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J. K. Colbourne,
M. E. Pfrender,
D. Gilbert,
W. K. Thomas,
A. Tucker,
T. H. Oakley,
S. Tokishita,
A. Aerts,
G. J. Arnold,
M. K. Basu, [......],
T. J. Crease,
H. Tang,
S. M. Lucas,
H. M. Robertson,
P. Bork,
E. V. Koonin,
E. M. Zdobnov,
I. V. Grigoriev,
M. Lynch,
J. L. Boore
[show abstract]
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ABSTRACT: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia’s genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.
Science. 02/2011; 331(6017):555-561.
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J. A. Banks,
T. Nishiyama,
M. Hasebe,
J. L. Bowman,
M. Gribskov,
C. Depamphilis,
V. A. Albert,
N. Aono,
T. Aoyama,
B. A. Ambrose, [......],
U. Hellsten,
D. Loque,
R. Otillar, A. Salamov,
J. Schmutz,
H. Shapiro,
E. Lindquist,
S. Lucas,
D. Rokhsar,
I. V. Grigoriev
[show abstract]
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ABSTRACT: Vascular plants appeared ~410 million years ago, then diverged into several lineages, of which only two survive: the euphyllophytes(ferns and seed plants) and the lycophytes. Here, we report the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionary diverse taxa, we found that the transition from a gametophyte- to sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, while secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the tasiRNA pathway and extensive RNA editing of organellar genes.
Science. 01/2011; 5:5.
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R. Sucgang,
W. Salerno,
A. Parikh,
C. L. Feasley,
E. Dalin,
H. Tu,
E. Huang,
K. Barry,
E. Lindquist,
H. Shapiro, [......],
F. Rivero,
N. H. Putnam,
C. M. West,
W. F. Loomis,
R. L. Chisholm,
G. Shaulsky,
J. E. Strassmann,
D. C. Queller,
A. Kuspa,
I. V. Grigoriev
[show abstract]
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ABSTRACT: ABSTRACT: BACKGROUND: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. RESULTS: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 x coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. CONCLUSIONS: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.
Genome Biol. 01/2011; 12(2):R20.
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F Martin,
A Aerts,
D Ahrén,
A Brun,
E G J Danchin,
F Duchaussoy,
J Gibon,
A Kohler,
E Lindquist,
V Pereda, [......],
G K Podila,
A Polle,
P J Pukkila,
P M Richardson,
P Rouzé,
I R Sanders,
J E Stajich,
A Tunlid,
G Tuskan,
I V Grigoriev
[show abstract]
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ABSTRACT: Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
Nature 04/2008; 452(7183):88-92. · 36.28 Impact Factor
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G A Tuskan,
S Difazio,
S Jansson,
J Bohlmann,
I Grigoriev,
U Hellsten,
N Putnam,
S Ralph,
S Rombauts, A Salamov, [......],
J Vahala,
K Wall,
S Wessler,
G Yang,
T Yin,
C Douglas,
M Marra,
G Sandberg,
Y Van de Peer,
D Rokhsar
[show abstract]
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ABSTRACT: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
Science 10/2006; 313(5793):1596-604. · 31.20 Impact Factor
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R.A. Ohm,
J.F. de Jong,
L.G. Lugones,
A. Aerts,
E. Kothe,
J.E. Stajich,
R.P. de Vries,
E Record,
A Levasseur,
S. E. Baker, [......],
J. K. Magnuson,
F. Piumi,
M. Raudaskoski, A. Salamov,
J Schmutz,
F.W. Schwarze,
P.A. Vankuyk,
J.S. Horton,
I.V. Grigoriev,
H.A.B. Wösten
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M G Kalyuzhnaya,
A. Lapidus,
N. Ivanova,
A. C. Copeland,
Alice McHardy,
E. Szeto, A. Salamov,
I.V. Grigoriev,
D. Suciu,
S. R. Levine,
V.M. Markowitz,
I. Rigoutsos,
S G Tringe,
D. C. Bruce,
P M Richardson,
M E Lidstrom,
L Chistoserdova
Nature biotechnology, v.26, 1029-34 (2008).
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K. Mavromatis,
N. Ivanova,
K. Barry,
H. Shapiro,
E. Goltsman,
Alice McHardy,
I. Rigoutsos, A. Salamov,
F. Korzeniewski,
M. Land,
A. Lapidus,
I. Grigoriev,
P Richardson,
P Hugenholtz,
N C Kyrpides
Nature Methods, v.4, 495-500 (2007).
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G Martin,
Kunin,
N. Ivanova,
Warnecke,
B Peterson,
W Barry,
C McHardy,
C Yeates,
He, A. Salamov,
E. Szeto,
E Dalin,
N. Putnam,
I. Rigoutsos,
C Kyrpides,
L. L. Blackall,
K. McMahon,
Hugenholtz
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F. Warnecke,
P. Luginbühl,
N. Ivanova,
M. Ghassemian,
T. H. Richardson,
J. T. Stege,
M. Cayouette,
Alice McHardy,
G. Djordjevic,
N. Aboushadi, [......],
L. G. Acosta,
I. Rigoutsos,
G. Tamayo,
B. D. Green,
C Chang,
E M Rubin,
E. J. Mathur,
D. E. Robertson,
P Hugenholtz,
J. R. Leadbetter
Nature, v.450, 560-565 (2007).
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[show abstract]
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ABSTRACT: Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast. The mechanism and regulation of xylose metabolism in P. stipitis have been characterized and genes from P. stipitis have been used to engineer xylose metabolism in Saccharomyces cerevisiae. We have sequenced and assembled the complete genome of P. stipitis. The sequence data have revealed unusual aspects of genome organization, numerous genes for bioconversion, a preliminary insight into regulation of central metabolic pathways and several examples of colocalized genes with related functions. The genome sequence provides insight into how P. stipitis regulates its redox balance while very efficiently fermenting xylose under microaerobic conditions.
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U. Hellsten,
R. M. Harland,
M. J. Gilchrist,
D. Hendrix,
J. Jurka,
V. Kapitonov,
I. Ovcharenko,
N. H. Putnam,
S. Shu,
L. Taher, [......],
D. Wells,
A. Wills,
R. K. Wilson,
L. B. Zimmerman,
A. M. Zorn,
R. Grainger,
T. Grammer,
M. K. Khokha,
P. M. Richardson,
D. S. Rokhsar
[show abstract]
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ABSTRACT: The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.
Science. 328(5978):633-6.
