Tag Archives: RNA-Seq

Summer 2013 Bioinformatics Workshop Roundup Part Two

Here’s a couple more promising bioinformatics workshops taking place in the summer of 2013:

Metagenomics: From The Bench To Data Analysis, Heidelberg, Germany, April 14th to April 20th, 2013

EMBO course header

Joint EU-US Training in Marine Bioinformatics, Newark, Delaware, USA, June 16th to June 29th, 2013

EU-US Course Header

Summer 2013 Bioinformatics Workshop Roundup Part One

The summer is a great time to learn some new skills and really hone data analysis techniques.  I think it’s best to learn some topics — bioinformatic tools and data analysis scripting in particular — as intense multi-day workshops or a week- or two-week long short courses.  Here’s a few courses that are being held this summer that may be of interest to you.  I’ll be sure to post more as I hear about them.

Programming for Evolutionary Biology, Leipzig, Germany, April 3rd to April 19th, 2013

course one

Informatics for RNA-sequence Analysis, Toronto, Canada, June 3rd to June 4th, 2013

course two

Pathway & Network Analysis of -Omics Data, Toronto, Canada, June 10th to June 12th, 2013

course two

A Genome Sequence for Tomato

The average person in the United States eats more than 10 kilograms of tomatoes a year – underscoring the fact that the fruit is one of the most important plant crops in cultivation.  To improve taste, texture, and disease resistance – just to name a few traits – a large consortium of researchers has initiated and provided a draft tomato genome.  In fact, the research consortium has published the genome sequence from two varieties of tomatoes: the domesticated inbred Solanum lycopersicum strain Heinz 1706 – the variety famous for ketchup – and the wild breeding Peruvian ancestor, Solanum pimpinellifolium.

The consortium published the draft genome sequences with a paper entitled “The tomato genome sequence provides insights into fleshy fruit evolution” in the journal Nature.  The consortium started sequencing the genome officially in 2003, but heterozygosity and duplication events made assembling the genome difficult.  The tomato genome is approximately 900 Mb – smaller than the Human genome – but certainly not small by eukaryotic standards.  Genetically and phenotypically diverse, the genus Solanum is one of the largest in the angiosperms.

The genomes of Solanum lycopersicum and S. pimpinellifolium only show 0.6% divergence and there is evidence of recent hybridization between the two species.  Both species show approximately 8% genome divergence compared against close relative potato, Solanum tuberosum.  Across the genus Solanum there has been two genome triplications with subsequent gene loss: one genome triplication is ancient and shared with all the rosid clade and another triplication is shared within the Solanaceae, which appear to be highly syntenic across the family.  The genomes were completed with both Sanger- and Illumina-derived sequences and assembled with the help of physical and genetic maps developed from a long history of tomato breeding efforts.

There are 34,727 and 35,004 genes identified across the genomes of Solanum lycopersicum and S. pimpinellifolium respectively.  These findings are similar to other plant genomes as 8,615 of these genes are found to be common to tomato, potato, rice, grape, and Arabidopsis.  Expression was assessed by replicated RNA-Seq of root, leaf, flower, and fruit tissues.  A total of 18,320 orthologous gene pairs were found in tomato and potato indicating diversifying selection between the two species of Solanum.

The consortium specifically compared tomato to grape in this study, as grape and tomato shared a common ancestor at approximately 100 million years ago, before the first whole genome triplication event that preceded the rosid-asterid divergence.  Additionally, both grape and tomato have similar molecular fruit maturation mechanisms.  When comparing the genomes of tomato and grape, approximately 73% of gene models are orthologous.  By estimating genome triplication events, the researchers conclude that the genome duplication event within the Solanaceae occurred roughly 71 million years ago and approximately 7 million years prior to the tomato-potato divergence.

Having a draft genome sequence is an important mechanism to understanding the molecular biology of the tomato plant.  Genome duplication events gave rise to the diversification of genes responsible for enhanced fruit physiological and chemical development – such as lycopene synthesis – and include photoreceptors and transcription factors that influence fruit ripening.  Additionally, tomato has had a contraction in the number of gene families associated with toxic alkaloid synthesis – the chemical hallmarks of many members of the Solanaceae.  One interesting question not answered by this research is the genomic mechanism by which the tomato regulates nutrient investment in above-ground fruits while the potato regulates starch investment in below-ground tubers.

These two tomato genomes, along with the genomes of fellow Nightshades completed or in the works (potato, pepper, tobacco, petunia, eggplant, etc.), will help breeders to develop traits desired by producers, like long shelf life, and fruit quality traits desired by tomato-consumers, such as taste, color, and texture.  In addition to these benefits, the draft tomato genomes will provide insights into the biology and nutrition of the Solanaceous plants, and provide more information for comparative genomics within this important economic group of plants.