January 2015

MM: Funded by illy and Lavazza - competing companies. Both SE/PE NGS and BAC clones as pools 2012 Nature http://t.co/nb1jhJxr0L #PAGXXIII

7:55pm January 11th 2015 via Hootsuite

MM:He starts with 'I admit that I'm not much of a coffee drinker' (elicits a reaction from the audience) #PAGXXIII

7:52pm January 11th 2015 via Hootsuite

Michele Morgante (Univ di Udine Italy) "Progress report on the sequencing and assembly of the allotetraploid Coffea arabica" #PAGXXIII

7:52pm January 11th 2015 via Hootsuite

MC: Making RNA-Seq resources from 36 hybrids available. Showed diff gene exp between shadow & sun in hybrids #PAGXXIII

7:43pm January 11th 2015 via Hootsuite

MC: Did Sanger on BACs of C. arabica w/ Rod Wing of Univ AZ. Was able to order using FPC method. #PAGXXIII

7:39pm January 11th 2015 via Hootsuite

MC: C. arabica: also on @PacBio, 57x coverage; N50 13kb; still being analyzed; First effort on tetraploid genome assy #PAGXXIII

7:35pm January 11th 2015 via Hootsuite

MC: Using P6/C4 @PacBio chemistry, N50 15kb #PAGXXIII

7:33pm January 11th 2015 via Hootsuite

MC: Extend work with @PacBio and moleculo technologies; work in-progress. Moleculo: 5.4kb ave readlength, 3.4x coverage #PAGXXIII

7:32pm January 11th 2015 via Hootsuite

MC: Collab w/Roche: FLX+ 700bp reads; 16x overall coverage (both SE and PE reads). N50 109kb (502 scaffolds). Error ~1.4% #PAGXXIII

7:31pm January 11th 2015 via Hootsuite

Marco Cristancho (colleague of AG): Coffea eugenoidides - 670Mbp; C. canephora 710Mbp; C. arabica 1.3Gbp. Cenicafe/Cornell groups #PAGXXIII

7:29pm January 11th 2015 via Hootsuite

AG:Large family tree illustrated canephora, robustas, etc. Genomics the foundation - facing climate var & yield/productivity #PAGXXIII

7:25pm January 11th 2015 via Hootsuite

AG: Need for younger and rust-resistant varieties. 60% rust-resistant now, ave <5y old. Adjust via local microclimates #PAGXXIII

7:24pm January 11th 2015 via Hootsuite

AG:Looking at 110y of Pacific Oscillation weather patterns: published 2011 'Climate Smart Coffee Cultivation' booklet #PAGXXIII

7:23pm January 11th 2015 via Hootsuite

AG: Production and consumption both rising; qty sufficient, but a quality problem due to climate changes #PAGXXIII

7:22pm January 11th 2015 via Hootsuite

AG: Points out this 2012 @sciam piece http://t.co/excQ5uEiqV that mentions 2020 the threat. But real threats much sooner #PAGXXIII

7:21pm January 11th 2015 via Hootsuite

Alvaro Gaitan (CENICAFE Columbia) "Long-Read Deep Sequencing and Assembly of the Allotetraploid Coffea arabica..." #PAGXXIII

7:19pm January 11th 2015 via Hootsuite

Oops - Perla Hamon speaking: describes association between Brazil, Cornell. Still need in funds; Int'l Devel Bank. #PAGXXIII

7:18pm January 11th 2015 via Hootsuite

MY: Initial: 80% of 710MB c. canephora genome completed; now on their way to finish C. eugenoides & tetraploid C. arabica #PAGXXIII

7:15pm January 11th 2015 via Hootsuite

MY: C. canephora seq paper in Science 2014 http://t.co/o88EyzRs02 Hybrid 454, Sanger CE on BAC libraries, and short reads. #PAGXXIII

7:12pm January 11th 2015 via Hootsuite

MY: >100 spp. 1.3GB genome; allotetraploid. Merged two diploid spp: C. canephora & C. eugenoides. Need fn. sig of polyploidy #PAGXXII

7:10pm January 11th 2015 via Hootsuite

Marcela Yepes (Cornell): Narrow genetic pool also a problem; much work left for positional cloning, char new gene families #PAGXXIII

7:09pm January 11th 2015 via Hootsuite

Coffee is second only to oil; Global US$90B/y. US consumption growing +2%/yr. Vulnerable to climate change; abiotic stress #PAGXXIII

7:08pm January 11th 2015 via Hootsuite

Int'l Coffee Genome Network:113 members; their site: http://t.co/ScyZHl1wgH Recognized founders from 2005 mtg; support from USDA #PAGXXIII

7:03pm January 11th 2015 via Hootsuite

SR: Now have 866 hybrids, grafted onto cacao; already field-testing. Examples of hybrid flowers shown #PAGXXIII

