Showing papers by "Sean Humphray published in 2009"
United States Department of Agriculture1, Seoul National University2, Chinese Academy of Sciences3, Imperial College London4, Seattle Children's Research Institute5, Wellcome Trust6, Illumina7, University of Delhi8, Wageningen University and Research Centre9, Institut national de la recherche agronomique10, University of Málaga11, Polytechnic University of Valencia12, Huazhong Agricultural University13, China Agricultural University14, ENEA15, Max Planck Society16, Rutgers University17, Ghent University18, Hebrew University of Jerusalem19
TL;DR: This first snapshot of the emerging tomato genome and its annotation is presented, a short comparison with potato sequence data, and the tools available for the researchers to exploit this new resource are presented.
Abstract: The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato (Solanum tuberosum L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.
105 citations
TL;DR: The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.
Abstract: Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15–18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.
92 citations
TL;DR: The sequencing of the myoblast enriched cDNA library has significantly increased the number of zebrafish ESTs, facilitating the prediction of new spliced transcripts in the genome assembly and providing a transcriptome of an in vivoMyoblast cell.
8 citations