PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-6 (6)
 

Clipboard (0)
None

Select a Filter Below

Journals
Year of Publication
Document Types
1.  Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution 
Archaea  2013;2013:202358.
The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life.
doi:10.1155/2013/202358
PMCID: PMC3852633  PMID: 24348093
2.  Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i 
PLoS ONE  2013;8(10):e76376.
The ancestor of Gloeobacter violaceus PCC 7421T is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of G. violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cyanobacteria evolution can be investigated. No other Gloeobacter species has been described since the genus was established in 1974 (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have been reported in environmental DNA libraries, but only the type strain's genome has been sequenced. However, we report here the cultivation of a new Gloeobacter species, G. kilaueensis JS1T, from an epilithic biofilm in a lava cave in Kīlauea Caldera, Hawai'i. The strain's genome was sequenced from an enriched culture resembling a low-complexity metagenomic sample, using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1T and G. violaceus PCC 7421T genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes shows they do not belong to the same species. Our results support establishing a new species to accommodate JS1T, for which we propose the name Gloeobacter kilaueensis sp. nov. Strain JS1T has been deposited in the American Type Culture Collection (BAA-2537), the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and the Belgian Coordinated Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the Algal Collection of the US National Herbarium (US# 217948). The JS1T genome sequence has been deposited in GenBank under accession number CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G. kilaueensis JS1T may further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic photosynthesis.
doi:10.1371/journal.pone.0076376
PMCID: PMC3806779  PMID: 24194836
3.  Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium 
Standards in Genomic Sciences  2012;6(1):84-93.
Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as ‘ixotrophy’. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.
doi:10.4056/sigs.2445005
PMCID: PMC3368406  PMID: 22675601
Saprospira grandis; predatory; RsbR; gliding motility; globin-coupled sensors; rhapidosomes
4.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) 
Ming, Ray | Hou, Shaobin | Feng, Yun | Yu, Qingyi | Dionne-Laporte, Alexandre | Saw, Jimmy H. | Senin, Pavel | Wang, Wei | Ly, Benjamin V. | Lewis, Kanako L. T. | Salzberg, Steven L. | Feng, Lu | Jones, Meghan R. | Skelton, Rachel L. | Murray, Jan E. | Chen, Cuixia | Qian, Wubin | Shen, Junguo | Du, Peng | Eustice, Moriah | Tong, Eric | Tang, Haibao | Lyons, Eric | Paull, Robert E. | Michael, Todd P. | Wall, Kerr | Rice, Danny W. | Albert, Henrik | Wang, Ming-Li | Zhu, Yun J. | Schatz, Michael | Nagarajan, Niranjan | Acob, Ricelle A. | Guan, Peizhu | Blas, Andrea | Wai, Ching Man | Ackerman, Christine M. | Ren, Yan | Liu, Chao | Wang, Jianmei | Wang, Jianping | Na, Jong-Kuk | Shakirov, Eugene V. | Haas, Brian | Thimmapuram, Jyothi | Nelson, David | Wang, Xiyin | Bowers, John E. | Gschwend, Andrea R. | Delcher, Arthur L. | Singh, Ratnesh | Suzuki, Jon Y. | Tripathi, Savarni | Neupane, Kabi | Wei, Hairong | Irikura, Beth | Paidi, Maya | Jiang, Ning | Zhang, Wenli | Presting, Gernot | Windsor, Aaron | Navajas-Pérez, Rafael | Torres, Manuel J. | Feltus, F. Alex | Porter, Brad | Li, Yingjun | Burroughs, A. Max | Luo, Ming-Cheng | Liu, Lei | Christopher, David A. | Mount, Stephen M. | Moore, Paul H. | Sugimura, Tak | Jiang, Jiming | Schuler, Mary A. | Friedman, Vikki | Mitchell-Olds, Thomas | Shippen, Dorothy E. | dePamphilis, Claude W. | Palmer, Jeffrey D. | Freeling, Michael | Paterson, Andrew H. | Gonsalves, Dennis | Wang, Lei | Alam, Maqsudul
Nature  2008;452(7190):991-996.
Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree1 to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far2–5, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.
doi:10.1038/nature06856
PMCID: PMC2836516  PMID: 18432245
5.  Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1 
Genome Biology  2008;9(11):R161.
Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation.
Background
Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life.
Results
We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres.
Conclusions
Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.
doi:10.1186/gb-2008-9-11-r161
PMCID: PMC2614493  PMID: 19014707
6.  Assembling the Marine Metagenome, One Cell at a Time 
PLoS ONE  2009;4(4):e5299.
The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.
doi:10.1371/journal.pone.0005299
PMCID: PMC2668756  PMID: 19390573

Results 1-6 (6)