In vivo interference of pea aphid endosymbiont Buchnera groEL gene by synthetic peptide nucleic acids

The unculturable nature of intracellular obligate symbionts presents a significant challenge for elucidating gene functionality, necessitating the development of gene manipulation techniques. One of the best-studied obligate symbioses is that between aphids and the bacterial endosymbiont Buchnera aphidicola. Given the extensive genome reduction observed in Buchnera, the remaining genes are crucial for understanding the host-symbiont relationship, but a lack of tools for manipulating gene function in the endosymbiont has significantly impeded the exploration of the molecular mechanisms underlying this mutualism. In this study, we introduced a novel gene manipulation technique employing synthetic single-stranded peptide nucleic acids (PNAs). We targeted the critical Buchnera groEL using specially designed antisense PNAs conjugated to an arginine-rich cell-penetrating peptide (CPP). Within 24 h of PNA administration via microinjection, we observed a significant reduction in groEL expression and Buchnera cell count. Notably, the interference of groEL led to profound morphological malformations in Buchnera, indicative of impaired cellular integrity. The gene knockdown technique developed in this study, involving the microinjection of CPP-conjugated antisense PNAs, provides a potent approach for in vivo gene manipulation of unculturable intracellular symbionts, offering valuable insights into their biology and interactions with hosts.

Host-specific co-evolution likely driven by diet in Buchnera aphidicola

BACKGROUND

Russian wheat aphid (Diuraphis noxia Kurd.) is a severe pest to wheat, and even though resistance varieties are available to curb this pest, they are becoming obsolete with the development of new virulent aphid populations. Unlike many other aphids, D noxia only harbours a single endosymbiont, Buchnera aphidicola. Considering the importance of Buchnera, this study aimed to elucidate commonalities and dissimilarities between various hosts, to better understand its distinctiveness within its symbiotic relationship with D. noxia. To do so, the genome of the D. noxia's Buchnera was assembled and compared to those of other aphid species that feed on diverse host species.

RESULTS

The overall importance of several features such as gene length and percentage GC content was found to be critical for the maintenance of Buchnera genes when compared to their closest free-living relative, Escherichia coli. Buchnera protein coding genes were found to have percentage GC contents that tended towards a mean of ~ 26% which had strong correlation to their identity to their E. coli homologs. Several SNPs were identified between different aphid populations and multiple isolates of Buchnera were confirmed in single aphids.

CONCLUSIONS

Establishing the strong correlation of percentage GC content of protein coding genes and gene identity will allow for identifying which genes will be lost in the continually shrinking Buchnera genome. This is also the first report of a parthenogenically reproducing aphid that hosts multiple Buchnera strains in a single aphid, raising questions regarding the benefits of maintaining multiple strains. We also found preliminary evidence for post-transcriptional regulation of Buchnera genes in the form of polyadenylation.

Direct sequencing of insect symbionts via nanopore adaptive sampling

Insect symbionts can alter their host phenotype and their effects can range from beneficial to pathogenic. Moreover, many insects exhibit co-infections, making their study more challenging. Less than 1% of insect species have high-quality referenced genomes available and fewer still also have their symbionts sequenced. Two methods are commonly used to sequence symbionts: whole-genome sequencing to concomitantly capture the host and bacterial genomes, or isolation of the symbiont's genome before sequencing. These methods are limited when dealing with rare or poorly characterized symbionts. Long-read technology is an important tool to generate high-quality genomes as they can overcome high levels of heterozygosity, repeat content, and transposable elements that confound short-read methods. Oxford Nanopore (ONT) adaptive sampling allows a sequencing instrument to select or reject sequences in real time. We describe a method based on ONT adaptive sampling (subtractive) approach that readily permitted the sequencing of the complete genomes of mitochondria, Buchnera and its plasmids (pLeu, pTrp), and Wolbachia genomes in two aphid species, Aphis glycines and Pentalonia nigronervosa. Adaptive sampling is able to retrieve organelles such as mitochondria and symbionts that have high representation in their hosts such as Buchnera and Wolbachia, but is less successful at retrieving symbionts in low concentrations.

Genome evolution of Buchnera aphidicola (Gammaproteobacteria): Insights into strand compositional asymmetry, codon usage bias, and phylogenetic implications

Taxa of Buchnera aphidicola (hereafter "Buchnera") are mutualistic intracellular symbionts of aphids, known for their remarkable biological traits such as genome reduction, strand compositional asymmetry, and symbiont-host coevolution. With the growing availability of genomic data, we performed a comprehensive analysis of 103 genomes of Buchnera strains from 12 host subfamilies, focusing on the genomic characterizations, codon usage patterns, and phylogenetic implications. Our findings revealed consistent features among all genomes, including small genome sizes, low GC contents, and gene losses. We also identified strong strand compositional asymmetries in all strains at the genome level. Further investigation suggested that mutation pressure may have played a crucial role in shaping codon usage of Buchnera. Moreover, the genomic asymmetries were reflected in asymmetric codon usage preferences within chromosomal genes. Notably, the levels of these asymmetries were varied among strains and were significantly influenced by the degrees of genome shrinkages. Lastly, our phylogenetic analyses presented an alternative topology of Aphididae, based on the Buchnera symbionts, providing robust confirmation of the paraphylies of Eriosomatinae, and Macrosiphini. Our objectives are to further understand the strand compositional asymmetry and codon usage bias of Buchnera taxa, and provide new perspectives for phylogenetic studies of Aphididae.

