Moran Yassour, Tommy Kaplan, Hunter B. Fraser, Joshua Z. Levin, Jenna Pfiffner, Xian Adiconis, Gary Schroth, Shujun Luo, Irina Khrebtukova, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, Aviv Regev.
PNAS 106, 3264-3269 (2009) | doi:10.1073/pnas.0812841106 | PMID:19208812
Defining the transcriptome, the repertoire of transcribed regions encoded in the genome, is a challenging experimental task. Current approaches, relying on sequencing of ESTs or cDNA libraries, are expensive and labor-intensive. Here, we present a general approach for ab initio discovery of the complete transcriptome of the budding yeast, based only on the unannotated genome sequence and millions of short reads from a single massively parallel sequencing run. Using novel algorithms, we automatically construct a highly accurate transcript catalog. Our approach automatically and fully defines 86% of the genes expressed under the given conditions, and discovers 160 previously undescribed transcription units of 250 bp or longer. It correctly demarcates the 5′ and 3′ UTR boundaries of 86 and 77% of expressed genes, respectively. The method further identifies 83% of known splice junctions in expressed genes, and discovers 25 previously uncharacterized introns, including 2 cases of condition-dependent intron retention. Our framework is applicable to poorly understood organisms, and can lead to greater understanding of the transcribed elements in an explored genome.
Naomi L. Ward, Jean F. Challacombe, Peter H. Janssen, Bernard Henrissat, Pedro M. Coutinho, Martin Wu, Gary Xie, Daniel H. Haft, Michelle Sait, Jonathan Badger, Ravi D. Barabote, Brent Bradley, Thomas S. Brettin, Lauren M. Brinkac, David Bruce, Todd Creasy, Sean C. Daugherty, Tanja M Davidsen, Robert T. DeBoy, J. Chris Detter, Robert J. Dodson, A. Scott Durkin, Anuradha Ganapathy, Michelle Gwinn-Giglio, Cliff S. Han, Hoda Khouri, Hajnalka Kiss, Sagar P. Kothari, Ramana Madupu, Karen Nelson, William C. Nelson, Ian Paulsen, Kevin Penn, Qinghu Ren, M. J. Rosovitz, Jeremy D. Selengut, Susmita Shrivastava, Steven A. Sullivan, Roxanne Tapia, L. Sue Thompson, Kisha L. Watkins, Qi Yang, Chunhui Yu, Nikhat Zafar, Liwei Zhou, Cheryl R. Kuske.
Appl. Environ. Microbiol., AEM accepts | doi:10.1128/AEM.02294-08 | PMID:19201974
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose and chitin. The genomes encode low-specificity MFS transporters and high-affinity ABC transporters for sugars, suggesting they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N2 fixation or denitrification. The genomes contained numerous genes encoding siderophore receptors, but no evidence was found for siderophore production, suggesting they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes, and a large class of novel high molecular weight excreted proteins suggest potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes encoding a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide, and the breadth of potential carbon use by the sequenced strains, suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates in low-nutrient conditions, and are well equipped to tolerate fluctuations hydration in soil.
Masaaki Seki, Ikuro Honda, Isao Fujita, Ikuya Yano, Saburo Yamamoto, Akira Koyama.
Vaccine 27, 1710-1716 (2009) | doi:10.1016/j.vaccine.2009.01.034 | PMID:19200449
To investigate the molecular characteristics of bacillus Calmette–Guérin (BCG) vaccines, the complete genomic sequence of Mycobacterium bovis BCG Tokyo 172 was determined, and the results were compared with those for BCG Pasteur and other M. tuberculosis complex. The genome of BCG Tokyo had a length of 4,371,711 bp and contained 4033 genes, including 3950 genes coding for proteins (CDS). There were 18 regions of difference (showing differences of more than 20 bp), 20 insertion or deletion (ins/del) mutations of less than 20 bp, and 68 SNPs between the two BCG substrains. These findings are useful for better understanding of the genetic differences in BCG substrains due to in vitro evolution of BCG.
Jarone Pinhassi, María J. Pujalte, Javier Pascual, José M. González, Itziar Lekunberri, Carlos Pedrós-Alió, David R. Arahal.
Int J Syst Evol Microbiol 59, 373-377 (2009) | DOI:10.1099/ijs.0.002113-0 | PMID:19196781
A novel heterotrophic, marine, strictly aerobic, motile bacterium was isolated from the Red Sea at a depth of 1 m. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to the genera Oleispira, Oceanobacter and Thalassolituus, each of which contains a single species, within the class Gammaproteobacteria. Phenotypic, genotypic and phylogenetic analyses supported the creation of a novel genus and species to accommodate this bacterium, for which the name Bermanella marisrubri gen. nov., sp. nov. is proposed. The type strain of Bermanella marisrubri is RED65T (=CECT 7074T =CCUG 52064T).
Andreas Gnirke, Alexandre Melnikov, Jared Maguire, Peter Rogov, Emily M LeProust, William Brockman, Timothy Fennell, Georgia Giannoukos, Sheila Fisher, Carsten Russ, Stacey Gabriel, David B Jaffe, Eric S Lander, Chad Nusbaum.
Nature Biotechnology 27, 182 - 189 (2009) | doi:10.1038/nbt.1523 | PMID:19182786
Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA 'baits' to fish targets out of a 'pond' of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to 50% lay on exons proper. The uniformity was such that 60% of target bases in the exonic 'catch', and 80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space.
