downstream of the source element, in a process called 3′ transduction 7-9. L1 retrotransposons can also promote the somatic transmobilization of Alu elements, SINE-VNTR-Alu (SVA) elements and processed pseudogenes, which are copies of mRNAs that have been reverse transcribed into DNA and inserted into the genome with the machinery of active L1 elements 10-12. Approximately 50% of human tumors contain somatic retrotranspositions of L1 elements 7,13-15. Previous analyses indicate that although a fraction of somatically acquired L1 insertions in cancer may influence gene function, the majority of retrotransposon integrations in a single tumor represent passenger mutations with little or no effect on cancer development 7,13. Nonetheless, L1 elements are capable of promoting other types of genomic structural alterations in the germline and somatically, in addition to canonical L1 insertion events 16-18 ; the effect of these alterations remains largely unexplored in the context of human cancer 19,20 .

About half of all cancers have somatic integrations of retrotransposons. To characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 37 histological cancer subtypes. We identified 19,166 somatically acquired retrotransposition events, affecting 35% of samples, and spanning a range of event types. L1 insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, sometimes removing tumour suppressor genes, as well as inducing complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage-fusion-bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications in the development of human tumours.Long interspersed nuclear element (LINE)-1 (L1) retrotransposons are widespread repetitive elements in the human genome, representing 17% of the entire DNA content 1,2 . Using a combination of cellular enzymes and self-encoded proteins with endonuclease and reverse transcriptase activity, L1 elements copy and insert themselves at new genomic sites, a process called retrotransposition. Most of the ~500,000 L1 copies in the human reference genome are truncated, inactive elements not able to retrotranspose. A small subset of them, maybe 100-150 L1 loci, remain active in the average human genome, acting as source elements, of which a small number are highly active copies termed hot-L1s 3-5 . These L1 source elements are usually transcriptionally repressed, but epigenetic changes occurring in tumours may promote their expression and allow them to retrotranspose 6,7 . Somatic L1 retrotransposition most often introduces a new copy of the 3' end of the L1 sequence, and can also mobilize unique DNA sequences located immediately downstream of the source element, a process called 3' transduction 7-9 . L1 retrotransposons can also promote the somatic trans-mobilization of Alu, SVA and processed pseudogenes, which are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome using the machinery of active L1 elements 10-12 .6 Approximately 50% of human tumours have somatic retrotransposition of L1 elements 7,13-15 .Previous analyses indicate that although a fraction of somatically acquired L1 insertions in cancer may influence gene function, the majority of retrotransposon integrations in a single tumour represent passenger mutations with little or no effect on cancer development 7,13 .Nonetheless, L1 insertions are capable of promoting other types of genomic structural alterations in the germline and somatically, apart from canonical L1 insertion events [16][17][18] , which remain largely unexplored in human cancer 19,20 .To further understand the roles...

Freshwater fungi are a poorly studied ecological group that includes a high taxonomic diversity. Most studies on aquatic fungal diversity have focused on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in the meso-oligotrophic, temperate Lake Stechlin in North-East Germany. These included the pelagic and littoral water column, sediments, and biotic substrates. We performed high throughput sequencing using the Roche 454 platform, employing a universal eukaryotic marker region within the large ribosomal subunit (LSU) to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1027 fungal OTUs (97% sequence similarity). Richness estimates were highest in the sediment, biofilms, and benthic samples (189-231 OTUs), intermediate in water samples (42-85 OTUs), and lowest in plankton samples (8 OTUs). NMDS grouped the eight studied habitats into six clusters, indicating that community composition was strongly influenced RESEARCH ARTICLEChristian Wurzbacher et al. / MycoKeys 16: 17-44 (2016) 18 by turnover among habitats. Fungal communities exhibited changes at the phylum and order levels along three different substrate categories from littoral to pelagic habitats. The large majority of OTUs (> 75%) could not be classified below the order level due to the lack of aquatic fungal entries in public sequence databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition. Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body.

Deciphering the genes involved in disease resistance is essential if we are to understand host-pathogen coevolutionary processes. The rabbit haemorrhagic disease virus (RHDV) was imported into Australia in 1995 as a biocontrol agent to manage one of the most successful and devastating invasive species, the European rabbit (Oryctolagus cuniculus). During the first outbreaks of the disease, RHDV caused mortality rates of up to 97%. Recently, however, increased genetic resistance to RHDV has been reported. Here, we have aimed to identify genomic differences between rabbits that survived a natural infection with RHDV and those that died in the field using a genomewide next-generation sequencing (NGS) approach. We detected 72 SNPs corresponding to 133 genes associated with survival of a RHD infection. Most of the identified genes have known functions in virus infections and replication, immune responses or apoptosis, or have previously been found to be regulated during RHD. Some of the genes identified in experimental studies, however, did not seem to play a role under natural selection regimes, highlighting the importance of field studies to complement the genomic background of wildlife diseases. Our study provides a set of candidate markers as a tool for the future scanning of wild rabbits for their resistance to RHDV. This is important both for wild rabbit populations in southern Europe where RHD is regarded as a serious problem decimating the prey of endangered predator species and for assessing the success of currently planned RHDV variant biocontrol releases in Australia.

The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.

Freshwater fungi are a poorly studied paraphyletic group that include a high diversity of phyla.Most studies of aquatic fungal diversity have focussed on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in meso-oligotrophic, temperate Lake Stechlin in northern Germany, including the pelagic and littoral water column, sediments, and biotic substrates.We pyrosequenced with an universal eukaryotic marker within the ribosomal large subunit (LSU) in order to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1024 fungal OTUs (97% criterion). Diversity was highest in the sediment, biofilms, and benthic samples (293-428 OTUs), intermediate in water and reed samples (36-64 OTUs), and lowest in plankton (8 OTUs) samples. NMDS clustering clearly grouped the eight studied habitats into six clusters, indicating that total diversity was strongly influenced by turnover among habitats. Fungal communities exhibited pronounced changes at the levels of phylum and order along a gradient from littoral to pelagic habitats. The large majority of OTUs could not be classified below the order level due to the lack of aquatic fungal entries in taxonomic databases.Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat-specificity to total fungal diversity. This remarkable diversity is probably an underestimate, because most lakes undergo seasonal changes and previous studies have uncovered differences in fungal communities among lakes.

The free-living amoeba Balamuthia mandrillaris is a rare but highly lethal agent of amoebic encephalitis in humans and many other mammalian species. Here, we announce the first draft genome sequence of the original 1990 isolate cultured from the brain of a deceased mandrill baboon.

29The study of processes driving diversification requires a fully sampled and well resolved 30 phylogeny. Multilocus approaches to the study of recent diversification provide a powerful 31 means to study the evolutionary process, but their application remains restricted because 32 multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not 33 available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA 34 (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic 35 insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. 36 Whole-genome sequencing data from one member of the species complex were used to 37 identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals 38 sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent 39 analyses established six putative species. Three island species formed a monophyletic clade, 40 with one species occurring on the Azores, Europe and North America. Ancestral state 41 reconstruction indicated at least two colonization events from the mainland (Canaries, 42Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets 43 of the 59 loci showed a positive linear relationship between number of loci and node support. 44In contrast, node support in the multispecies coalescent tree was negatively correlated with 45 mean number of phylogenetically informative sites per locus, suggesting a complex 46 relationship between tree resolution and marker variability. Our approach highlights the value 47 of combining coalescent-based phylogeography, species delimitation, and phylogenetic 48 reconstruction to resolve recent diversification events in an archipelago species complex. 49