Data from: Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming
Contributors: Ebner, Joshua Niklas, Ritz, Danilo, von Fumetti, Stefanie, Ebner, Joshua
... Species’ ecological preferences are often deduced from habitat characteristics thought to represent more or less optimal conditions for physiological functioning. Evolution has led to stenotopic and eurytopic species, the former having decreased niche breadths and lower tolerances to environmental variability. Species inhabiting freshwater springs are often described as being stenotopic specialists, adapted to the stable thermal conditions found in these habitats. Whether due to past local adaptation these species have evolved or have lost intra-generational adaptive mechanisms to cope with increasing thermal variability has, to our knowledge, never been investigated. By studying how the proteome of a stenotopic species changes as a result of increasing temperatures we investigate if the absence or attenuation of molecular mechanisms is indicative of local adaptation to freshwater springs. An understanding of compensatory mechanisms is especially relevant as spring-specialists will experience thermal conditions beyond their physiological limits due to climate change. In this study, the stenotopic species Crunoecia irrorata (Trichoptera: Lepidostomatidae, Curtis 1834) was acclimated to 10, 15 and 20 °C for 168 h. We constructed a homology-based database, and via liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based shotgun proteomics identified 1358 proteins. Differentially abundant proteins and protein norms of reaction revealed candidate proteins and molecular mechanisms facilitating compensatory responses such as trehalose metabolism, tracheal system alteration, and heat shock protein regulation. A species-specific understanding of compensatory physiologies challenges the characterization of species as having narrow tolerances to environmental variability if that characterization is based on occurrences and habitat characteristics alone.
Data from: Genome sequence of Striga asiatica provides insight into the evolution of plant parasitism
Contributors: Yoshida, Satoko, Kim, Seungill, Wafula, Eric K., Tanskanen, Jaakko, Kim, Yong-Min, Honaas, Loren, Yang, Zhenzhen, Spallek, Thomas, Conn, Caitlin E., Ichihashi, Yasunori
... Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialised penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.
Data from: Social spider webs harbor largely consistent bacterial communities across broad spatial scales
Contributors: Keiser, Carl N., Hammer, Tobin J., Pruitt, Jonathan N.
... Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbor microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbors compositionally distinct microbes from the more ephemeral capture webs in the desert social spider Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harbored similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey, and web samples. These data suggest that social spider webs can harbor characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.
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Data from: Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage
Contributors: Hostager, Reilly, Raggonet-Cronin, Manon, Murrell, Ben, Hedskog, Charlotte, Osinusi, Anu, Susser, Simone, Sarrazin, Christoph, Svarovskaia, Evguenia, Wertheim, Joel
... Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced 21 full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; n=109) sampled in 19 countries from public databases (102 individuals), additional newly sequenced genomic regions (from 48 of these 102 individuals), unpublished isolates with newly sequenced regions (5 additional individuals), and novel complete genomes (2 additional individuals) generated in this study. Analysis of this expanded dataset reconfirmed the monophyletic origin of 2k/1b with a recombination breakpoint at position 3,187 (95% confidence interval: 3,172–3,202; HCV GT1a reference strain H77). Phylogeography is a valuable tool used to reveal viral migration dynamics. Inference of the timed history of spread in a Bayesian framework identified Russia as the ancestral source of the CRF 2k/1b clade. Further, we found evidence for migration routes leading out of Russia to other former Soviet Republics or countries under the Soviet sphere of influence. These findings suggest an interplay between geopolitics and the historical spread of CRF 2k/1b.
Data from: Evidence of genetic erosion in a peripheral population of a North American game bird: the Montezuma quail (Cyrtonyx montezumae)
Contributors: Mathur, Samarth, Tomeček, John M., Heniff, Ashlyn, Luna, Ryan, DeWoody, J. Andrew
... Population extirpations are often precursors to species extinctions. Anthropogenic activities often lead to smaller populations that are more prone to extirpations and advocates for active conservation management have recently called for the preservation and monitoring of genetic diversity, particularly with regard to the adaptive potential of vulnerable populations. We used genomics and curated arrays of molecular markers, including those expected to impact key fitness traits, to quantify evidence of genomic erosion in core and peripheral populations of a gallinaceous bird. The Montezuma quail (Cyrtonyx montezumae) is a game species considered vulnerable to extirpation in Texas, but core populations in Arizona and New Mexico are robust and have the potential to serve as genetic reservoirs. We sequenced the Montezuma quail genome then developed a single nucleotide polymorphism (SNP) assay to quantify genetic variation, effective population sizes, signatures of natural selection, and population structure. We genotyped SNPs from gene deserts and from genes associated with fitness traits and found the isolated Texas population exhibits an extremely small effective population size, is genetically distinct from our Arizona and New Mexico samples, and has reduced heterozygosity at the fitness-related markers. Thus, our samples from Texas exhibit symptoms of genetic erosion that could exacerbate future risk of local extirpation. Management agencies must decide if active conservation efforts such as assisted gene flow or genetic rescue are now warranted. This decision may not be straightforward because the current conservation status of the Texas population reflects its isolated geographic locale on the periphery of the species’ range.
