Genome Sequencer System Used To Sequence, Assemble the Pinot Noir Genome

A variety of red wine grape's genome has been sequenced and assembled in an effort to help growers breed grapes for resistance against aggressive microorganisms.

454 Life Sciences (Branford, CT, USA), a part of Roche Applied Science (Basel, Switzerland;), announced that researchers from the Istituto Agrario San Michele all'Adige (Italy) and Myriad Genetics (Salt Lake City, UT, USA) have used the company's first-generation instrument, the Genome Sequencer 20 system, to sequence and assemble the genome of the grape species Pinot Noir. 454 Sequence data were used in conjunction with Sanger data to produce an assembled genome of 477 million bases in length with 29,585 predicted genes. The study was published December 20, 2007, in the journal PLoS ONE.

Pinot Noir is a red wine grape from the species Vitis vinifera and is one of the most popular varietals in the world. The red grape is mainly associated with the Burgundy region of France, but is also widely grown in many regions throughout the world. The Grapevine Genome Initiative was established with the aim of accelerating the breeding of this difficult perennial species. The Pinot Noir genome sequence will aid growers breed grapes for resistance against aggressive microorganisms, which are currently controlled by massive use of agrochemicals, without altering wine quality.

"Sequencing of the Pinot Noir genome will introduce a new era in the molecular breeding of grape, and further grape's potential as a model for fruit tree genetics.” said Dr. Riccardo Velasco, Ph.D., lead author of the study and head of genetics and molecular biology at the Istituto Agrario San Michele all'Adige. "Highly efficient 454 Sequencing enabled us to quickly generate whole genome shotgun data, which was crucial in identifying polymorphic sites throughout the genome, and in conjunction with Sanger sequencing, allowed us to assemble a high quality draft genome.”

The Pinot noir genome was assembled into 2,093 metacontigs, which spanned 477.1 million nucleotides, anchored to 19 linkage groups; 29,585 genes were predicted from the sequence with many candidate genes implicated in traits relevant to grapevine cultivation such as those influencing wine quality and those connected with susceptibility to grape pathogens. Approximately 2,000,000 single nucleotide polymorphisms (SNPs) were identified with one or more SNPs detected in 87% of genes. Furthermore, the study described the genome content in repeats and transposons, miRNAs, tRNAs, snRNAs, rRNAs, snoRNAs, and transcription factor genes.

"Pinot Noir has a highly complex heterozygous genome, which presents significant challenges to any sequence and assembly effort,” said Dr. Michael Egholm, Ph.D., vice president of research and development at 454 Life Sciences. "Using highly accurate, unbiased 454 Sequencing, the researchers were able to quickly produce the data needed to resolve the complete genome sequence. This project serves as a model for the sequencing of plant and other complex genomes using the long read 454 Sequencing platform.”

454 Life Sciences develops and commercializes the innovative Genome Sequencer system for ultra-high-throughput DNA sequencing. Specific applications include de novo sequencing and re-sequencing of genomes, metagenomics, RNA analysis, and targeted sequencing of DNA regions of interest. The hallmarks of 454 Sequencing are its simple, unbiased sample preparation and long, highly accurate sequence reads, including paired reads.


Related Links:
454 Life Sciences
Istituto Agrario San Michele all'Adige
Myriad Genetics