Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages

Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages–Powerpuff, Lego, and YesChef–which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ, Microbacterium Cluster EH, and the former Microbacterium singleton Zeta1847 exhibited low nucleotide similarity. However, their gene content similarity was in excess of the recently adopted Microbacterium clustering parameter, which ultimately resulted in the reassignment of Zeta1847 to Cluster EH. This finding further highlights the importance of using multiple metrics to capture phage relatedness. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle. In the first experimental verification of a Cluster AZ phage’s life cycle, we show that phage Powerpuff is a true temperate phage. It forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages may be temperate as well. Our findings provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.

KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population

The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. Through regulation of natural killer (NK) cell activity KIRs participate in tumour surveillance and clearing viral infections. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Inferring KIR gene content from genetic variant data is therefore desirable for immunogenetic analysis, particularly in the context of growing biobank genome data collections that rely on genotyping by microarray. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 807 Finnish biobank samples genotyped for 5900 KIR-region SNPs and analysed for KIR gene content with targeted sequencing. Cross-validation results demonstrate a high mean overall accuracy of 98.5% (95% CI [97.0–99.2]%) which compares favourably with previous methods including short-read sequencing based approaches.

Yield is negatively correlated with nucleotide-binding leucine-rich repeat gene content in soybean

The availability of increasing quantities of crop pangenome data permits the detailed association of gene content with agronomic traits. Here, we investigate disease resistance gene content of diverse soybean cultivars and report a significant negative correlation between the number of NLR resistance (R) genes and yield. We find no association between R-genes with seed weight, oil or protein content, and we find no correlation between yield and the number of RLK, RLP genes, or the total number of genes. These results suggest that recent yield improvement in soybean may be partially associated with the selective loss of NLR genes. Three quarters of soybean NLR genes do not show presence/absence variation, limiting the ability to select for their absence, and so the deletion or disabling of select NLR genes may support future yield improvement.

Investigating diversity, evolution, development and physiology of red algal parasites from New Zealand

<p>Red algal parasites have evolved independently over a 100 times and grow only on other red algal hosts. Most parasites are closely related to their host based on the similarity of their reproductive structures. Secondary pit connections between red algal parasites and their hosts are used to transfer parasite organelles and nuclei into host cells. Morphological and physiological changes in infected host cells have been observed in some species. Parasite mitochondrial genomes are similar in size and gene content to free-living red algae whereas parasite plastids are highly reduced. Overall, red algal parasites are poorly studied and thus the aim of this study was to increase the general knowledge of parasitic taxa with respect to their diversity, evolutionary origin, development, physiology, and organelle evolution. Investigation of the primary literature showed that most species descriptions of red algal parasites were poor and did not meet the criteria for defining a parasitic relationship. This literature study also revealed a lack of knowledge of many key parasitic processes including early parasite development, host cell “control”, and parasite origin. Many of these poorly studied research areas were addressed in this thesis. Phylogenetic analyses, using a range of markers from all three genomes (cpDNA: rbcL, nDNA: actin, LSU rRNA; mtDNA: cox1), showed different patterns of phylogenetic relationships for the four new red algal parasites and their hosts. The parasites Phycodrys novae-zelandiophila sp. nov. and Vertebrata aterrimophila sp. nov. closest relative is its host species. Cladhymenia oblongifoliophila sp. nov. closest relative is its host species based on nuclear and mitochondrial markers whereas the plastid markers group the parasite with Cladhymenia lyallii, suggesting that the parasite plastid was acquired when previously parasitizing C. lyallii. Judithia parasitica sp. nov. grows on two Blastophyllis species but the parasites’ closest relative is the non-host species Judithia delicatissima. Developmental studies of the parasite Vertebrata aterrimophila, showed a unique developmental structure (“trunk-like” cell) not known in other parasites, plus localised infection vi and few changes in infected host cells. High-throughput-sequencing revealed mitochondrial genomes of similar size, gene content and order in the parasite Pterocladiophila hemisphaerica to its host Pterocladia lucida, and a reduced non-photosynthetic plastid in the parasite. Mitochondrial (mt) and plastid (cp) genome phylogenies placed Pterocladiophila hemisphaerica on long branches, either as sister to Ceramiales (mt) or Gracilariales (cp). Further analyses, filtering non-elevated plastid genes grouped the parasite neither with the Gracilariales (mt) or Gelidiales (cp) on shorter branches but without support. Nuclear phylogeny grouped P. hemisphaerica as sister to the Gelidiales and other red algal orders and was the only phylogenetic relationship with support. Investigations of photosystem II capacity using PAM fluorometry, and quantifying chlorophyll a content in three pigmented parasites, showed different host nutrient dependencies. Rhodophyllis parasitica and Vertebrata aterrimophila are not able to photosynthesize and are fully dependent on host nutrients. Pterocladiophila hemisphaerica is able to photosynthesize independently, even though it has a reduced non-photosynthetic plastid genome, and therefore is only partially dependent on its host. This study advances our current understanding of red algal parasites and highlights many possibilities for future research including genome evolution and understanding parasite diversity.</p>

Investigating diversity, evolution, development and physiology of red algal parasites from New Zealand

