Adaptation by Deletogenic Replication Slippage in a Nascent Symbiont

Intracellular Bacterial Symbionts in Corals: Challenges and Future Directions

Corals are the main primary producers of coral reefs and build the three-dimensional reef structure that provides habitat to more than 25% of all marine eukaryotes. They harbor a complex consortium of microorganisms, including bacteria, archaea, fungi, viruses, and protists, which they rely on for their survival. The symbiosis between corals and bacteria is poorly studied, and their symbiotic relationships with intracellular bacteria are only just beginning to be acknowledged. In this review, we emphasize the importance of characterizing intracellular bacteria associated with corals and explore how successful approaches used to study such microorganisms in other systems could be adapted for research on corals. We propose a framework for the description, identification, and functional characterization of coral-associated intracellular bacterial symbionts. Finally, we highlight the possible value of intracellular bacteria in microbiome manipulation and mitigating coral bleaching.

Enhanced Mutation Rate, Relaxed Selection, and the "Domino Effect" are associated with Gene Loss in Blattabacterium, A Cockroach Endosymbiont

Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete genome sequences of a representative set of 67 Blattabacterium strains, with sizes ranging between 511 and 645 kb. We found that 200 of the 566 analyzed protein-coding genes were lost in at least one lineage of Blattabacterium, with the most extreme case being one gene that was lost independently in 24 lineages. We found evidence for three mechanisms influencing gene loss in Blattabacterium. First, gene loss rates were found to increase exponentially with the accumulation of substitutions. Second, genes involved in vitamin and amino acid metabolism experienced relaxed selection in Cryptocercus and Mastotermes, possibly triggered by their vertically inherited gut symbionts. Third, we found evidence of epistatic interactions among genes leading to a "domino effect" of gene loss within pathways. Our results highlight the complexity of the process of genome erosion in an endosymbiont.

Multiple concurrent and convergent stages of genome reduction in bacterial symbionts across a stink bug family

Nutritional symbioses between bacteria and insects are prevalent and diverse, allowing insects to expand their feeding strategies and niches. A common consequence of long-term associations is a considerable reduction in symbiont genome size likely influenced by the radical shift in selective pressures as a result of the less variable environment within the host. While several of these cases can be found across distinct insect species, most examples provide a limited view of a single or few stages of the process of genome reduction. Stink bugs (Pentatomidae) contain inherited gamma-proteobacterial symbionts in a modified organ in their midgut and are an example of a long-term nutritional symbiosis, but multiple cases of new symbiont acquisition throughout the history of the family have been described. We sequenced the genomes of 11 symbionts of stink bugs with sizes that ranged from equal to those of their free-living relatives to less than 20%. Comparative genomics of these and previously sequenced symbionts revealed initial stages of genome reduction including an initial pseudogenization before genome reduction, followed by multiple stages of progressive degeneration of existing metabolic pathways likely to impact host interactions such as cell wall component biosynthesis. Amino acid biosynthesis pathways were retained in a similar manner as in other nutritional symbionts. Stink bug symbionts display convergent genome reduction events showing progressive changes from a free-living bacterium to a host-dependent symbiont. This system can therefore be used to study convergent genome evolution of symbiosis at a scale not previously available.

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes

Bacterial symbionts bring a wealth of functions to the associations they participate in, but by doing so, they endanger the genes and genomes underlying these abilities. When bacterial symbionts become obligately associated with their hosts, their genomes are thought to decay towards an organelle-like fate due to decreased homologous recombination and inefficient selection. However, numerous associations exist that counter these expectations, especially in marine environments, possibly due to ongoing horizontal gene flow. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine chemosynthetic bacterial-bivalve endosymbioses that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory. We found that transmission mode strongly predicts homologous recombination rates, and that exceedingly low recombination rates are associated with moderate genome degradation in the marine symbionts with nearly strict vertical transmission. Nonetheless, even the most degraded marine endosymbiont genomes are occasionally horizontally transmitted and are much larger than their terrestrial insect symbiont counterparts. Therefore, horizontal transmission and recombination enable efficient natural selection to maintain intermediate symbiont genome sizes and substantial functional genetic variation.

