The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

International audienceCurrent sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans

A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination

Haematobia irritans, commonly known as the horn fly, is a globally distributed blood-feeding pest of cattle that is responsible for significant economic losses to cattle producers. Chemical insecticides are the primary means for controlling this pest but problems with insecticide resistance have become common in the horn fly. To provide a foundation for identification of genomic loci for insecticide resistance and for discovery of new control technology, we report the sequencing, assembly, and annotation of the horn fly genome. The assembled genome is 1.14 Gb, comprising 76,616 scaffolds with N50 scaffold length of 23 Kb. Using RNA-Seq data, we have predicted 34,413 gene models of which 19,185 have been assigned functional annotations. Comparative genomics analysis with the Dipteran flies Musca domestica L., Drosophila melanogaster, and Lucilia cuprina, show that the horn fly is most closely related to M. domestica, sharing 8,748 orthologous clusters followed by D. melanogaster and L. cuprina, sharing 7,582 and 7,490 orthologous clusters respectively. We also identified a gene locus for the sodium channel protein in which mutations have been previously reported that confers target site resistance to the most common class of pesticides used in fly control. Additionally, we identified 276 genomic loci encoding members of metabolic enzyme gene families such as cytochrome P450s, esterases and glutathione S-transferases, and several genes orthologous to sex determination pathway genes in other Dipteran species

Supplemental Material for Konganti et al., 2018

File S1 - S5, Figure S1 - S4 and Tables S1-S14

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans

A schematic of the major lineages in the eukaryotic tree of life, showing the relationships between lineages for which genomic resources are currently available and those that have been targeted by the MMETSP.

<p>Lineages with complete genomes according to the GOLD database, as summarized in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001889#pbio.1001889-Burki1" target="_blank">[3]</a>, are indicated by a solid line leading to that group, whereas lineages with no complete genome are represented by a dashed line. Lineages where at least one MMETSP transcriptome is complete or underway are indicated with a red dot by the name. Major lineages discussed in the text have been named and color-coded, but for clarity, some major lineages have not been labeled.</p

Comparing the diversity of microbial eukaryotes at one marine site with that represented in genome data and the MMETSP project.

<p>(A) Taxon assignments for 930 Small Subunit (SSU) rRNA gene sequences from environmental clone libraries built using DNA from three size fractions in sunlit surface waters of the North Pacific Ocean. Four hundred and five sequences corresponding to Syndiniales (nonphotosynthetic members of the dinoflagellate lineage, often referred to as MALV1 and MALV2) were excluded for visualization purposes. Syndiniales are not represented in any complete genome data or the MMETSP, and the vast majority are only known as sequences from uncultivated taxa that often dominate clone libraries <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001889#pbio.1001889-Massana1" target="_blank">[22]</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001889#pbio.1001889-Massana2" target="_blank">[31]</a>. Filter size fractions were 0.1 to <0.8 µm, 0.8 to <3 µm, and 3 to <20 µm. This graph is only intended to give a snapshot of one marine sample; relative distributions vary based on distance from shore and depth, and several studies provide more detailed reviews of available SSU rRNA gene sequence surveys, see e.g., <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001889#pbio.1001889-Amin1" target="_blank">[21]</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001889#pbio.1001889-Not1" target="_blank">[32]</a>. (B) Taxonomic diversity of eukaryotes with complete genome sequences, as summarized in the Genomes Online Database (GOLD: <a href="http://genomesonline.org" target="_blank">http://genomesonline.org</a>). Note that multicellular organisms are included (unlike in A or C); animals, land plants, and multicellular rhodophytes are included in the opisthokont, viridiplantae, and rhodophyte categories, respectively. (C) Taxon breakdown of the MMETSP sequencing project, collapsed at the strain level (for some strains, cells were grown under multiple conditions and these have been counted only once). (D) Comparison of currently available complete genomes and MMETSP transcriptomes by Class for two diverse and well-studied groups of algae, prasinophytes <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001889#pbio.1001889-Marin1" target="_blank">[14]</a> and dinoflagellates <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001889#pbio.1001889-Fensome1" target="_blank">[15]</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001889#pbio.1001889-Saldarriagaa1" target="_blank">[16]</a>. For both lineages, genomes are broken down by Class on the left and MMETSP transcriptomes on the right.</p