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

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

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

Comparing the emergence of Echinochloa crus-galli populations in different locations. Part II: similarities and threshold parameters

The variability in the emergence process of different populations was confirmed for two Echinochloa crus-galli populations, one from Italy (IT) and the second from Norway (NO). Seeds were sown in 12 localities over Europe and the Middle East, and the emergence patterns of IT and NO were compared with those of several local populations at each location. Seeds of each population were sown in pots buried to the ground level. The base temperature (Tb) for emergence was estimated by (1) analysing logistic models applied to the field emergence of IT and NO, and (2) a germination assay set in winter 2020 at constant temperatures (8, 11, 14, 17, 20, 26, 29°C) with newly collected seeds in 2019 from the same fields where IT and NO had previously been harvested in 2015. The logistic models developed for IT and NO in each location showed that the emergence pattern of IT was similar to that of the local populations in Poland, Italy, Spain, Turkey South and Iran, while NO fitted better to those in Sweden and Latvia. No germination was obtained for IT in a germination chamber, but the estimated Tb with the logistic model was 11.2°C. For NO, the estimated Tb was 8.8°C in the germination chamber and 8.1°C in the field. Results suggest that adaptation to local environmental conditions has led to inter-population differences in Tb and parameter estimates of thermal-time models to predict the emergence of E. crus-galli should only be used for populations with similar climatic and habitat conditions.The authors thank all the technicians, students and institutions that have contributed to establishing and maintaining the field experiment. We also thank Dr. Frank Forcella and James Eklund, from the USDA‐ARS in Morris (MN), for providing the dataloggers and facilitating the collection of soil temperature data in each location. Our thanks also to the Spanish Ministry of Economy and Competitiveness for funding to Royo‐Esnal through the AGL2017‐83325‐C4‐2‐R; Duzce Üniversitesi, Turkey, for funding to Uludag (Project No: 2015.11.02.375); and the Norwegian Research Funding for Agriculture and the Food Industry and project partners in Research Council of Norway Project no. 267700 for supporting Tørresen in the experiment. Uludag thank his two graduate students, Miss Buyukkurt and Zambak, and Murdoch thank MSc student, Mr Guangxing Xie, who carried out some of the germination assays. Royo‐Esnal thank Jordi Izquierdo for providing the seeds of L3 population for the experiment in Lleida. Finally, the authors are also grateful to the EWRS, for providing funds to enable the working group participants to meet and discuss the collaborative experiment

Residue cover, soil structure, weed infestation and spring cereal yields as affected by tillage and straw management on three soils in Norway

Four field trials (spring wheat and oats) were conducted (one on clay soil, one on loam soil and two on silt soil) for three years in important cereal growing districts, to investigate the influence of tillage regimes (ploughing versus reduced tillage in either autumn or spring) and straw management (removed and retained) on plant residue amounts, weed populations, soil structural parameters and cereal yields. The effect of tillage on soil structure varied, mainly due to the short trial period. In general, the amount of small soil aggregates increased with tillage intensity. Reduced soil tillage, and in some cases spring ploughing, gave significantly higher aggregate stability than autumn ploughing, thus providing protection against erosion. However, decreasing tillage intensity increased the amounts of weeds, particularly of Poa annua on silt soil. Straw treatment only slightly affected yields, while effects of tillage varied between both year and location. Reduced tillage, compared to ploughing, gave only small yield differences on loam soil, while it was superior on clay soil and inferior on silt soil. Our results suggest that shallow spring ploughing is a good alternative to autumn ploughing, since it gave comparable yields, better protection against erosion and was nearly as effective against weeds

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

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