Dataset Information

Insular organization of gene space in grass genomes.

ABSTRACT: Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands "gene insulae" to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.

SUBMITTER: Gottlieb A

PROVIDER: S-EPMC3543359 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Insular organization of gene space in grass genomes.

Gottlieb Andrea A Müller Hans-Georg HG Massa Alicia N AN Wanjugi Humphrey H Deal Karin R KR You Frank M FM Xu Xiangyang X Gu Yong Q YQ Luo Ming-Cheng MC Anderson Olin D OD Chan Agnes P AP Rabinowicz Pablo P Devos Katrien M KM Dvorak Jan J

PloS one 20130111 1

Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density ...[more]

PMID: 23326580

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Project description:Understanding the mechanisms of species distribution within ecosystems is a fundamental question of ecological research. The current worldwide changes and loss of habitats associated with a decline in species richness render this topic a key element for developing mitigation strategies. Ecological niche theory is a widely accepted concept to describe species distribution along environmental gradients where each taxon occupies its own distinct set of environmental parameters, that is, its niche. Niche occupation has been described in empirical studies for different closely related taxa, like ant, ungulate, or skink species, just to name a few. However, how species assemblages of whole ecosystems across multiple taxa are structured and organized has not been investigated thoroughly, although considering all taxa of a community would be essential when analyzing realized niches. Here, we investigated the organization of niche occupation and species distribution for the whole ground-associated invertebrate community of small tropical insular ecosystems. By correlating environmental conditions with species occurrences using partial canonical correspondence analysis (pCCA), we demonstrated that the ground-associated invertebrate community does not spread evenly across the overall niche space, but instead is compartmentalized in four distinct clusters: crustacean and gastropod taxa occurred in one cluster, attributable to the beach habitat, whereas hexapods and spider taxa occurred in three distinct inland clusters, attributable to distinct inland habitats, that is, grassland, open forest, and dense forest. Within the clusters, co-occurrence pattern analysis suggested only a few negative interactions between the different taxa. By studying ground-associated insular invertebrate communities, we have shown that species distribution and niche occupation can be, similar to food webs, organized in a compartmentalized way. The compartmentalization of the niche space might thereby be a mechanism to increase ecosystem resilience, as disturbances cascade more slowly throughout the ecosystem.

Dataset Information

Insular organization of gene space in grass genomes.

Publications

Insular organization of gene space in grass genomes.

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