Posts Tagged ‘Next Generation Sequencing’

Analyzing complex plant genomes with the newest next-generation DNA sequencing techniques

 :: Posted by American Biotechnologist on 02-27-2012

Richard Cronn and colleagues (from the USDA Forest Service, Oregon State University, Brigham Young University, and Linfield College) have published an overview of newly developed, up-and-coming DNA sequencing techniques as one of a series of articles in a Special Issue on Methods and Applications of Next-Generation Sequencing in Botany in the American Journal of Botany. In their article, Cronn and co-authors summarize “targeted enrichment” strategies that can be used to obtain specific DNA sequences from complex plant genomes. Articles in the Special Issue provide a detailed snapshot of how “next-generation” sequencing is transforming plant biology.

“Plant genomes range from simple to exceptionally complex,” noted Cronn. “Combining next-generation sequencing with targeted enrichment allows plant scientists to reduce the complexity of plant genomes and focus on specific genes or unique regions that are easy to analyze.”

Read more…

The special issue also includes a comprehensive review article on NGS technologies. Click here to read the review.

Giving Thanks for Turkey Science

 :: Posted by American Biotechnologist on 11-24-2010

What does the domesticated Turkey have in common with the mouse, rat, chimpanzee and Human? Give up? The answer is that its genome can now be added to the long list of species that have had their genomes sequenced thanks to advances in Next Generation Sequencing.

Earlier this year, a team of 34 scientists published their findings regarding the Sequencing of Meleagris gallopavo (i.e domesticated turkey) in PLoS Biology. Not surprisingly, the team found that a comparative analysis of the turkey, chicken, and zebra finch genomes revealed that although the Turkey is indeed genetically different from the Chicken it contains many genes that are unique to the avian lineage.

When comparing these three species by genomic alignment, 92.39% of the turkey genome, 91.92% of the chicken genome and 81.51% of the zebra finch genome align. Furthermore, avian genomes have been relatively stable to rearrangements during the course of avian evolution with the chicken and turkey being much closer to each other in the evolutionary process than the rhesus macaque and the human. These findings are supported by common personal experience. Although it may be difficult to detect differences between some people and rhesus monkeys, this tends to be a much easier task than discerning between a roasted chicken and a roasted turkey which are both covered in cranberry sauce.

Whatever the case may be, understanding the turkey genome will help improve meat quality, animal health and disease resistance. According to turkey breeders (see video below), the science of turkey breeding has already given us birds that are fifteen pounds bigger than they were four decades ago. Nonetheless, increasing public demand for antibiotic-free meat has required scientists to come up with genetic tools for studying alternate ways of disease resistance. Hence, the sequencing of the turkey genome coincides well with the laws of supply and demand and places turkey scientists at the forefront of economic homeostasis.

So when your sitting around the dinner table this coming Thanksgiving, be sure to tell your family why you are thankful for next generation sequencing and Turkey science.

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Ann Blomberg L, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, & Reed KM (2010). Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS biology, 8 (9) PMID: 20838655