Co-option of a conserved host glutamine transporter facilitates aphid/Buchnera metabolic integration

Organisms across the tree of life colonize novel environments by partnering with bacterial symbionts. These symbioses are characterized by intimate integration of host/endosymbiont biology at multiple levels, including metabolically. Metabolic integration is particularly important for sap-feeding insects and their symbionts, which supplement nutritionally unbalanced host diets. Many studies reveal parallel evolution of host/endosymbiont metabolic complementarity in amino acid biosynthesis, raising questions about how amino acid metabolism is regulated, how regulatory mechanisms evolve, and the extent to which similar mechanisms evolve in different systems. In the aphid/Buchnera symbiosis, the transporter ApGLNT1 (Acyrthosiphon pisum glutamine transporter 1) supplies glutamine, an amino donor in transamination reactions, to bacteriocytes (where Buchnera reside) and is competitively inhibited by Buchnera-supplied arginine-consistent with a role regulating amino acid metabolism given host demand for Buchnera-produced amino acids. We examined how ApGLNT1 evolved a regulatory role by functionally characterizing orthologs in insects with and without endosymbionts. ApGLNT1 orthologs are functionally similar, and orthology searches coupled with homology modeling revealed that GLNT1 is ancient and structurally conserved across insects. Our results indicate that the ApGLNT1 symbiotic regulatory role is derived from its ancestral role and, in aphids, is likely facilitated by loss of arginine biosynthesis through the urea cycle. Given consistent loss of host arginine biosynthesis and retention of endosymbiont arginine supply, we hypothesize that GLNT1 is a general mechanism regulating amino acid metabolism in sap-feeding insects. This work fills a gap, highlighting the broad importance of co-option of ancestral proteins to novel contexts in the evolution of host/symbiont systems.

Arsenophonus Interacts with Buchnera to Improve Growth Performance of Aphids under Amino Acid Stress

Amino acids play a crucial role in the growth and development of insects. Aphids cannot ingest enough amino acids in plant phloem to meet their requirements, and therefore, they are mainly dependent on the obligate symbiont Buchnera aphidicola to synthesize essential amino acids. Besides Buchnera, aphids may harbor another facultative symbiont, Arsenophonus, which alters the requirement of the cotton-melon aphid Aphis gossypii for amino acid. However, it is unclear how Arsenophonus regulates the requirement. Here, we found that Arsenophonus ameliorated growth performance of A. gossypii on an amino acid-deficient diet. A deficiency in lysine (Lys) or methionine (Met) led to changes in the abundance of Arsenophonus. Arsenophonus suppressed the abundance of Buchnera when aphids were fed a normal amino acid diet, but this suppression was eliminated or reversed when aphids were on a Lys- or Met-deficient diet. The relative abundance of Arsenophonus was positively correlated with that of Buchnera, but neither of them was correlated with the body weight of aphids. The relative expression levels of Lys and Met synthase genes of Buchnera were affected by the interaction between Arsenophonus infections and Buchnera abundance, especially in aphids reared on a Lys- or Met-deficient diet. Arsenophonus coexisted with Buchnera in bacteriocytes, which strengthens the interaction. IMPORTANCE The obligate symbiont Buchnera can synthesize amino acids for aphids. In this study, we found that a facultative symbiont, Arsenophonus, can help improve aphids' growth performance under amino acid deficiency stress by changing the relative abundance of Buchnera and the expression levels of amino acid synthase genes. This study highlights the interaction between Arsenophonus and Buchnera to ameliorate aphid growth under amino acid stress.

Phylosymbiotic Structures of the Microbiota in Mollitrichosiphum tenuicorpus (Hemiptera: Aphididae: Greenideinae)

Aphids harbor an array of symbionts that provide hosts with ecological benefits. Microbial community assembly generally varies with respect to aphid species, geography, and host plants. However, the influence of host genetics and ecological factors on shaping intraspecific microbial community structures has not been fully understood. In the present study, using Illumina sequencing of the V3 - V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions associated with Mollitrichosiphum tenuicorpus from different regions and plants in China. The primary symbiont Buchnera aphidicola and the secondary symbiont Arsenophonus dominated the microbial flora in M. tenuicorpus. Ordination analyses and statistical tests suggested that geography and aphid genetics primarily contributed to the variation in the microbiota of M. tenuicorpus. We further confirmed the combined effect of aphid genetics and geography on shaping the structures of symbiont and secondary symbiont communities. Moreover, the significant correlation between aphid genetic divergence and symbiont community dissimilarity provides evidence for intraspecific phylosymbiosis in natural systems. Our study helped to elucidate the eco-evolutionary relationship between symbiont communities and aphids within one given species.

Compartmentalized into Bacteriocytes but Highly Invasive: the Puzzling Case of the Co-Obligate Symbiont Serratia symbiotica in the Aphid Periphyllus lyropictus

