Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Variability of Symbiodinium Communities in Waters, Sediments, and Corals of Thermally Distinct Reef Pools in American Samoa.

Reef-building corals host assemblages of symbiotic algae (Symbiodinium spp.) whose diversity and abundance may fluctuate under different conditions, potentially facilitating acclimatization to environmental change. The composition of free-living Symbiodinium in reef waters and sediments may also be environmentally labile and may influence symbiotic assemblages by mediating supply and dispersal. The magnitude and spatial scales of environmental influence over Symbiodinium composition in different reef habitat compartments are, however, not well understood. We used pyrosequencing to compare Symbiodinium in sediments, water, and ten coral species between two backreef pools in American Samoa with contrasting thermal environments. We found distinct compartmental assemblages of clades A, C, D, F, and/or G Symbiodinium types, with strong differences between pools in water, sediments, and two coral species. In the pool with higher and more variable temperatures, abundance of various clade A and C types differed compared to the other pool, while abundance of D types was lower in sediments but higher in water and in Pavona venosa, revealing an altered habitat distribution and potential linkages among compartments. The lack of between-pool effects in other coral species was due to either low overall variability (in the case of Porites) or high within-pool variability. Symbiodinium communities in water and sediment also showed within-pool structure, indicating that environmental influences may operate over multiple, small spatial scales. This work suggests that Symbiodinium composition is highly labile in reef waters, sediments, and some corals, but the underlying drivers and functional consequences of this plasticity require further testing with high spatial resolution biological and environmental sampling

Data from: Variability of Symbiodinium communities in waters, sediments, and corals of thermally distinct reef pools in American Samoa

Reef-building corals host assemblages of symbiotic algae (Symbiodinium spp.) whose diversity and abundance may fluctuate under different conditions, potentially facilitating acclimatization to environmental change. The composition of free-living Symbiodinium in reef waters and sediments may also be environmentally labile and may influence symbiotic assemblages by mediating supply and dispersal. The magnitude and spatial scales of environmental influence over Symbiodinium composition in different reef habitat compartments are, however, not well understood. We used pyrosequencing to compare Symbiodinium in sediments, water, and ten coral species between two backreef pools in American Samoa with contrasting thermal environments. We found distinct compartmental assemblages of clades A, C, D, F, and/or G Symbiodinium types, with strong differences between pools in water, sediments, and two coral species. In the pool with higher and more variable temperatures, abundance of various clade A and C types differed compared to the other pool, while abundance of D types was lower in sediments but higher in water and in Pavona venosa, revealing an altered habitat distribution and potential linkages among compartments. The lack of between-pool effects in other coral species was due to either low overall variability (in the case of Porites) or high within-pool variability. Symbiodinium communities in water and sediment also showed within-pool structure, indicating that environmental influences may operate over multiple, small spatial scales. This work suggests that Symbiodinium composition is highly labile in reef waters, sediments, and some corals, but the underlying drivers and functional consequences of this plasticity require further testing with high spatial resolution biological and environmental sampling

Cunning_PLoSONE_Dryad_Archive

This archive file contains all data and scripts necessary to reproduce the analyses and figures presented in this manuscript

<i>Symbiodinium</i> clade composition for complete dataset.

<p>Bars represent the proportion of sequences in each sample from each clade.</p

Differentiation of <i>Symbiodinium</i> communities between pools.

<p>NMDS biplots on Bray-Curtis dissimilarities are shown for water (A), sediment (B), and coral (C). Samples from pool 300 and pool 400 are represented by circles and triangles, respectively. Taxa are plotted in the same ordination space and colored by clade (A = green, C = yellow, D = purple, F = red, G = orange) to show their role in driving the differentiation between samples (e.g., clade D in association with sediment samples from pool 400). Three sediment samples are plotted with arrows indicating they lie outside the plot range. For corals, 90% confidence ellipses surround groups of species categorized qualitatively as low (< 0.4), intermediate (0.4–0.6), or high (> 0.6) overall dissimilarity (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145099#pone.0145099.t001" target="_blank">Table 1</a>) to illustrate the range of observed variability in different coral species. Coral species whose symbiont communities were significantly different between pools (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145099#pone.0145099.t001" target="_blank">Table 1</a>) are represented by filled symbols (gray = <i>Psammacora contigua</i>, black = <i>Pavona venosa</i>).</p

Altered compartmental distributions of <i>Symbiodinium</i> between pools.

<p>The inner ring shows <i>Symbiodinium</i> taxa (clade A = green, C = yellow, D = purple, F = red, G = orange) that were differentially abundant in each compartment (middle ring: water = blue, sediment = gray, coral = pink, <i>Pavona venosa</i> = Pv, <i>Psammocora contigua</i> = Pc) between pools. The outer ring indicates whether taxa were more or less abundant in each pool, and ribbons connect instances where taxa were differentially abundant in multiple compartments. Ribbons reveal different compartmental distributions of taxa in each pool: in pool 300 (vs. 400), 8 taxa (including 4 clade D) were less abundant in sediments and more abundant in water and/or coral, while 2 other clade C taxa were more abundant in sediments and less abundant in water.</p

Location and <i>Symbiodinium</i> clade composition of water, coral, and sediment samples in each pool.

<p>Points represent sample positions and pie charts represent clade composition (A = green, C = yellow, D = purple, F = red, G = orange). Water samples (A) showed more clade A near shore, while sediments (C) showed more clade A further from shore, and clusters of more similar communities (e.g., clades D and F in the northeast and clade G in the southwest corners of pool 300; similar mixtures of C, D, and A in northwest corner of pool 400). Corals (B) tended to have more clade D near pool edges, especially in pool 400. Clade composition for <i>Porites</i> spp. (i.e., species with the lowest dissimilarity, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145099#pone.0145099.t001" target="_blank">Table 1</a>) is not shown here, but can be seen in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145099#pone.0145099.g001" target="_blank">Fig 1</a>. While data are visualized at the clade level, spatial autocorrelation tests reflect patterns in total diversity.</p