Newswire (US) • 04/16/2024 12:05:00 PM
- Estonia National Biobank Selects PacBio to Sequence 10,000 Whole Genomes • PR Newswire (US) • 03/27/2024 12:00:00 PM
- PacBio Grants Equity Incentive Award to New Employee • PR Newswire (US) • 03/22/2024 08:30:00 PM
VHAI - Vocodia Partners with Leading Political Super PACs to Revolutionize Fundraising Efforts • VHAI • Sep 19, 2024 11:48 AM
Dear Cashmere Group Holding Co. AKA Swifty Global Signs Binding Letter of Intent to be Acquired by Signing Day Sports • DRCR • Sep 19, 2024 10:26 AM
HealthLynked Launches Virtual Urgent Care Through Partnership with Lyric Health. • HLYK • Sep 19, 2024 8:00 AM
Element79 Gold Corp. Appoints Kevin Arias as Advisor to the Board of Directors, Strengthening Strategic Leadership • ELMGF • Sep 18, 2024 10:29 AM
Mawson Finland Limited Further Expands the Known Mineralized Zones at Rajapalot: Palokas step-out drills 7 metres @ 9.1 g/t gold & 706 ppm cobalt • MFL • Sep 17, 2024 9:02 AM
PickleJar Announces Integration With OptCulture to Deliver Holistic Fan Experiences at Venue Point of Sale • PKLE • Sep 17, 2024 8:00 AM