Dependence on multiple nutritional symbionts that form a metabolic unit has evolved many times in insects. Although it has been postulated that host dependence on these metabolically interconnected symbionts is sustained by their high degree of anatomical integration (these symbionts are often housed in distinct symbiotic cells, the bacteriocytes, assembled into a common symbiotic organ, the bacteriome), the developmental aspects of such multipartner systems have received little attention. Aphids of the subfamilies Chaitophorinae and Lachninae typically harbor disymbiotic systems in which the metabolic capabilities of the ancient obligate symbiont Buchnera aphidicola are complemented by those of a more recently acquired nutritional symbiont, often belonging to the species Serratia symbiotica. Here, we used microscopy approaches to finely characterize the tissue tropism and infection dynamics of the disymbiotic system formed by B. aphidicola and S. symbiotica in the Norway maple aphid Periphyllus lyropictus (Chaitophorinae). Our observations show that, in this aphid, the co-obligate symbiont S. symbiotica exhibits a dual lifestyle: intracellular by being housed in large syncytial bacteriocytes embedded between B. aphidicola-containing bacteriocytes in a well-organized compartmentalization pattern, and extracellular by massively invading the digestive tract and other tissues during embryogenesis. This is the first reported case of an obligate aphid symbiont that is internalized in bacteriocytes but simultaneously adopts an extracellular lifestyle. This unusual infection pattern for an obligate insect symbiont suggests that some bacteriocyte-associated obligate symbionts, despite their integration into a cooperative partnership, still exhibit invasive behavior and escape strict compartmentalization in bacteriocytes. IMPORTANCE Multipartner nutritional endosymbioses have evolved many times in insects. In Chaitophorinae aphids, the eroded metabolic capabilities of the ancient obligate symbiont B. aphidicola are complemented by those of more recently acquired symbionts. Here, we report the atypical case of the co-obligate S. symbiotica symbiont associated with P. lyropictus. This bacterium is compartmentalized into bacteriocytes nested into the ones harboring the more ancient symbiont B. aphidicola, reflecting metabolic convergences between the two symbionts. At the same time, S. symbiotica exhibits highly invasive behavior by colonizing various host tissues, including the digestive tract during embryogenesis. The discovery of this unusual phenotype for a co-obligate symbiont reveals a new face of multipartner nutritional endosymbiosis in insects. In particular, it shows that co-obligate symbionts can retain highly invasive traits and suggests that host dependence on these bacterial partners may evolve prior to their strict compartmentalization into specialized host structures.

Elucidation of host and symbiont contributions to peptidoglycan metabolism based on comparative genomics of eight aphid subfamilies and their Buchnera

Pea aphids (Acyrthosiphon pisum) are insects containing genes of bacterial origin with putative functions in peptidoglycan (PGN) metabolism. Of these, rlpA1-5, amiD, and ldcA are highly expressed in bacteriocytes, specialized aphid cells that harbor the obligate bacterial symbiont Buchnera aphidicola, required for amino acid supplementation of the host's nutrient-poor diet. Despite genome reduction associated with endosymbiosis, pea aphid Buchnera retains genes for the synthesis of PGN while Buchnera of many other aphid species partially or completely lack these genes. To explore the evolution of aphid horizontally-transferred genes (HTGs) and to elucidate how host and symbiont genes contribute to PGN production, we sequenced genomes from four deeply branching lineages, such that paired aphid and Buchnera genomes are now available for 17 species representing eight subfamilies. We identified all host and symbiont genes putatively involved in PGN metabolism. Phylogenetic analyses indicate that each HTG family was present in the aphid shared ancestor, but that each underwent a unique pattern of gene loss or duplication in descendant lineages. While four aphid rlpA gene subfamilies show no relation to symbiont PGN gene repertoire, the loss of aphid amiD and ldcA HTGs coincides with the loss of symbiont PGN metabolism genes. In particular, the coincident loss of host amiD and symbiont murCEF in tribe Aphidini, in contrast to tribe Macrosiphini, suggests either 1) functional linkage between these host and symbiont genes, or 2) Aphidini has lost functional PGN synthesis and other retained PGN pathway genes are non-functional. To test these hypotheses experimentally, we used cell-wall labeling methods involving a d-alanine probe and found that both Macrosiphini and Aphidini retain Buchnera PGN synthesis. Our results imply that compensatory adaptations can preserve PGN synthesis despite the loss of some genes considered essential for this pathway, highlighting the importance of the cell wall in these symbioses.

Aphid hologenomics: current status and future challenges

Aphids are important model organisms in ecological, developmental, and evolutionary studies of, for example, symbiosis, insect-plant interactions, pest management, and developmental polyphenism. Here, we review the recent progress made in the genomics of aphids and their symbionts: hologenomics. The reference genome of Acyrthosiphon pisum has been greatly improved, and chromosome-level assembly is now available. The genomes of over 20 aphid species have been sequenced, and comparative genomic analyses have revealed pervasive gene duplication and dynamic chromosomal rearrangements. Over 120 symbiont genomes (both obligate and facultative) have been sequenced, and modern deep-sequencing technologies have identified novel symbionts. The advances in hologenomics have helped to elucidate the dynamic evolution of facultative and co-obligate symbionts with the ancient obligate symbiont Buchnera.

The boom and bust of the aphid's essential amino acid metabolism across nymphal development

Within long-term symbioses, animals integrate their physiology and development with their symbiont. In a model nutritional mutualism, aphids harbor the endosymbiont, Buchnera, within specialized bacteriocyte cells. Buchnera synthesizes essential amino acids (EAAs) and vitamins for their host, which are lacking from the aphid's plant sap diet. It is unclear if the aphid host differentially expresses aphid EAA metabolism pathways and genes that collaborate with Buchnera for the production of EAA and vitamins throughout nymphal development when feeding on plants. It is also unclear if aphid bacteriocytes are differentially methylated throughout aphid development as DNA methylation may play a role in gene regulation. By analyzing aphid gene expression, we determined that the bacteriocyte is metabolically more active in metabolizing Buchnera's EAAs and vitamins early in nymphal development compared to intermediate or later immature and adult lifestages. The largest changes in aphid bacteriocyte gene expression, especially for aphid genes that collaborate with Buchnera, occurred during the 3rd to 4th instar transition. During this transition, there is a huge shift in the bacteriocyte from a high energy "nutrient-consuming state" to a "recovery and growth state" where patterning and signaling genes and pathways are upregulated and differentially methylated, and de novo methylation is reduced as evidenced by homogenous DNA methylation profiles after the 2nd instar. Moreover, bacteriocyte number increased and Buchnera's titer decreased throughout aphid nymphal development. These data suggest in combination that bacteriocytes of older nymphal and adult lifestages depend less on the nutritional symbiosis compared to early nymphal lifestages.

Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing

Aphids are known to be associated with a variety of symbiotic bacteria. To improve our knowledge of the bacterial diversity of polyphagous aphids, in the present study, we investigated the microbiota of the cosmopolitan agricultural pest Myzus persicae (Sulzer). Ninety-two aphid samples collected from different host plants in various regions of China were examined using high-throughput amplicon sequencing. We comprehensively characterized the symbiont diversity of M. persicae and assessed the variations in aphid-associated symbiont communities. We detected a higher diversity of symbionts than has been previously observed. M. persicae hosted the primary endosymbiont Buchnera aphidicola and seven secondary symbionts, among which Wolbachia was the most prevalent and Rickettsia, Arsenophonus, and Spiroplasma were reported for the first time. Ordination analyses and statistical tests revealed that the symbiont flora associated with M. persicae did not change with respect to host plant or geography, which may be due to frequent migrations between different aphid populations. These findings will advance our knowledge of the microbiota of polyphagous insects and will enrich our understanding of assembly of host-microbiome systems.

Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts

The evolution of bacterial endosymbiont genomes is strongly influenced by host-driven selection. Factors affecting host genome evolution will potentially affect endosymbiont genomes in similar ways. One potential outcome is correlations in molecular rates between the genomes of the symbiotic partners. Recently, we presented the first evidence of such correlations between the mitochondrial genomes of cockroaches and the genomes of their endosymbiont (Blattabacterium cuenoti). Here we investigate whether similar patterns are found in additional host-symbiont partners. We use partial genome data from multiple strains of the bacterial endosymbionts Buchnera aphidicola and Sulcia muelleri, and the mitochondrial genomes of their sap-feeding insect hosts. Both endosymbionts show phylogenetic congruence with the mitochondria of their hosts, a result that is expected due to their identical mode of inheritance. We compared root-to-tip distances and branch lengths of phylogenetically independent species pairs. Both analyses showed a highly significant correlation of molecular rates between the genomes of Buchnera and the mitochondrial genomes of their hosts. A similar correlation was detected between Sulcia and their hosts, but was not statistically significant. Our results indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.

B-vitamin nutrition in the pea aphid-Buchnera symbiosis

Various insects that utilize vitamin-deficient diets derive a supplementary supply of these micronutrients from their symbiotic microorganisms. Here, we tested the inference from genome annotation that the symbiotic bacterium Buchnera aphidicola in the pea aphid Acyrthosiphon pisum provides the insect with vitamins B₂ and B₅ but no other B-vitamins. Contrary to expectation, aphid survival over five days of larval development on artificial diets individually lacking each B-vitamin not synthesized by Buchnera was not significantly reduced, despite significantly lower carcass B₁, B₃, B₆ and B₇ concentrations in the aphids on diets lacking each of these B-vitamins than on the vitamin-complete diet. Aphid survival was, however, significantly reduced on diet containing low concentrations (≤0.2 mM) or no pantothenate (B₅). Complementary transcriptome analysis revealed low abundance of the sense-transcript, but high abundance of the antisense transcript, of the Buchnera gene panC encoding the enzyme mediating the terminal reaction in pantothenate synthesis. We hypothesize that metabolic constraints or antisense transcripts may reduce Buchnera-mediated production of pantothenate, resulting in poor aphid performance on pantothenate-free diets. The discrepancy between predictions from genome data and empirical data illustrates the need for physiological study to test functional inferences made from genome annotations.

No evidence for Wolbachia as a nutritional co-obligate endosymbiont in the aphid Pentalonia nigronervosa

Obligate symbiotic associations are present in a wide variety of animals with a nutrient-restricted diet. Aphids (hemiptera: Aphididae) almost-universally host Buchnera aphidicola bacteria in specialised organs (called bacteriomes). These bacteria supply the aphid with essential nutrients lacking from their diet (i.e. essential amino acids and some B vitamins). Some aphid lineages, such as species from the Lacninae subfamily, have evolved co-obligate associations with secondary endosymbionts, deriving from a loss of biotin- and riboflavin-biosynthetic genes. In this study, I re-analyse previously published sequencing data from the banana aphid Pentalonia nigronervosa. I show that the metabolic inference results from De Clerck et al. (Microbiome 3:63, 2015) are incorrect and possibly arise from the use of inadequate methods. Additionally, I discuss how the seemingly biased interpretation of their antibiotic treatment analyses together with an incorrect genome-based metabolic inference resulted in the erroneous suggestion "that a co-obligatory symbiosis between B. aphidicola and Wolbachia occurs in the banana aphid".

Host and symbiont genetic determinants of nutritional phenotype in a natural population of the pea aphid

A defining feature of the nutritional ecology of plant sap-feeding insects is that the dietary deficit of essential amino acids (EAAs) in plant sap is supplemented by EAA-provisioning microbial symbionts in the insect. Here, we demonstrated substantial variation in the nutritional phenotype of 208 genotypes of the pea aphid Acyrthosiphon pisum collected from a natural population. Specifically, the genotypes varied in performance (larval growth rates) on four test diets lacking the EAAs arginine, histidine and methionine or aromatic EAAs (phenylalanine and tryptophan), relative to the diet containing all EAAs. These data indicate that EAA supply from the symbiotic bacteria Buchnera can meet total aphid nutritional demand for only a subset of the EAA/aphid genotype combinations. We then correlated single nucleotide polymorphisms (SNPs) identified in the aphid and Buchnera genomes by reduced genome sequencing against aphid performance for each EAA deletion diet. This yielded significant associations between performance on the histidine-free diet and Buchnera SNPs, including metabolism genes predicted to influence histidine biosynthesis. Aphid genetic correlates of performance were obtained for all four deletion diets, with associations on the arginine-free diet and aromatic-free diets dominated by genes functioning in the regulation of metabolic and cellular processes. The specific aphid genes associated with performance on different EAA deletion diets are largely nonoverlapping, indicating some independence in the regulatory circuits determining aphid phenotype for the different EAAs. This study demonstrates how variation in the phenotype of associations collected from natural populations can be applied to elucidate the genetic basis of ecologically important traits in systems intractable to traditional forward/reverse genetic techniques.