<p>Red algal parasites have evolved independently over a 100 times and grow only on other red algal hosts. Most parasites are closely related to their host based on the similarity of their reproductive structures. Secondary pit connections between red algal parasites and their hosts are used to transfer parasite organelles and nuclei into host cells. Morphological and physiological changes in infected host cells have been observed in some species. Parasite mitochondrial genomes are similar in size and gene content to free-living red algae whereas parasite plastids are highly reduced. Overall, red algal parasites are poorly studied and thus the aim of this study was to increase the general knowledge of parasitic taxa with respect to their diversity, evolutionary origin, development, physiology, and organelle evolution. Investigation of the primary literature showed that most species descriptions of red algal parasites were poor and did not meet the criteria for defining a parasitic relationship. This literature study also revealed a lack of knowledge of many key parasitic processes including early parasite development, host cell “control”, and parasite origin. Many of these poorly studied research areas were addressed in this thesis. Phylogenetic analyses, using a range of markers from all three genomes (cpDNA: rbcL, nDNA: actin, LSU rRNA; mtDNA: cox1), showed different patterns of phylogenetic relationships for the four new red algal parasites and their hosts. The parasites Phycodrys novae-zelandiophila sp. nov. and Vertebrata aterrimophila sp. nov. closest relative is its host species. Cladhymenia oblongifoliophila sp. nov. closest relative is its host species based on nuclear and mitochondrial markers whereas the plastid markers group the parasite with Cladhymenia lyallii, suggesting that the parasite plastid was acquired when previously parasitizing C. lyallii. Judithia parasitica sp. nov. grows on two Blastophyllis species but the parasites’ closest relative is the non-host species Judithia delicatissima. Developmental studies of the parasite Vertebrata aterrimophila, showed a unique developmental structure (“trunk-like” cell) not known in other parasites, plus localised infection vi and few changes in infected host cells. High-throughput-sequencing revealed mitochondrial genomes of similar size, gene content and order in the parasite Pterocladiophila hemisphaerica to its host Pterocladia lucida, and a reduced non-photosynthetic plastid in the parasite. Mitochondrial (mt) and plastid (cp) genome phylogenies placed Pterocladiophila hemisphaerica on long branches, either as sister to Ceramiales (mt) or Gracilariales (cp). Further analyses, filtering non-elevated plastid genes grouped the parasite neither with the Gracilariales (mt) or Gelidiales (cp) on shorter branches but without support. Nuclear phylogeny grouped P. hemisphaerica as sister to the Gelidiales and other red algal orders and was the only phylogenetic relationship with support. Investigations of photosystem II capacity using PAM fluorometry, and quantifying chlorophyll a content in three pigmented parasites, showed different host nutrient dependencies. Rhodophyllis parasitica and Vertebrata aterrimophila are not able to photosynthesize and are fully dependent on host nutrients. Pterocladiophila hemisphaerica is able to photosynthesize independently, even though it has a reduced non-photosynthetic plastid genome, and therefore is only partially dependent on its host. This study advances our current understanding of red algal parasites and highlights many possibilities for future research including genome evolution and understanding parasite diversity.</p>

What makes a megaplasmid?

Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids—known as megaplasmids—are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms. Why are megaplasmids so big? What other features come with large plasmid size that could affect bacterial ecology and evolution? Are megaplasmids 'just' big plasmids, or do they have distinct characteristics? In this perspective, we reflect on the distribution, diversity, biology, and gene content of megaplasmids, providing an overview to these large, yet often overlooked, mobile genetic elements. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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

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’.

Genome Sequence and Characteristics of Cluster C1 Mycobacterium smegmatis Phage EasyJones

Bacteriophage EasyJones is a myovirus infecting Mycobacterium smegmatis mc 2 155, with a genome length and gene content similar to those of phages grouped in subcluster C1. Interestingly, EasyJones contains a gene found in a subset of C1 genomes that is similar to the well-characterized immunity repressor of subcluster A1 mycobacteriophage Bxb1.

Complete Mitochondrial Genomes of Three Mangifera Species, Their Genomic Structure And Gene Transfer From Chloroplast Genomes

BackgroundAmong the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species. Results Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63-69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24-27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7-10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407-6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value. ConclusionsWe sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content of Mangifera mitochondrial genomes is similar across various species. Gene transferred from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex

Sex chromosome gene content frequently differs from that of the autosomes, a phenomenon that can be informative of the effects of chromatin environment, sex-specific selection, recombination, and ploidy on genome evolution. For example, the Drosophila X chromosome is depauperate in genes with male-biased expression or limited expression in specific tissues—in particular those expressed in the accessory gland of the male reproductive tract. Multiple hypotheses have been put forth to explain the unique gene content of the X chromosome, including selection against male-beneficial X-linked alleles, expression limits imposed by the haploid dosage of the X in males, and interference by the dosage compensation complex (DCC) on expression in males. Here, we investigate these hypotheses by examining differential gene expression in Drosophila melanogaster following several treatments known to have widespread transcriptomic effects: bacterial infection, viral infection, and abiotic stress. We found that genes that are induced (up-regulated) by these biotic and abiotic treatments are frequently under-represented on the X chromosome, but so are those that are repressed (down-regulated) following treatment. We further show that whether a gene is bound by the DCC in males can largely explain the paucity of both up- and down-regulated genes on the X chromosome. Specifically, genes that are bound by the DCC are unlikely to be up- or down-regulated after treatment. Moreover, genes that are closer to a high-affinity site where the DCC is thought to initiate binding to the X chromosome experience a smaller change in expression following treatment. This relationship, however, could partially be explained by a correlation between differential expression and breadth of expression across tissues. Nonetheless, our results suggest that DCC binding, or the associated chromatin modifications, inhibit both up- and down-regulation of X chromosome gene expression within specific contexts. This effect could explain why the Drosophila X chromosome is depauperate in genes with tissue-specific expression, in addition to the paucity of X-linked genes differentially expressed after biotic or abiotic treatments. We propose multiple possible mechanisms of action for the effect, including a role of Males absent on the first (Mof), a component of the DCC, as a dampener of gene expression variance in both males and females.