D. P. R. Herlemann, O. Geissinger, W. Ikeda-Ohtsubo, V. Kunin, H. Sun, A. Lapidus, P. Hugenholtz, A. Brune.
Appl. Environ. Microbiol., AEM Accepts | doi:10.1128/AEM.02698-08 | PMID:19270133
The candidate phylum Termite group 1 (TG1), is regularly encountered in termite hindguts but is present also in many other habitats. Here we report the complete genome sequence (1.64 Mbp) of Elusimicrobium minutum strain Pei191T, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut and discuss the findings in light of physiological data. E. minutum has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading to the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a Gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60 pilE-like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, non-ribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of Elusimicrobia (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.
Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, Knut Reinert.
Bioinformatics, Advance Access | doi:10.1093/bioinformatics/btp131 | PMID:19269990
Motivation: Novel high-throughput sequencing technologies pose new algorithmic challenges in handling massive amounts of shortread, high-coverage data. A robust and versatile consensus tool is of particular interest for such data since a sound multi-read alignment is a prerequisite for variation analyses, accurate genome assemblies and insert sequencing.
Results: A multi-read alignment algorithm for de novo or reference-guided genome assembly is presented. The program identifies segments shared by multiple reads and then aligns these segments using a consistency-enhanced alignment graph. On real de novo sequencing data, obtained from the newly established NCBI Short Read Archive, the program performs similarly in quality to other comparable programs. On more challenging simulated data sets for insert sequencing and variation analyses our program outperforms the other tools.
Availability: Availability: The consensus program can be downloaded from http://www.seqan.de/projects/consensus.html. It can be used stand-alone or in conjunction with the Celera Assembler. Both application scenarios as well as the usage of the tool are described in the documentation.
Chao Xie, Martti T Tammi.
BMC Bioinformatics 10, 80 (2009) | doi:10.1186/1471-2105-10-80 | PMID:19267900
Background
DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations.
Results
Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads.
Conclusion
Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.
Siân Jones, Ralph H. Hruban, Mihoko Kamiyama, Michael Borges, Xiaosong Zhang, D. Williams Parsons, Jimmy Cheng-Ho Lin, Emily Palmisano, Kieran Brune, Elizabeth M. Jaffee, Christine A. Iacobuzio-Donahue, Anirban Maitra, Giovanni Parmigiani, Scott E Kern, Victor E. Velculescu, Kenneth W. Kinzler, Bert Vogelstein, James R. Eshleman, Michael Goggins, Alison P. Klein.
Science 324, 217 (2009) | DOI:10.1126/science.1171202 | PMID:19264984
Through complete sequencing of the protein-coding genes in a patient with familial pancreatic cancer, we identified a germline, truncating mutation in PALB2 that appeared responsible for this patient's predisposition to the disease. Analysis of 96 additional patients with familial pancreatic cancer revealed three distinct protein-truncating mutations, thereby validating the role of PALB2 as a susceptibility gene for pancreatic cancer. PALB2 mutations have been previously reported in patients with familial breast cancer, and the PALB2 protein is a binding partner for BRCA2. These results illustrate that complete, unbiased sequencing of protein-coding genes can lead to the identification of a gene responsible for a hereditary disease.
Yong Zhang, Xue Zhou, Xie Ge, Jianhao Jiang, Muwang Li, Shihai Jia, Xiaonan Yang, Yunchao Kan, Xuexia Miao, Guoping Zhao, Fei Li, Yongping Huang.
PLoS ONE 4, e4677 (2009) | doi:10.1371/journal.pone.0004677 | PMID:19262741
MicroRNAs (miRNAs) are endogenous non-coding genes that participate in post-transcription regulation by either degrading mRNA or blocking its translation. It is considered to be very important in regulating insect development and metamorphosis. We conducted a large-scale screening for miRNA genes in the silkworm Bombyx mori using sequence-by-synthesis (SBS) deep sequencing of mixed RNAs from egg, larval, pupal, and adult stages. Of 2,227,930 SBS tags, 1,144,485 ranged from 17 to 25 nt, corresponding to 256,604 unique tags. Among these non-redundant tags, 95,184 were matched to the silkworm genome. We identified 3,750 miRNA candidate genes using a computational pipeline combining RNAfold and TripletSVM algorithms. We confirmed 354 miRNA genes using miRNA microarrays and then performed expression profile analysis on these miRNAs for all developmental stages. While 106 miRNAs were expressed in all stages, 248 miRNAs were egg- and pupa-specific, suggesting that insect miRNAs play a significant role in embryogenesis and metamorphosis. We selected eight miRNAs for quantitative RT-PCR analysis; six of these were consistent with our microarray results. In addition, we searched for orthologous miRNA genes in mammals, a nematode, and other insects and found that most silkworm miRNAs are conserved in insects, whereas only a small number of silkworm miRNAs has orthologs in mammals and the nematode. These results suggest that there are many miRNAs unique to insects.