Genome Evolution of the Obligate Endosymbiont Buchnera aphidicola

An evolutionary consequence of uniparentally transmitted symbiosis is degradation of symbiont genomes. We use the system of aphids and their maternally inherited obligate endosymbiont, Buchnera aphidicola, to explore the evolutionary process of genome degradation. We compared complete genome sequences for 39 Buchnera strains, including 23 newly sequenced symbiont genomes from diverse aphid hosts. We reconstructed the genome of the most recent shared Buchnera ancestor, which contained 616 protein-coding genes, and 39 RNA genes. The extent of subsequent gene loss varied across lineages, resulting in modern genomes ranging from 412 to 646 kb and containing 354-587 protein-coding genes. Loss events were highly nonrandom across loci. Genes involved in replication, transcription, translation, and amino acid biosynthesis are largely retained, whereas genes underlying ornithine biosynthesis, stress responses, and transcriptional regulation were lost repeatedly. Aside from losses, gene order is almost completely stable. The main exceptions involve movement between plasmid and chromosome locations of genes underlying tryptophan and leucine biosynthesis and supporting nutrition of aphid hosts. This set of complete genomes enabled tests for signatures of positive diversifying selection. Of 371 Buchnera genes tested, 29 genes show strong support for ongoing positive selection. These include genes encoding outer membrane porins that are expected to be involved in direct interactions with hosts. Collectively, these results indicate that extensive genome reduction occurred in the ancestral Buchnera prior to aphid diversification and that reduction has continued since, with losses greater in some lineages and for some loci.

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems

Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera's. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera's. Additionally, we found that the Erwinia vitamin-biosynthetic genes not only compensate for Buchnera's deficiencies, but also provide a new nutritional function; whose genes have been horizontally acquired from a Sodalis-related bacterium. A subset of these genes have been subsequently transferred to a new Hamiltonella co-obligate symbiont in one specific Cinara lineage. These results show that the establishment and dynamics of multi-partner endosymbioses can be mediated by lateral gene transfers between co-ocurring symbionts.

Changes in Aphid Host Plant Diet Influence the Small-RNA Expression Profiles of Its Obligate Nutritional Symbiont, Buchnera

Plants are a difficult food resource to use, and herbivorous insects have evolved a variety of mechanisms that allow them to fully exploit this poor nutritional resource. One such mechanism is the maintenance of bacterial symbionts that aid in host plant feeding and development. The majority of these intracellular symbionts have highly eroded genomes that lack many key regulatory genes; consequently, it is unclear if these symbionts can respond to changes in the insect's diet to facilitate host plant use. There is emerging evidence that symbionts with highly eroded genomes express small RNAs (sRNAs), some of which potentially regulate gene expression. In this study, we sought to determine if the reduced genome of the nutritional symbiont (Buchnera) in the pea aphid responds to changes in the aphid's host plant diet. Using transcriptome sequencing (RNA-seq), Buchnera sRNA expression profiles were characterized within two Buchnera life stages when pea aphids fed on either alfalfa or fava bean. Overall, this study demonstrates that Buchnera sRNA expression changes not only with life stage but also with changes in aphid host plant diet. Of the 321 sRNAs characterized in this study, 47% were previously identified and 22% showed evidence of conservation in two or more Buchnera taxa. Functionally, 13 differentially expressed sRNAs were predicted to target genes related to pathways involved in essential amino acid biosynthesis. Overall, results from this study reveal that host plant diet influences the expression of conserved and lineage-specific sRNAs in Buchnera and that these sRNAs display distinct host plant-specific expression profiles among biological replicates.IMPORTANCE In general, the genomes of intracellular bacterial symbionts are reduced compared to those of free-living relatives and lack many key regulatory genes. Many of these reduced genomes belong to obligate mutualists of insects that feed on a diet that is deficient in essential nutrients, such as essential amino acids. It is unclear if these symbionts respond with their host to changes in insect diet, because of their reduced regulatory capacity. Emerging evidence suggests that these symbionts express small RNAs (sRNAs) that regulate gene expression at the posttranscriptional level. Therefore, in this study, we sought to determine if the reduced genome of the nutritional symbiont Buchnera in the pea aphid responds to changes in the aphid's host plant diet. This study demonstrates for the first time that Buchnera sRNAs, some conserved in two or more Buchnera lineages, are differentially expressed when aphids feed on different plant species and potentially target genes within essential amino acid biosynthesis pathways.

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

BACKGROUND

Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.

RESULTS

We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.

CONCLUSIONS

We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.

