The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR 2 , http://ssurrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of hightroughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total,

/pdf/the-protist-ribosomal-reference-database-pr2-a-catalog-of-1jfpu9ej1a.pdf

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Motivation: Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically estimate the best k to use and/or quickly generate histograms of k-mer abundances that would allow the user to make an informed decision. Results: We develop a fast and accurate sampling method that constructs approximate abundance histograms with several orders of magnitude performance improvement over traditional methods. We then present a fast heuristic that uses the generated abundance histograms for putative k values to estimate the best possible value of k. We test the effectiveness of our tool using diverse sequencing datasets and find that its choice of k leads to some of the best assemblies. Availability: Our tool KMERGENIE is freely available at: http://kmergenie.

/pdf/informed-and-automated-k-mer-size-selection-for-genome-4p90e4avmu.pdf

Informed and automated k-mer size selection for genome assembly

Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically estimate the best k to use and/or quickly generate histograms of k-mer abundances that would allow the user to make an informed decision. 
We develop a fast and accurate sampling method that constructs approximate abundance histograms with a several orders of magnitude performance improvement over traditional methods. We then present a fast heuristic that uses the generated abundance histograms for putative k values to estimate the best possible value of k. We test the effectiveness of our tool using diverse sequencing datasets and find that its choice of k leads to some of the best assemblies. 
Our tool KmerGenie is freely available at: this http URL

Informed and Automated k-Mer Size Selection for Genome Assembly

▪ Abstract Oysters have been introduced worldwide to 73 countries, but the ecological consequences of the introductions are not fully understood. Economically, introduced oysters compose a majority of oyster harvests in many areas. Oysters are ecosystem engineers that influence many ecological processes, such as maintenance of biodiversity, population and food web dynamics, and nutrient cycling. Consequently, both their loss, through interaction of overharvest, habitat degradation, disease, poor water quality, and detrimental species interactions, and their gain, through introductions, can cause complex changes in coastal ecosystems. Introductions can greatly enhance oyster population abundance and production, as well as populations of associated native species. However, introduced oysters are also vectors for non-native species, including disease-causing organisms. Thus, substantial population, community, and habitat changes have accompanied new oysters. In contrast, ecosystem-level consequences of oyste...

Introduction of Non-Native Oysters: Ecosystem Effects and Restoration Implications

Funding information NSF Konza LTER, Grant/Award Numbers: NSF OIA-1656006, NSF DEB 1065255; Dimensions of Biodiversity, Grant/Award Numbers: 1831096, 1240851; US National Science Foundation, Grant/Award Numbers: CBET 1230543, 1840715, OCE 9905723, DEB 9815495; Ecology Center at Utah State University Abstract Agricultural, urban and industrial activities have dramatically increased aquatic nitrogen and phosphorus pollution (eutrophication), threatening water quality and biotic integrity from headwater streams to coastal areas world-wide. Eutrophication creates multiple problems, including hypoxic “dead zones” that reduce fish and shellfish production; harmful algal blooms that create taste and odor problems and threaten the safety of drinking water and aquatic food supplies; stimulation of greenhouse gas releases; and degradation of cultural and social values of these waters. Conservative estimates of annual costs of eutrophication have indicated $1 billion losses for European coastal waters and $2.4 billion for lakes and streams in the United States. Scientists have debated whether phosphorus, nitrogen, or both need to be reduced to control eutrophication along the freshwater to marine continuum, but many management agencies worldwide are increasingly opting for dual control. The unidirectional flow of water and nutrients through streams, rivers, lakes, estuaries and ultimately coastal oceans adds additional complexity, as each of these ecosystems may be limited by different factors. Consequently, the reduction of just one nutrient upstream to control eutrophication can allow the export of other nutrients downstream where they may stimulate algal production. The technology exists for controlling eutrophication, but many challenges remain for understanding and managing this global environmental problem.