Data from: Maintenance of high genome integrity over vegetative growth in the fairy-ring mushroom Marasmius oreades
Contributors: Hiltunen, Markus, Grudzinska-Sterno, Magdalena, Wallerman, Ola, Ryberg, Martin, Johannesson, Hanna
... Most mutations in coding regions of the genome are deleterious, causing selection to favor mechanisms that minimize the mutational load over time [1–5]. DNA replication during cell division is a major source of new mutations. It is therefore important to limit the number of cell divisions between generations, particularly for large and long-lived organisms [6–9]. The germline cells of animals and the slowly dividing cells in plant meristems are adaptations to control the number of mutations that accumulate over generations [9–11]. Fungi lack a separated germline while harboring species with very large and long-lived individuals that appear to maintain highly stable genomes within their mycelia [8,12,13]. Here, we studied genomic mutation accumulation in the fairy-ring mushroom Marasmius oreades. We generated a chromosome-level genome assembly using a combination of cutting-edge DNA sequencing technologies, and re-sequenced 40 samples originating from six individuals of this fungus. The low number of mutations recovered in the sequencing data suggests the presence of an unknown mechanism that works to maintain extraordinary genome integrity over vegetative growth in M. oreades. The highly structured growth pattern of M. oreades allowed us to estimate the number of cell divisions leading up to each sample [14,15], and from this data we infer an incredibly low per mitosis mutation rate (3.8 × 10-12 mutations per site and cell division) as one of several possible explanations for the low number of identified mutations.
Data from: The monocotyledonous underground: global climatic and phylogenetic patterns of geophyte diversity
Contributors: Howard, Cody Coyotee, Folk, Ryan A., Beaulieu, Jeremy M., Cellinese, Nico
... Geophytes—plants typically with a bulb, corm, tuber or rhizome—are economically and evolutionarily important; however, the drivers of their morphological diversity remain unknown. Using a comprehensive phylogeny of monocots, we test for correlations between climate and growth form to better understand why we observe such a diversity of geophyte underground traits. Understanding the evolutionary factors promoting independent origins of these organs will lend insights into how plants adapt to environmental hardships. Using a phylogeny incorporated with global occurrence and climate data for the monocots, we investigated whether climatic patterns could explain differences between geophytes and non-geophytes, as well as differences among bulbous, cormous, tuberous, rhizomatous, and non-geophytic taxa. We used phylogenetically-informed ANOVAs, MANOVAs and PCAs to test differences in climatic variables between growth forms. Geophytes inhabit cooler, drier and thermally variable climates compared to non-geophytes. Although some underground traits (i.e., bulb, corm, and tuber) appear to inhabit particular niches, our data has limited evidence for an overall role of climate in the evolution of these traits. However, temperature may be a driving force in rhizome evolution, as well as the evolution of taxa considered here as non-geophytes. Our results suggest that temperature should be more strongly considered as a factor promoting the evolution of belowground bud placement, specifically as it relates to rhizomatous taxa. Bulbous, cormous and tuberous taxa need closer examination of other mechanisms, such as anatomical constraints or genetic controls, in order to begin to understand the causes behind the evolution of their underground morphology. In compliance with data protection regulations, you may request that we remove your personal registration details at any time. (Use the following URL: https://www.editorialmanager.com/ajb/login.asp?a=r) Please contact the publication office if you have any questions.
Contributors: Koski, Matthew, Prior, Carly, Layman, Nathan, Busch, Jeremiah, Galloway, Laura
... Colonization at expanding range edges often involves few founders, reducing effective population size. This process can promote the evolution of self-fertilization, but implicating historical processes as drivers of trait evolution is often difficult and requires an explicit model of biogeographic history. In plants, contemporary limits to outcrossing are often invoked as evolutionary drivers of self-fertilization, but historical expansions may shape mating system diversity, with leading-edge populations evolving elevated selfing ability. In a widespread plant, Campanula americana, we identified a glacial refugium in the southern Appalachian Mountains from spatial patterns of genetic drift among 24 populations. Populations farther from this refugium have smaller effective sizes and fewer rare alleles. They also displayed elevated heterosis in among-population crosses, reflecting the accumulation of deleterious mutations during range expansion. While populations with elevated heterosis had reduced segregating mutation load, the magnitude of inbreeding depression lacked geographic pattern. The ability to self-fertilize was strongly positively correlated with the distance from the refugium and mutation accumulation—a pattern that contrasts sharply with contemporary mate and pollinator limitation. In this and other species, diversity in sexual systems may reflect the legacy of evolution in small, colonizing populations, with little or no relation to the ecology of modern populations.
