The Hyphal Tip: Fungal Genomes and Comparative Genomics

Digesting the fungal genomes

The Hyphal Tip: Fungal Genomes and Comparative Genomics header image 4

Fungal genome assembly from short-read sequences

Posted on June 16th, 2008 by Jason Stajich · 6 Comments

This is a research blog so I though I'd post some quick numbers we are seeing for de novo assembly of the [[Neurospora crassa]] genome using Velvet. The genome of N.crassa is about 40Mb and sequencing of several flow cells using Solexa/Illumina technology to see what kind of de novo reconstruction we'd get.

Click to continue reading "Fungal genome assembly from short-read sequences"

[Read more →]

Categories: bioinformatics · neurospora · resequencing · short-read

Deep EST sequencing = RNA-Seq

Posted on May 6th, 2008 by Jason Stajich · No Comments

The transcriptional landscape of yeast has been (further) defined with [[Solexa]] sequencing in a method deemed "RNA-Seq", but what I would call "deep EST sequencing".  This approach for transcriptional profiling by sequencing alone is sure to be used by many labs looking for lower and more complete ways to describe and quantitate the full population of transcripts in an organism.

Click to continue reading "Deep EST sequencing = RNA-Seq"

[Read more →]

Categories: genome sequencing · saccharomyces · yeast

Aspergillus comparative transcriptional profiling

Posted on March 12th, 2008 by Jason Stajich · 1 Comment

ResearchBlogging.org

Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.

Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.

Click to continue reading "Aspergillus comparative transcriptional profiling"

[Read more →]

Categories: aspergillus · evolution · gene regulation · microarray

New Saccharomyces resequencing assembly

Posted on February 21st, 2008 by Jason Stajich · No Comments

SGRP LogoDavid Carter at the Sanger Centre emailed a message that new assemblies of Saccharomyces strain resequencing project have been posted including a new three-way alignment of S. bayanus-S.paradoxus-S.cerevisiae. This updates the Dec 2007 release.
Click to continue reading "New Saccharomyces resequencing assembly"

[Read more →]

Categories: SGRP · genome · genome sequencing · population genomics · resequencing · saccharomyces

Next gen sequencing technology

Posted on October 4th, 2007 by Jason Stajich · No Comments

Nature has an overview of what goes in and out of next generation sequencers with an interview with a smiling Chad Nusbaum from the Broad Institute. Most of these have been out and about for a while, but it seems that the hayride/bandwagon is starting to pick up more steam as GT's Genome Scan has several posts about sequencing referencing J. Craig V, George
Click to continue reading "Next gen sequencing technology"

[Read more →]

Categories: genome sequencing · news · resequencing