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Host life-history traits influence the distribution of prophages and the genes they carry.

ABSTRACT: Bacterial strains with a short minimal doubling time-'fast-growing' hosts-are more likely to contain prophages than their slow-growing counterparts. Pathogenic bacterial species are likewise more likely to carry prophages. We develop a bioinformatics pipeline to examine the distribution of prophages in fast- and slow-growing lysogens, and pathogenic and non-pathogenic lysogens, analysing both prophage length and gene content for each class. By fitting these results to a mathematical model of the evolutionary forces acting on prophages, we predict whether the observed differences can be attributed to different rates of lysogeny among the host classes, or other evolutionary pressures. We also test for significant differences in gene content among prophages, identifying genes that are preferentially lost or maintained in each class. We find that fast-growing hosts and pathogens have a greater fraction of full-length prophages, and our analysis predicts that induction rates are significantly reduced in slow-growing hosts and non-pathogenic hosts. Consistent with previous results, we find that several proteins involved in the packaging of new phage particles and lysis are preferentially lost in cryptic prophages. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.

SUBMITTER: Pattenden T

PROVIDER: S-EPMC8628077 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Host life-history traits influence the distribution of prophages and the genes they carry.

Pattenden Tyler T Eagles Christine C Wahl Lindi M LM

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 20211129 1842

Bacterial strains with a short minimal doubling time-'fast-growing' hosts-are more likely to contain prophages than their slow-growing counterparts. Pathogenic bacterial species are likewise more likely to carry prophages. We develop a bioinformatics pipeline to examine the distribution of prophages in fast- and slow-growing lysogens, and pathogenic and non-pathogenic lysogens, analysing both prophage length and gene content for each class. By fitting these results to a mathematical model of the ...[more]

PMID: 34839698

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Project description:BackgroundVisual opsins are expressed in the compound eyes and ocelli of insects and enable light detection. Three distinct phylogenetic groups of visual opsins are found in insects, named long (LW), short (SW) and ultraviolet (UV) wavelength sensitive opsins. Recently, the LW group was found to be duplicated into the LW2b and the LW2a opsins. The expression of LW2b opsins is ocelli specific in some insects (e.g., bees, cricket, scorpion flies), but the gene was not found in other orders possessing three or less ocelli (e.g., dragonflies, beetles, moths, bugs). In flies, two LW2b homologs have been characterised, with one expressed in the ocelli and the other in the compound eyes. To date, it remains unclear which evolutionary forces have driven gains and losses of LW opsins in insects. Here we take advantage of the recent rapid increase in available sequence data (i.e., from insect genomes, targeted PCR amplification, RNAseq) to characterize the phylogenetic relationships of 1000 opsin sequences in 18 orders of Insects. The resulting phylogeny discriminates between four main groups of opsins, and onto this phylogeny we mapped relevant morphological and life history traits.ResultsOur results demonstrate a conserved LW2b opsin only present in insects with three ocelli. Only two groups (Brachycera and Odonata) possess more than one LW2b opsin, likely linked to their life history. In flies, we hypothesize that the duplication of the LW2b opsin occurred after the transition from aquatic to terrestrial larvae. During this transition, higher flies (Brachycera) lost a copy of the LW2a opsin, still expressed and duplicated in the compound eyes of lower flies (Nematocera). In higher flies, the LW2b opsin has been duplicated and expressed in the compound eyes while the ocelli and the LW2b opsin were lost in lower flies. In dragonflies, specialisation of flight capabilities likely drove the diversification of the LW2b visual opsins.ConclusionThe presence of the LW2b opsin in insects possessing three ocelli suggests a role in specific flight capabilities (e.g., stationary flight). This study provides the most complete view of the evolution of visual opsin genes in insects yet, and provides new insight into the influence of ocelli and life history traits on opsin evolution in insects.

Project description:Global changes are thought to affect most Arctic species, yet some populations are more at risk. Today, the Barents Sea ecoregion is suffering the strongest sea ice retreat ever measured; and these changes are suspected to modify food access and thus diet of several species. Biochemical diet tracers enable investigation of diet in species such as polar bears (Ursus maritimus). We examined individual diet variation of female polar bears in Svalbard, Norway, and related it to year, season (spring and autumn), sampling area and breeding status (solitary, with cubs of the year or yearlings). Sampling areas were split according to their ice cover: North-West (less sea ice cover), South-East (larger amplitude in sea ice extent) and North-East/South-West (NESW) as bears from that zone are more mobile among all regions of Svalbard. We measured fatty acid (FA) composition in adipose tissue and carbon (δ13C) and nitrogen (δ15N) stable isotopes in plasma and red blood cells. Females feeding in the North-West area had lower δ15N values than those from the NESW. In South-East females, δ13C values were lower in autumn compared to spring and females seemed less selective in their diet as depicted by large variances in stable isotope values. Considering the differences in FA composition and stable isotope values, we suggest that females from the North-West and South-East could ingest a higher proportion of avian prey. With regard to breeding status, solitary females had higher δ15N values and smaller variance in their stable isotopic values than females with cubs, suggesting that solitary females were more selective and prey on higher trophic level species (i.e. seals). Overall, our results indicate that prey availability for Svalbard polar bears varies according to geographical area and prey selectivity differs according to breeding status. Our findings suggest that complex changes in sea ice and prey availability will interact to affect Svalbard polar bear feeding patterns and associated nutrition.

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Host life-history traits influence the distribution of prophages and the genes they carry.

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Host life-history traits influence the distribution of prophages and the genes they carry.

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