At our PAG Educational Seminar
“Examples of new NGS-Enabled Plant Research and Opportunities for Global Gene Banking Partnerships”
Monday, January 16, 6:10 – 8:20PM, in the Sunset Meeting House
Prof. Joshua Udall
Re-sequenced genomes reveal the genetic diversity of polyploid cotton.
Joshua A. Udall, Daojun Yuan, Mengqiao Pan, Evan Long, Spencer Hunt, Samantha McCord, Logan Brase, Lori Hinze, Jonathan F. Wendel, Vasu Kuraparthy, Richard Percy
By deep-sequencing many accessions of cotton, we have revealed detailed genetic information and phylogeographic patterns demonstrating the diversity in the cotton genome. We have re-sequenced more than 600 accessions, including 431 accessions of G. hirsutum, 165 accessions of G. barbadense, and other species. We detected the variation among these accessions and identified genetic variation between cultivars and wild species, also between the different species. This wealth of sequence information will allows us to identify which specific gene or genome region have been selected during domestication of cotton. Understanding the location of these loci will allow us to further improve the cotton genome for agricultural improvement.
Prof. Sally Mackenzie
Integrating genome-wide methylome and gene expression data in plant genomes
Mon-Ray Shao, Vikas Shedge, Robersy Sanchez, Xiaodong Yang, Sally Mackenzie
Genome-wide methylome analysis in plants conducted by bisulfite sequencing produces a highly heterogenous dataset that is difficult to associate with gene expression changes. Part of the data heterogeneity is dynamic DNA methylation behavior that serves to stabilize DNA, but which confounds analysis of methylation signal deriving from experimental treatment. We have conducted genome-wide bisulfite sequencing together with RNAseq in Arabidopsis and tomato lines that have undergone epigenetic reprogramming by suppression of the gene MSH1. We have developed a strategy for data analysis that permits more robust discrimination of signal to noise in methylome data, and integrated these data with transcriptome analysis to identify genes that display altered gene expression in association with intragenic DNA methylation changes. These analyses were also invaluable in detection of methylation changes that were aberrant in pattern, revealing them to be the consequence of germplasm contamination. We will present the various methodologies we have employed for mining these large datasets.
Dr. Xin Liu,
Large scale genomic studies at China National GeneBank
After 5 years of construction, the China National GeneBank (CNGB) was opened in September 2016.
CNGB, the first of its kind in China, is operated by BGI and will provide an open platform for global scientific research. So far, CNGB has established a bio-repository with the capacity to store tens of millions of samples, a database with a storage capacity of 20Pb as well as a living biobank. CNGB also offers an in-house sequencing infrastructure with the capacity to generate 10 Tb of data per day.
With this infrastructure, we have initiated several large scale genomic studies, including an avian genome project that will be introduced here, along with other examples of large scale genome projects currently under way.
As the CNGB is rapidly ramping up, we are open for additional global collaborations in which our infrastructure can add value.