Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.

ABSTRACT: Identification of small polymorphisms from next generation sequencing short read data is relatively easy, but detection of larger deletions is less straightforward. Here, we analyzed four divergent Arabidopsis accessions and found that intersection of absent short read coverage with weak tiling array hybridization signal reliably flags deletions. Interestingly, individual deletions were frequently observed in two or more of the accessions examined, suggesting that variation in gene content partly reflects a common history of deletion events.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. We generated 10,010 RSRs from a metagenomic library of microorganisms found in human faecal samples. Then searched them using the program BLASTN against a prokaryotic sequence database to assign a taxon to each RSR. The results were compared with those obtained by screening and analysing the clones containing 16S rDNA sequences in the whole library. We found that the biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA. We also show that RSRs are suitable to compare the biodiversity between different metagenomic libraries. RSRs can thus provide a good estimate of the biodiversity of a metagenomic library and, as an alternative to 16S, this approach is both faster and cheaper.

Quick Reads, Jan 2, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, Jan 24, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, Feb 12, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, Mar 6, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, Mar 27, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, April 14, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, May 8, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, May 29, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, June 23, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, July 15, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, Aug 14, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.

Quick Reads, October 2, 2008

IDPH Quick Reads is an electronic newsletter produced by the Director’s Office at the Iowa Department of Public Health. IDPH Quick Reads are published every three to four weeks.