Insect-bacteria parallel evolution in multiple-co-obligate-aphid association: a case in Lachninae (Hemiptera: Aphididae)

Parallel phylogenies between aphid and its obligate symbiont Buchnera are hot topics which always focused on aphid lower taxonomic levels. Symbionts in the subfamily Lachninae are special. Buchnera in many lachnine species has undergone functional and genome size reduction that was replaced by other co-obligate symbionts. In this study, we constructed the phylogenetic relationships of Lachninae with a combined dataset of five genes sequenced from Buchnera to estimate the effects of a dual symbiotic system in the aphid-Buchnera cospeciation association. The phylogeny of Buchnera in Lachninae was well-resolved in the combined dataset. Each of the genera formed strongly supported monophyletic groups, with the exception of the genus Cinara. The phylogeny based on sequences from Buchnera was divided into five tribes according to the clades of the Lachninae hosts tree, with the phylogenies of Buchnera and Lachninae being generally congruent. These results first provided evidence of parallel evolution at the aphid subfamily level comprehensively and supported the view that topological congruence between the phylogenies of Buchnera and Lachninae would not be interfered with the other co-obligate symbionts, such as Sarretia, in aphid-entosymbiont association. These results also provided new insight in understanding host-plant coevolution in lachnine lineages.

EF-1α DNA Sequences Indicate Multiple Origins of Introduced Populations of Essigella californica (Hemiptera: Aphididae)

Aphids in the pine-feeding Nearctic genus Essigella (Sternorrhyncha, Aphididae, Lachninae) have been introduced in Europe, North Africa, Oceania, and South America. Mitochondrial, nuclear, and endosymbiont DNA sequences of 12 introduced populations from three continents confirm they all belong to Essigella californica (Essig, 1909). Intron sequence variation of the nuclear gene EF-1α has revealed the existence of four distinct groups. Group I gathers one population from China, where the species is newly reported, and several from Europe (France and Italy); Group II is represented by one population from Argentina; Group III includes two populations from Southern Australia with one from New Zealand; and Group IV corresponds to five populations from Eastern and South-Eastern Australia. These results indicate that introduced populations of E. californica have at least four source populations. They also show that intron variation of EF-1α can be a method to discriminate populations of asexually reproducing aphids.

Symbiont Diversity of Aphis (Toxoptera) citricidus (Hemiptera: Aphididae) as Influenced by Host Plants

Aphids are well known for their association with endosymbiont bacteria. Almost all aphids harbor Buchnera aphidicola as an obligate symbiont and several other bacteria as facultative symbionts. Associations of facultative symbionts and aphids are quite variable in terms of diversity and prevalence across aphid species. Facultative symbionts can have a major impact on aphid bioecological traits. A number of factors shape the outcome of the facultative symbiont-aphid association, including aphid clone, bacterial genotype, geography, and host plant association. The effects of host plant on aphid-facultative symbiont associations are the least understood. We performed deep sequencing of the bacterial community associated with field populations of the oligophagous aphid Aphis (Toxoptera) citricidus collected from different host plants. We demonstrate that (i) A. citricidus has low symbiont diversity, (ii) symbiont diversity is affected by host plant, and (iii) host plants affect the relative abundance of the obligate symbiont Buchnera and an unknown genus of Enterobacteriaceae.

Reinventing the Wheel and Making It Round Again: Evolutionary Convergence in Buchnera-Serratia Symbiotic Consortia between the Distantly Related Lachninae Aphids Tuberolachnus salignus and Cinara cedri

Virtually all aphids (Aphididae) harbor Buchnera aphidicola as an obligate endosymbiont to compensate nutritional deficiencies arising from their phloem diet. Many species within the Lachninae subfamily seem to be consistently associated also with Serratia symbiotica We have previously shown that both Cinara (Cinara) cedri and Cinara (Cupressobium) tujafilina (Lachninae: Eulachnini tribe) have indeed established co-obligate associations with both Buchnera and S. symbiotica However, while Buchnera genomes of both Cinara species are similar, genome degradation differs greatly between the two S. symbiotica strains. To gain insight into the essentiality and degree of integration of S. symbiotica within the Lachninae, we sequenced the genome of both Buchnera and S. symbiotica endosymbionts from the distantly related aphid Tuberolachnus salignus (Lachninae: Tuberolachnini tribe). We found a striking level of similarity between the endosymbiotic system of this aphid and that of C. cedri In both aphid hosts, S. symbiotica possesses a highly reduced genome and is found exclusively intracellularly inside bacteriocytes. Interestingly, T. salignus' endosymbionts present the same tryptophan biosynthetic metabolic complementation as C. cedri's, which is not present in C. tujafilina's. Moreover, we corroborate the riboflavin-biosynthetic-role take-over/rescue by S. symbiotica in T. salignus, and therefore, provide further evidence for the previously proposed establishment of a secondary co-obligate endosymbiont in the common ancestor of the Lachninae aphids. Finally, we propose that the putative convergent split of the tryptophan biosynthetic role between Buchnera and S. symbiotica could be behind the establishment of S. symbiotica as an obligate intracellular symbiont and the triggering of further genome degradation.

A metagenomic approach from aphid's hemolymph sheds light on the potential roles of co-existing endosymbionts

BACKGROUND

Aphids are known to live in symbiosis with specific bacteria, called endosymbionts which can be classified as obligate or accessory. Buchnera aphidicola is generally the only obligatory symbiont present in aphids, supplying essential nutrients that are missing in the plants phloem to its host. Pentalonia nigronervosa is the main vector of the banana bunchy top virus, one of the most damageable viruses in banana. This aphid is carrying two symbionts: B. aphidicola (BPn) and Wolbachia sp. (wPn). The high occurrence of Wolbachia in the banana aphid raises questions about the role it plays in this insect. The goal of this study was to go further in the understanding of the role played by the two symbionts in P. nigronervosa. To do so, microinjection tests were made to see the effect of wPn elimination on the host, and then, high-throughput sequencing of the haemolymph was used to analyze the gene content of the symbionts.