Data from: Analysis of head and neck carcinoma progression reveals novel and relevant stage-specific changes associated with immortalisation and malignancy
Contributors: Veeramachaneni, Ratna, Walker, Thomas, Revil, Timothée, De Weck, Antoine, Badescu, Dunarel, O'Sullivan, James, Higgins, Catherine, Elliot, Louise, Liloglou, Triantafillos, Risk, Janet M.
... Head and neck squamous cell carcinoma (HNSCC) is a widely prevalent cancer globally with high mortality and morbidity. We report here changes in the genomic landscape in the development of these tumours from potentially premalignant lesions (PPOLS) to malignancy and lymph node metastases. Frequent likely pathological mutations are restricted to a relatively small set of genes including TP53, CDKN2A, FBXW7, FAT1, NOTCH1 and KMT2D; these arise early in tumour progression and are present in PPOLs with NOTCH1 mutations restricted to cell lines from lesions that subsequently progressed to HNSCC. The most frequent genetic changes are of consistent somatic copy number alterations (SCNA). The earliest SCNAs involved deletions of CSMD1 (8p23.2), FHIT (3p14.2) and CDKN2A (9p21.3) together with gains of chromosome 20. CSMD1 deletions or promoter hypermethylation were present in all of the immortal PPOLs and occurred at high frequency in the immortal HNSCC cell lines (promoter hypermethylation ~63%, hemizygous deletions ~75%, homozygous deletions ~18%). Forced expression of CSMD1 in the HNSCC cell line H103 showed significant suppression of proliferation (p=0.0053) and invasion in vitro (p=5.98X10-5) supporting a role for CSMD1 inactivation in early head and neck carcinogenesis. In addition, knockdown of CSMD1 in the CSMD1-expressing BICR16 cell line showed significant stimulation of invasion in vitro (p=1.82 x 10-5) but not cell proliferation (p=0.239). HNSCC with and without nodal metastases showed some clear differences including high copy number gains of CCND1, hsa-miR-548k and TP63 in the metastases group. GISTIC peak SCNA regions showed significant enrichment (adj P<0.01) of genes in multiple KEGG cancer pathways at all stages with disruption of an increasing number of these involved in the progression to lymph node metastases. Sixty-seven genes from regions with statistically significant differences in SCNA/LOH frequency between immortal PPOL and HNSCC cell lines showed correlation with expression including 5 known cancer drivers.
Contributors: Soontararak, Sirikul, Chow, Lyndah, Johnson, Valerie, Coy, Jonathan, Webb, Craig, Wennogle, Sara, Dow, Steven
... Inflammatory bowel disease (IBD) in dogs is associated with clinical signs of intestinal dysfunction, as well as abnormal lymphocytic and myeloid cell infiltrates in the small and/or large intestine. Thus, in many respects IBD in dogs resembles IBD in humans. However, the factors that trigger intestinal inflammation in dogs with IBD are not well understood and have been variously attributed to immune responses against dietary antigens or intestinal antigens. Previous studies in humans with IBD have documented increased production of IgG and IgA antibodies specific to intestinal bacteria, and this abnormal immune response has been linked to disease pathogenesis. Therefore, we investigated the humoral immune response against gut bacteria in dogs with IBD, using flow cytometry to quantitate IgG and IgA binding. Studies were also done to investigate the source of these antibodies (locally produced versus systemic production) and whether greater antibody binding to bacteria is associated with increased inflammatory responses. We found that dogs with IBD had significantly higher percentages and overall amounts of IgG bound to their intestinal bacteria compared to healthy dogs. Similarly, significantly higher percentages of bacteria were IgA+ bacteria were also found in dogs with IBD. Serum antibody recognition of gut bacteria was not different between healthy dogs and dogs with IBD, suggesting that anti-bacterial antibodies were primarily produced locally in the gut rather than systemically. Importantly, bacteria in the Actinobacteria phylum and in particular the genus Collinsella had significantly greater levels of antibody binding in dogs with IBD. Based on these findings, we concluded that antibody binding to commensal gut bacteria was significantly increased in dogs with IBD, that particular phyla were preferential targets for gut antibodies, and that anti-bacterial antibody responses may play an important role in regulating gut inflammation.