Nutrients, eutrophication and harmful algal blooms along the freshwater to marine continuum

Mollusca evolutionary success can be attributed partly to their efficiency to sustain and protect their soft body with an external biomineralized structure, the shell. Current knowledge of the protein set responsible for the formation of the shell microstructural polymorphism and unique properties remains largely patchy. In Pinctada margaritifera and Pinctada maxima, we identified 80 shell matrix proteins, among which 66 are entirely unique. This is the only description of the whole "biomineralization toolkit" of the matrices that, at least in part, is thought to regulate the formation of the prismatic and nacreous shell layers in the pearl oysters. We unambiguously demonstrate that prisms and nacre are assembled from very different protein repertoires. This suggests that these layers do not derive from each other.

https://www.pnas.org/content/pnas/109/51/20986.full.pdf

Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell

The shell of the pearl-producing bivalve Pinctada margaritifera is composed of an organic cell-free matrix that plays a key role in the dynamic process of biologically-controlled biomineralization. In order to increase genomic resources and identify shell matrix proteins implicated in biomineralization in P. margaritifera, high-throughput Expressed Sequence Tag (EST) pyrosequencing was undertaken on the calcifying mantle, combined with a proteomic analysis of the shell. We report the functional analysis of 276 738 sequences, leading to the constitution of an unprecedented catalog of 82 P. margaritifera biomineralization-related mantle protein sequences. Components of the current "chitin-silk fibroin gel-acidic macromolecule" model of biomineralization processes were found, in particular a homolog of a biomineralization protein (Pif-177) recently discovered in P. fucata. Among these sequences, we could show the localization of two other biomineralization protein transcripts, pmarg-aspein and pmarg-pearlin, in two distinct areas of the outer mantle epithelium, suggesting their implication in calcite and aragonite formation. Finally, by combining the EST approach with a proteomic mass spectrometry analysis of proteins isolated from the P. margaritifera shell organic matrix, we demonstrated the presence of 30 sequences containing almost all of the shell proteins that have been previously described from shell matrix protein analyses of the Pinctada genus. The integration of these two methods allowed the global composition of biomineralizing tissue and calcified structures to be examined in tandem for the first time. This EST study made on the calcifying tissue of P. margaritifera is the first description of pyrosequencing on a pearl-producing bivalve species. Our results provide direct evidence that our EST data set covers most of the diversity of the matrix protein of P. margaritifera shell, but also that the mantle transcripts encode proteins present in P. margaritifera shell, hence demonstrating their implication in shell formation. Combining transcriptomic and proteomic approaches is therefore a powerful way to identify proteins involved in biomineralization. Data generated in this study supply the most comprehensive list of biomineralization-related sequences presently available among protostomian species, and represent a major breakthrough in the field of molluskan biomineralization.

/pdf/transcriptome-and-proteome-analysis-of-pinctada-78g6aob7m8.pdf

Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization

Bonamia sp. is a pathogenic parasite that occurs in the haemocytes of dredge oysters Ostrea chilensis Philippi in New Zealand. Ultrastructurally it resembles other haplosporidians in the possession of haplosporosomes, haplosporogenesis, persistence of mitotic microtubules during interphase and of the nuclear envelope during mitosis, and occurrence of a diplokaryotic or multi-nucleate plasmodial stage. Another stage containing a large vacuole derived from enlargement of 1 or more mitochondria has not previously been described from other haplosporidians. It most closely resembles B. ostreae Pichot et al., 1979, which parasitises and is pathogenic in haemocytes of European flat oysters, O. edulis. However, B. ostreae is smaller and denser, and has fewer lipoid bodies and haplosporosomes. We have nearly completely sequenced the small ribosomal gene of the organism from O. chilensis. Initial comparisons of these sequences with those of other protozoans showed similarities to B. ostreae. Polymorphism within Bonamia sp. was confirmed by restriction fragment length polymorphism analysis. On the basis of ultrastructural and molecular considerations it is proposed that this organism be named Bonamia exitiosus sp. nov.

/pdf/bonamia-exitiosus-n-sp-haplosporidia-infecting-flat-oysters-201y9glu3w.pdf

Bonamia exitiosus n.sp. (Haplosporidia) infecting flat oysters Ostrea chilensis in New Zealand

Changes in circulating and tissue-infiltrating hemocyte parameters of European flat oysters, Ostrea edulis, naturally infected with Bonamia ostreae.

http://www.vliz.be/imisdocs/publications/ocrd/299466.pdf

Nathalie Cochennec-Laureau

Papers

Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell

Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization

Bonamia exitiosus n.sp. (Haplosporidia) infecting flat oysters Ostrea chilensis in New Zealand

Changes in circulating and tissue-infiltrating hemocyte parameters of European flat oysters, Ostrea edulis, naturally infected with Bonamia ostreae.

Microcell parasites of oysters: Recent insights and future trends