RESULTS

We observed that the elimination of wPn systematically led to the death of aphids, suggesting that the bacterium could play a mutualistic role. In addition, we identify and annotate 587 and 250 genes for wPn and BPn, respectively, through high-throughput sequencing. Analysis of these genes suggests that the two bacteria are working together for the production of several essential nutrients. The most striking cases are for lysin and riboflavin which are usually provided by B. aphidicola alone to the host. In the banana aphid, the genes involved in the production pathways of these metabolites are shared between the two bacteria making them both essential for the survival of the aphid host.

CONCLUSIONS

Our results suggest that a co-obligatory symbiosis between B. aphidicola and Wolbachia occurs in the banana aphid, the two bacteria acting together to supply essential nutrients to the host. This is, to our knowledge, the first time Wolbachia is reported to play an essential role in aphids.

Phylogenetic Relationships of the Symbiotic Bacteria in the Aphid Sitobion avenae (Hemiptera: Aphididae)

Aphids have developed symbiotic associations with different bacterial species, and some morphological and molecular analyses have provided evidence of the host relationship between the primary symbiotic bacteria (Buchnera aphidicola) and the aphid while the contrary with the secondary symbiotic bacteria. In this study, we investigated the phylogenetic relationships of the bacterial endosymbionts in the aphid Sitobion avenae (F.). We characterized all bacterial endosymbionts in 10 genetically defined S. avenae clones by denaturing gradient gel electrophoresis and, from these clones, sequenced the 16S rRNA genes of both the primary endosymbiont, B. aphidicola (for the first time), and the secondary endosymbionts, Regiella insecticola and Hamiltonella defensa (for the first time). The phylogenetic analysis indicated that Buchnera from Sitobion related to those in Macrosiphoni. The analysis of the secondary endosymbionts indicated that there is no host relationship between H. defensa and R. insecticola from Sitobion and those from other aphid species. In this study, therefore, we identified further evidence for the relationship between Buchnera and its host and reported a relationship within the secondary endosymbionts of S. avenae from the same country, even though there were no relationships between the secondary bacteria and their host. We also discussed the diversity within the symbiotic bacteria in S. avenae clones.

Shifts in Buchnera aphidicola density in soybean aphids (Aphis glycines) feeding on virus-infected soybean

Vertically transmitted bacterial symbionts are common in arthropods. Aphids undergo an obligate symbiosis with Buchnera aphidicola, which provides essential amino acids to its host and contributes directly to nymph growth and reproduction. We previously found that newly adult Aphis glycines feeding on soybean infected with the beetle-transmitted Bean pod mottle virus (BPMV) had significantly reduced fecundity. We hypothesized that the reduced fecundity was attributable to detrimental impacts of the virus on the aphid microbiome, namely Buchnera. To test this, mRNA sequencing and quantitative real-time PCR were used to assay Buchnera transcript abundance and titre in A. glycines feeding on Soybean mosaic virus-infected, BPMV-infected, and healthy soybean for up to 14 days. Our results indicated that Buchnera density was lower and ultimately suppressed in aphids feeding on virus-infected soybean. While the decreased Buchnera titre may be associated with reduced aphid fecundity, additional mechanisms are probably involved. The present report begins to describe how interactions among insects, plants, and plant pathogens influence endosymbiont population dynamics.

Widespread expression of conserved small RNAs in small symbiont genomes

Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it remains unclear whether and how these small symbiont genomes regulate gene expression. Here, using a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of putative transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergent Buchnera lineages, spanning a variety of Buchnera life stages, reveals 140 novel intergenic and antisense small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for ∼65 million years. In addition, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together, these data suggest that gene regulation at the post-transcriptional level may be important in Buchnera. This is the first study to empirically identify Buchnera small RNAs, and we propose that these novel small RNAs may facilitate post-transcriptional regulation through translational inhibition/activation, and/or transcript stability. Ultimately, post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal's ecology and evolution.

Aphis (Hemiptera: Aphididae) species groups found in the Midwestern United States and their contribution to the phylogenetic knowledge of the genus

A phylogeny of the genus Aphis Linnaeus, 1 758 was built primarily from specimens collected in the Midwest of the United States. A data matrix was constructed with 68 species and 41 morphological characters with respective character states of alate and apterous viviparous females. Dendrogram topologies of analyses performed using UPGMA (Unweighted Pair Group Method with Arithmetic Mean), Maximum Parsimony and Bayesian analysis of Cytochrome Oxidase I, Elongation Factor 1-α and primary endosymbiont Buchnera aphidicola 16S sequences were not congruent. Bayesian analysis strongly supported most terminal nodes of the phylogenetic trees. The phylogeny was strongly supported by EF1-α, and analysis of COI and EF1-α molecular data combined with morphological characters. It was not supported by single analysis of COI or Buchnera aphidicola 16S. Results from the Bayesian phylogeny show 4 main species groups: asclepiadis, fabae, gossypii, and middletonii. Results place Aphis and species of the genera Protaphis Börner, 1952, Toxoptera Koch, and Xerobion Nevsky, 1928 in a monophyletic clade. Morphological characters support this monophyly as well. The phylogeny shows that the monophyletic clade of the North American middletonii species group belong to the genus Protaphis: P. debilicornis (Gillette & Palmer, 1929), comb. nov., P. echinaceae (Lagos and Voegtlin, 2009), comb. nov., and P. middletonii (Thomas, 1879). The genus Toxoptera should be considered a subgenus of Aphis (stat. nov.). The analysis also indicates that the current genus Iowana Frison, 1954 should be considered a subgenus of Aphis (stat. nov.).