The Life of an Insect Endosymbiont from the Cradle to the Grave

Host-beneficial endosymbioses, which are formed when a microorganism takes up residence inside another cell and provides a fitness advantage to the host, have had a dramatic influence on the evolution of life. These intimate relationships have yielded the mitochondrion and the plastid (chloroplast) - the ancient organelles that in part define eukaryotic life - along with many more recent associations involving a wide variety of hosts and microbial partners. These relationships are often envisioned as stable associations that appear cooperative and persist for extremely long periods of time. But recent evidence suggests that this stable state is often born from turbulent and conflicting origins, and that the apparent stability of many beneficial endosymbiotic relationships - although certainly real in many cases - is not an inevitable outcome of these associations. Here we review how stable endosymbioses form, how they are maintained, and how they sometimes break down and are reborn. We focus on relationships formed by insects and their resident microorganisms because these symbioses have been the focus of significant empirical work over the last two decades. We review these relationships over five life stages: origin, birth, middle age, old age, and death.

Identification of Arylphorin interacting with the insecticidal protein PirAB from Xenorhabdus nematophila by yeast two-hybrid system

PirAB toxin was initially found in the Photorhabdus luminescens TT01 strain and is a demonstrated binary toxin with high insecticidal activity. In this paper, we co-expressed the pirAB gene of Xenorhabdus nematophila HB310 in a prokaryotic expression system, and we found that the PirAB protein showed high hemocoel insecticidal activity against Galleria mellonella, Helicoverpa armigera and Spodoptera exigua. LD₅₀ values were 1.562, 2.003 and 2.17 μg/larvae for G. mellonella, H. armigera, and S. exigua, respectively (p > 0.05). Additionally, PirAB-interaction proteins were identified from G. mellonella by 6 × His Protein Pulldown combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Of which, arylphorin of G. mellonella showed the highest matching rate. A protein domain conservative structure analysis indicated that arylphorin has three domains including Hemocyanin-N, Hemocyanin-M, and Hemocyanin-C. Among these protein domains, Hemocyanin-C has immune and recognition functions. Further, Hemocyanin-C domain of arylphorin was identified to interact with PirA but not PirB by Yeast two-hybrid system. These findings reveal, for the first time, new host protein interacting with PirAB. The identification of interaction protein may serve as the foundation for further study on the function and insecticidal mechanism of this binary toxin from Xenorhabdus.

ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea

BACKGROUND

Narrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) in Brassica juncea (AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak, RSPR-01 and Urvashi) and Exotic (Donskaja IV, Zem 1 and EC287711) genepools.

RESULTS

Sequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set of B. juncea genotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes.

CONCLUSIONS

Despite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity in Brassica juncea.

Selective advantages favour high genomic AT-contents in intracellular elements

Extrachromosomal genetic elements such as bacterial endosymbionts and plasmids generally exhibit AT-contents that are increased relative to their hosts’ DNA. The AT-bias of endosymbiotic genomes is commonly explained by neutral evolutionary processes such as a mutational bias towards increased A+T. Here we show experimentally that an increased AT-content of host-dependent elements can be selectively favoured. Manipulating the nucleotide composition of bacterial cells by introducing A+T-rich or G+C-rich plasmids, we demonstrate that cells containing GC-rich plasmids are less fit than cells containing AT-rich plasmids. Moreover, the cost of GC-rich elements could be compensated by providing precursors of G+C, but not of A+T, thus linking the observed fitness effects to the cytoplasmic availability of nucleotides. Accordingly, introducing AT-rich and GC-rich plasmids into other bacterial species with different genomic GC-contents revealed that the costs of G+C-rich plasmids decreased with an increasing GC-content of their host’s genomic DNA. Taken together, our work identifies selection as a strong evolutionary force that drives the genomes of intracellular genetic elements toward higher A+T contents.

