A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum

Background Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates. Results We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae. Conclusions L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum

Innovation in Nucleotide-Binding Oligomerization-Like Receptor and Toll-Like Receptor Sensing Drives the Major Histocompatibility Complex-II Free Atlantic Cod Immune System

The absence of MHC class II antigen presentation and multiple pathogen recognition receptors in the Atlantic cod has not impaired its immune response however how underlying mechanisms have adapted remains largely unknown. In this study, ex vivo cod macrophages were challenged with various bacterial and viral microbe-associated molecular patterns (MAMP) to identify major response pathways. Cytosolic MAMP-PRR pathways based upon the NOD-like receptors (NLRs) and RIG-I-like receptors (RLRs) were identified as the critical response pathways. Our analyses suggest that internalization of exogenous ligands through scavenger receptors drives both pathways activating transcription factors like NF-kB (Nuclear factor-kappa B) and interferon regulatory factors (IRFs). Further, ligand-dependent differential expression of a unique TLR25 isoform and multiple NLR paralogues suggests (sub)neofunctionalization toward specific immune defensive strategies. Our results further demonstrate that the unique immune system of the Atlantic cod provides an unprecedented opportunity to explore the evolutionary history of PRR-based signaling in vertebrate immunity

Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change

The Arctic is experiencingthe fastest rates of globalwarming,leadingto shiftsin the distributionof its biotaandincreasingthe potentialfor hybridization. However, genomicevidenceof recenthybridization events in theArctic remainsunexpectedlyrare. Here, we use whole-genomesequencingof contemporary and 122-year-oldhistoricalspecimensto investigate the originof an Arctic hybridpopulation of Atlanticpuffins(Fr aterculaarctica)on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodiedsubspeciesF. a. naumanniand the temperate, smaller-sizedsubspeciesF. a. arcticabeganas recentlyas six generationsagodue to an unexpectedsouthward rangeexpansionofF. a. naumanni.Moreover, we find a significanttemporalloss of geneticdiversityacross Arctic and temperate puffinpopulations.Our observationsprovide compellinggenomicevidenceof the impacts of recentdistributionalshiftsand loss of diversityin Arctic communitiesduringthe 20th century.publishedVersio

Assemblies of icefishes

<div>File Family Species</div><div>fish_57.scf.fasta.gzEleginopsidae Eleginops maclovinus</div><div>fish_58.scf.fasta.gzNototheniidae Patagonotothen guntheri</div><div>fish_59.scf.fasta.gzNototheniidae Trematomus newnesi</div><div>fish_60.scf.fasta.gzNototheniidae Pleuragramma antarcticum</div><div>fish_62.scf.fasta.gzArtedidraconidae Artedidraco skottsbergi</div><div>fish_63.scf.fasta.gzHarpagiferidaeHarpagifer kerguelensis</div><div>fish_64.scf.fasta.gzBathydraconidaeGymnodraco acuticeps</div

Transcript and genome assemblies of Atlantic cod

<p>Described here: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3448-x</p><p>NEWB454: An assembly based on 454 sequencing reads and sequenced BAC-ends. Assembled with Newbler 3.0.</p> <p>CA454ILM: An assembly based on Illuminaand 454sequencing reads. Assembled with CeleraAssembler.</p> <p>CA454PB: An assembly based on Illumina,454 andPacBio sequencing reads. Assembled withCelera Assembler.</p> <p>ALPILM:An assembly based on Illumina reads. Assembled with ALLPATHS-LG.</p> <p>gadMor2: An assembly reconciliation of NEWB454,ALPILM,CA454PB, CA454ILM put into linkage groups. </p> <p>trinity_cod_rna: A Trinity assembly of IlluminaRNA reads from 10.1016/j.redox.2015.06.003.</p> <p>newbler_cod_rna: A Newbler assembly of 454 and Sanger reads from 10.1038/nature10342 and Sanger reads from 10.1186/1471-2164-13-443.</p> <p>isoseq_cod_rna:A IsoSeq clustering of PacBio RNA reads.</p><p>te_comprehensive_cod_replib: The repeat library used for annotation TEs.</p><p>repeatmodeler_cod_replib: The repeat library used for annotation. </p><p>gadMor2_predicted_*_filtered: The predicted proteins/transcripts, filtered at less than 0.5 AED.</p><p>gadMor2_predicted_transcripts_all: All predicted proteins/transcripts.</p><p>gadMor2_annotation_filtered_only_gene_models: Only the gene models from the annotation, genes with less than 0.5 AED.</p><p>gadMor2_annotation_filtered: Only genes with less 0.5 AED, plus everything else (exonerate, blast, repeats etc).</p><p>gadMor2_annotation_complete: Everything MAKER outputs.</p><p> </p><p><br></p

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts

Teleost genomic repeat landscapes in light of diversification rates and ecology

Abstract Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring

A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)

The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behavior in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here, we present a high-quality reference genome for the reed warbler, based on PacBio, 10×, and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of BUSCO genes were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, and a BUSCO analysis of the protein sequences indicated 97.5% completeness. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds.Peer reviewe

Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish

Background The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach loss has occurred independently multiple times in the course of evolution. By assembling the ballan wrasse genome and transcriptome we aimed to determine the genetic basis for its digestive system function and appetite regulation. Among other, this knowledge will aid the formulation of aquaculture diets that meet the nutritional needs of agastric species. Results Long and short read sequencing technologies were combined to generate a ballan wrasse genome of 805 Mbp. Analysis of the genome and transcriptome assemblies confirmed the absence of genes that code for proteins involved in gastric function. The gene coding for the appetite stimulating protein ghrelin was also absent in wrasse. Gene synteny mapping identified several appetite-controlling genes and their paralogs previously undescribed in fish. Transcriptome profiling along the length of the intestine found a declining expression gradient from the anterior to the posterior, and a distinct expression profile in the hind gut. Conclusions We showed gene loss has occurred for all known genes related to stomach function in the ballan wrasse, while the remaining functions of the digestive tract appear intact. The results also show appetite control in ballan wrasse has undergone substantial changes. The loss of ghrelin suggests that other genes, such as motilin, may play a ghrelin like role. The wrasse genome offers novel insight in to the evolutionary traits of this large family. As the stomach plays a major role in protein digestion, the lack of genes related to stomach digestion in wrasse suggests it requires formulated diets with higher levels of readily digestible protein than those for gastric species

SupplementaryData.zip

<div><div>Data analyzed and generated in submitted paper "Evolutionary adaptability linked to length variation in short genic tandem Repeats". View in context of scripts available on https://github.com/uio-cels/TandemRepeats/tree/master/scripts.</div><div><br></div><div>Preprint available on bioRxiv: https://doi.org/10.1101/310045</div><div><br></div><div>1001 genomes SNP data was downloaded from the 1001 Genomes Consortium Data Center (http://1001genomes.org/data/GMI-MPI/releases/).</div><div><br></div><div>The RNA-seq dataset: GSE80744_ath1001_tx_norm_2016-04-21-UQ_gNorm_normCounts_k4.tsv.gz</div><div><br></div><div>was downloaded from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80744</div><div><br></div><div>Originally produced in:</div><div>Kawakatsu T, Huang SC, Jupe F, Sasaki E et al. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell 2016 Jul 14;166(2):492-505. PMID: 27419873</div></div><div><br></div><div><br></div