6:09pm January 11th 2015 via Hootsuite

SR: Measured palmitic acid across hybrids generated fro 2012 and 2013; looked at SNP markers to ID potential transloc's as well #PAGXXIII

6:08pm January 11th 2015 via Hootsuite

MT @iontorrent: Visit Life Technologies (booth 111 #PAGXXIII) & get a gift (Terms & Conditions apply)

6:05pm January 11th 2015 via Hootsuite

SR: T. grandiflorum is low in palmitic acid, arachnidic acid higher than cacao. Photos of artificial pollinations #PAGXXIII

6:02pm January 11th 2015 via Hootsuite

SR: Goal is for hybrids - Theobroma grandiflorum native to Amazon; seeds used i cosmetics, pulp used for food #PAGXXIII

6:00pm January 11th 2015 via Hootsuite

Stefan Royaert (MARS Ctr for Cocoa Science) "Interspecific Hybridization Between Theobroma cacao and Theobroma grandiflorum" #PAGXXIII

5:59pm January 11th 2015 via Hootsuite

SA: Detailed phylogeny comparison across gene types; hydrolases, necrosis, RxLR effectors (increased retroelements) #PAGXXIII

5:57pm January 11th 2015 via Hootsuite

SA: Cp P. megakarya from Cameroon vs P. palmivora from Ivory Coast - 156Mb vs 180Mb genome size, about 25K genes in both #PAGXXIII

5:48pm January 11th 2015 via Hootsuite

SA: Nigeria caused 4-5% losses; showed map of Ghana and progression; 80-90% losses. Showed diversity of 119 spp, very similar #PAGXXIII

5:45pm January 11th 2015 via Hootsuite

SA: Black pod - WW distribution, P. megakarya in Africa. Nigeria '79, in '81 predominant. Moving west to Ghana and Ivory Coast #PAGXXIII

5:43pm January 11th 2015 via Hootsuite

SA: Phytophthera means 'plant destroyer'; epicillium similar to other fungi, but phylogentically closer to diatoms #PAGXXIII

5:41pm January 11th 2015 via Hootsuite

Shahin Ali (USDA-ARS Beltsville MD) "Biology and Genomics of Phytophthora spp.: Fight Against a Potential Global Chocolate Famine" #PAGXXIII

5:39pm January 11th 2015 via Hootsuite

RT @PlantEvolution: I Henderson @hendersi Recombination frequency downstream of TSS 150 bp nucleosome periodicity #PAGXXIII

5:36pm January 11th 2015 via Hootsuite

RT @KristaTernus: Orlando: Interested in studying ancient epigenomes http://t.co/mWurcYqdjS #PAGXXIII

5:34pm January 11th 2015 via Hootsuite

DB: Runs of homozygosity - effective population size est's. Imputation shown to work for that work too #PAGXXIII

5:04pm January 11th 2015 via Hootsuite

DB: Took 22x Neolithic genome and downsampled to 1x, imputed and compared. Of 600k SNPs, 99.2% matched #PAGXXIII

5:02pm January 11th 2015 via Hootsuite

DB: PCA plot of groups: shift occurs to metal ages (Bronze, then Iron). Further extended data w/ imputation #PAGXXIII

5:01pm January 11th 2015 via Hootsuite

DB: Showing data from C Gamba and R Pinhasi Nature Comm http://t.co/8BccnnSZeV What happens to genomes across 5K years? #PAGXXIII

4:59pm January 11th 2015 via Hootsuite

DB:Showed plot of percent endogenous reads against time years before present. Petrous 30-70%; non-petrous <10% #PAGXXIII

4:57pm January 11th 2015 via Hootsuite

DB: Anatomically informed: best part is the bone in the skull housing the inner ear - petrous bone #PAGXXIII

4:56pm January 11th 2015 via Hootsuite

DB: Methods - capture, 'privileged substrates' (parchment, permafrost), anatomically informed sampling, whole-genome imputation #PAGXXIII

4:53pm January 11th 2015 via Hootsuite

Dan Bradley (Trinity Coll Dublin) "The best bones, imputation and ancient Genomics" #PAGXXIII

4:52pm January 11th 2015 via Hootsuite

IB: a 'stamp-collecting phase' w/ poor understanding of DNA recovery; below 40-45N latitude, Pleistocene DNA recovery poor #PAGXXIII

4:45pm January 11th 2015 via Hootsuite

IB: Screened using MALDI-TOF MS, then protein seq using Orbitrap and maXis, able to resolve collagen phylogeny #PAGXXIII

4:43pm January 11th 2015 via Hootsuite

IB: Using proteomics for collagen type I - 27% of bone, possible via mass-spec, perhaps 10x life-span of DNA PAGXXIII

4:42pm January 11th 2015 via Hootsuite

IB: Mapped S Am thermal model predicts non-preservation; only southernmost Patagonia. Their samples: too far north. Not easy. #PAGXXIII

4:41pm January 11th 2015 via Hootsuite