Genomes of endosymbiotic bacteria are commonly more AT-rich than the ones of their free-living relatives. Interestingly, genomes of other intracellular elements like plasmids or bacteriophages also tend to be richer in AT than the genomes of their hosts. The AT-bias of endosymbiotic genomes is commonly explained by neutral evolutionary processes. However, since A+T nucleotides are both more abundant and energetically less expensive than G+C nucleotides, an alternative explanation is that selective advantages drive the nucleotide composition of intracellular elements. Here we provide strong experimental evidence that intracellular elements, whose genome is more AT-rich than the genome of the host, are selectively favoured on the host level. Thus, our results emphasize the importance of selection for shaping the DNA base composition of extrachromosomal genetic elements.

In it for the long haul: evolutionary consequences of persistent endosymbiosis

Phylogenetically independent bacterial lineages have undergone a profound lifestyle shift: from a free-living to obligately host-associated existence. Among these lineages, intracellular bacterial mutualists of insects are among the most intimate, constrained symbioses known. These obligate endosymbionts exhibit severe gene loss and apparent genome deterioration. Evolutionary theory provides a basis to link their unusual genomic features with shifts in fundamental mechanisms - selection, genetic drift, mutation, and recombination. This mini-review highlights recent comparative and experimental research of processes shaping ongoing diversification within these ancient associations. Recent work supports clear contributions of stochastic processes, including genetic drift and exceptionally strong mutational pressure, toward degenerative evolution. Despite possible compensatory mechanisms, genome degradation may constrain how persistent endosymbionts (and their hosts) respond to environmental fluctuations.

Parallel genome reduction in symbionts descended from closely related free-living bacteria

Endosymbiosis plays an important role in ecology and evolution, but fundamental aspects of the origin of intracellular symbionts remain unclear. The extreme age of many symbiotic relationships, lack of data on free-living ancestors and uniqueness of each event hinder investigations. Here, we describe multiple strains of the bacterium Polynucleobacter that evolved independently and under similar conditions from closely related, free-living ancestors to become obligate endosymbionts of closely related ciliate hosts. As these genomes reduced in parallel from similar starting states, they provide unique glimpses into the mechanisms underlying genome reduction in symbionts. We found that gene loss is contingently lineage-specific, with no evidence for ordered streamlining. However, some genes in otherwise disrupted pathways are retained, possibly reflecting cryptic genetic network complexity. We also measured substitution rates between many endosymbiotic and free-living pairs for hundreds of genes, which showed that genetic drift, and not mutation pressure, is the main non-selective factor driving molecular evolution in endosymbionts.

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r² = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.

PirAB protein from Xenorhabdus nematophila HB310 exhibits a binary toxin with insecticidal activity and cytotoxicity in Galleria mellonella

PirAB (Photorhabdus insect-related proteins, PirAB) toxin was initially found in the Photorhabdus luminescens TT01 strain and has been shown to be a binary toxin with high insecticidal activity. Based on GenBank data, this gene was also found in the Xenorhabdus nematophila genome sequence. The predicted amino acid sequence of pirA and pirB in the genome of X. nematophila showed 51% and 50% identity with those gene sequences from P. luminescens. The purpose of this experiment is to identify the relevant information for this toxin gene in X. nematophila. The pirA, pirB and pirAB genes of X. nematophila HB310 were cloned and expressed in Escherichia coli BL21 (DE3) using the pET-28a vector. A PirAB-fusion protein (PirAB-F) was constructed by linking the pirA and pirB genes with the flexible linker (Gly)₄ DNA encoding sequence and then efficiently expressed in E. coli. The hemocoel and oral insecticidal activities of the recombinant proteins were analyzed against the larvae of Galleria mellonella. The results show that PirA/B alone, PirA/B mixture, co-expressed PirAB protein, and PirAB-F all had no oral insecticidal activity against the second-instar larvae of G. mellonella. Only PirA/B mixture and co-expressed PirAB protein had hemocoel insecticidal activity against G. mellonella fifth-instar larvae, with an LD₅₀ of 2.718μg/larva or 1.566μg/larva, respectively. Therefore, we confirmed that PirAB protein of X. nematophila HB310 is a binary insecticidal toxin. The successful expression and purification of PirAB laid a foundation for further studies on the function, insecticidal mechanism and expression regulation of the binary toxin.

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r² = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.