PB: Computer tapes - shipped to Australia, printed out, then transferred. Now - the proteome of Ebola visualized in seconds #PAGXXIII
9:27pm January 11th 2015 via Hootsuite
PB: What is a digital enterprise? How quickly we've come: maintaining the Protein Data Bank - starting with 15 structures! #PAGXXIII
9:26pm January 11th 2015 via Hootsuite
Philip Bourne (NIH Bethesda Maryland) "NIH as a Digital Enterprise – Implications for PAG" #PAGXXIII @pebourne
9:24pm January 11th 2015 via Hootsuite
RG: SIRE retrotransposons my have accumulated in geographic-specific migration pattern: Indonesia to Mozambique to W Africa #PAGXXIII
8:48pm January 11th 2015 via Hootsuite
RG: Looking at SIRE retrotransposon family across 62 diploit spp - some groups amplified, others completely absent. #PAGXXIII
8:47pm January 11th 2015 via Hootsuite
RG: Sampled 10 diploid Coffea spp; using @rochesequencing at low-pass (6% - 15%), surprised that # of repeats constant #PAGXXIII
8:43pm January 11th 2015 via Hootsuite
RG: 188 Copia and 387 Gypsy LTR retrotransposon families in C canefora. Evidence is recent amplification #PAGXXIII
8:41pm January 11th 2015 via Hootsuite
RG: Tn elements in C canephora is >50%; LTR retroposons are 42% (!) A cut-and-paste mechanism #PAGXXIII
8:40pm January 11th 2015 via Hootsuite
RG: Genome size varies - smallest in E Africa, largest in W Africa. Madagascar: smaller in N, larger in S. Mechanism unk #PAGXXIII
8:39pm January 11th 2015 via Hootsuite
RG: 124 spp world-wide. (Coffea 104, Psilanthus 20 spp) Diverse fruit color, sie, flower morphology #PAGXXIII
8:36pm January 11th 2015 via Hootsuite
Romain Guyot (IRD UMR France) "Transposable Element Distribution, Abundance and Impact in Genome Evolution in the Genus Coffea" #PAGXXIII
8:35pm January 11th 2015 via Hootsuite
AK: Full-length cDNA seq using @pacbio - 4.6k consensus isoforms, ave readlength of isoform 7.5kb P6/C4 chemistry, 2 SMRTcells #PAGXXIII
8:30pm January 11th 2015 via Hootsuite
AK: Looked at 16 microsatellites, 135 Arabica accessions, cultivated ones cluster; wild accessions diverge #PAGXXIII
8:26pm January 11th 2015 via Hootsuite
AK: PacBio gave 9.8k contigs, N50 267Kb. Short reads: 119k contigs, N50 of 8.8kb. Both about 80% est genome size #PAGXXIII
8:23pm January 11th 2015 via Hootsuite
AK: A di-haploid is not tetraploid; C. canephora can create dihaploid 1n=22. Autofertile, but some cross-pollination #PAGXXIII
8:20pm January 11th 2015 via Hootsuite
AK: Shor read, long read (PacBio), GBS, RNA-Seq both short and long reads; high-density maps #PAGXXIII
8:18pm January 11th 2015 via Hootsuite
AK: Showed geographic distribution of canephora across Africa; 7 groups assessed, ancestor of arabica is Ugandan #PAGXXIII
8:17pm January 11th 2015 via Hootsuite
AK: One goal is to catalog diversity of C arabica via GBS and multiple wild and cultivated accessions #PAGXXIII
8:16pm January 11th 2015 via Hootsuite
Alexandre de Kochko (IRD UMR DIADE, Montpellier, France) "Dihaploid Coffea arabica Genome Sequencing and Assembly" #PAGXXIII
8:14pm January 11th 2015 via Hootsuite
MM: Presently they are merging BAC pool assy w/ short-read assy, and then align against canephora seq. #PAGXXIII
8:11pm January 11th 2015 via Hootsuite
MM: Uses 'alignment-free sequence comparison' - groups of kmers canephora- or -eugenioides specific for assigning contigs #PAGXXIII
8:07pm January 11th 2015 via Hootsuite
MM: Showed kmer analysis - large peak unique; secondary peak identical sequences in the tetraploid #PAGXXIII
8:00pm January 11th 2015 via Hootsuite
MM: Overall coverage was 98x w/short reads; 132x from BAC approach. #PAGXXIII
7:57pm January 11th 2015 via Hootsuite
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
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
.@pop_gen_JED I've used this tool http://t.co/fqfpxrAnNa to clean up inactive accounts I follow, if only to get around the follower limit
6:16pm January 11th 2015 via Hootsuite in reply to
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