Exploring the bacterial microbiota associated with native South American species of Aphis (Hemiptera: Aphididae)

Aphids harbor a variety of bacterial endosymbionts, including the obligate symbiont Buchnera aphidicola and diverse facultative symbionts. The former supplies its host with essential amino acids. The latter are not indispensable for insect survival, but often improve their host's fitness. To date, the study of such associations was restricted to aphids of Holarctic origin. The bacterial microbiota of seven Aphis species from Argentina was investigated. The presence of B. aphidicola was assessed by specific PCR. Additional symbionts were identified through PCR with eubacterial universal primers, cloning, and sequencing of nearly complete 16S rRNA gene, intergenic spacer region, and partial 23S rRNA gene and subjected to phylogenetic analysis. Infection with B. aphidicola was confirmed in every species analyzed. The facultative symbiont Serratia symbiotica was detected in Aphis malalhuina Mier Durante, Nieto Nafría & Ortego, 2003, Aphis senecionicoides Blanchard, 1944, and Aphis schinifoliae Blanchard, 1939, while Hamiltonella defensa was identified in Aphis mendocina Mier Durante, Ortego & Nieto Nafría, 2006. Arsenophonus sp. was found infecting Aphis melosae Mier Durante & Ortego, 1999, and a new, undescribed Aphis sp. In Aphis danielae Remaudière, 1994, no facultative symbionts could be recorded. When analyzing the highly conserved 16S rRNA gene, the phylogenetic tree grouped the S. symbiotica, H. defensa, and Arsenophonus isolates into three well-defined clusters showing little variability among clones corresponding to the same aphid host species. This article reports for the first time the endosymbionts associated with aphids native to South America. Despite their geographic origin, the qualitative composition of their microbiota revealed no evident differences from that described for aphids in the Northern Hemisphere.

Evolutionary relationships of Pemphigus and allied genera (Hemiptera: Aphididae: Eriosomatinae) and their primary endosymbiont, Buchnera aphidicola

Aphids harbor primary endosymbionts, Buchnera aphidicola, in specialized cells within their body cavities. Aphids and Buchnera have strict mutualistic relationships in nutrition exchange. This ancient association has received much attention from researchers who are interested in endosymbiotic evolution. Previous studies have found parallel phylogenetic relationships between non-galling aphids and Buchnera at lower taxonomic levels (genus, species). To understand whether relatively isolated habitats such as galls have effect on the parallel relationships between aphids and Buchnera, the present paper investigated the phylogenetic relationships of gall aphids from Pemphigus and allied genera, which induce pseudo-galls or galls on Populus spp. (poplar) and Buchnera. The molecular phylogenies inferred from three aphid genes (COI, COII and EF-1α) and two Buchnera genes (gnd, 16S rRNA gene) indicated significant congruence between aphids and Buchnera at generic as well as interspecific levels. Interestingly, both aphid and Buchnera phylogenies supported three main clades corresponding to the galling locations of aphids, namely leaf, the joint of leaf blade and petiole, and branch of the host plant. The results suggest phylogenetic conservatism of gall characters, which indicates gall characters are more strongly affected by aphid phylogeny, rather than host plants.

The combined effects of bacterial symbionts and aging on life history traits in the pea aphid, Acyrthosiphon pisum

While many endosymbionts have beneficial effects on hosts under specific ecological conditions, there can also be associated costs. In order to maximize their own fitness, hosts must facilitate symbiont persistence while preventing symbiont exploitation of resources, which may require tight regulation of symbiont populations. As a host ages, the ability to invest in such mechanisms may lessen or be traded off with demands of other life history traits, such as survival and reproduction. Using the pea aphid, Acyrthosiphon pisum, we measured survival, lifetime fecundity, and immune cell counts (hemocytes, a measure of immune capacity) in the presence of facultative secondary symbionts. Additionally, we quantified the densities of the obligate primary bacterial symbiont, Buchnera aphidicola, and secondary symbionts across the host's lifetime. We found life history costs to harboring some secondary symbiont species. Secondary symbiont populations were found to increase with host age, while Buchnera populations exhibited a more complicated pattern. Immune cell counts peaked at the midreproductive stage before declining in the oldest aphids. The combined effects of immunosenescence and symbiont population growth may have important consequences for symbiont transmission and maintenance within a host population.

Comparative analysis of genome sequences from four strains of the Buchnera aphidicola Mp endosymbion of the green peach aphid, Myzus persicae

BACKGROUND

Myzus persicae, the green peach aphid, is a polyphagous herbivore that feeds from hundreds of species of mostly dicot crop plants. Like other phloem-feeding aphids, M. persicae rely on the endosymbiotic bacterium, Buchnera aphidicola (Buchnera Mp), for biosynthesis of essential amino acids and other nutrients that are not sufficiently abundant in their phloem sap diet. Tobacco-specialized M. persicae are typically red and somewhat distinct from other lineages of this species. To determine whether the endosymbiotic bacteria of M. persicae could play a role in tobacco adaptation, we sequenced the Buchnera Mp genomes from two tobacco-adapted and two non-tobacco M. persicae lineages.

RESULTS

With a genome size of 643.5 kb and 579 predicted genes, Buchnera Mp is the largest Buchnera genome sequenced to date. No differences in gene content were found between the four sequenced Buchnera Mp strains. Compared to Buchnera APS from the well-studied pea aphid, Acyrthosiphon pisum, Buchnera Mp has 21 additional genes. These include genes encoding five enzymes required for biosynthesis of the modified nucleoside queosine, the heme pathway enzyme uroporphyrinogen III synthase, and asparaginase. Asparaginase, which is also encoded by the genome of the aphid host, may allow Buchnera Mp to synthesize essential amino acids from asparagine, a relatively abundant phloem amino acid.

CONCLUSIONS

Together our results indicate that the obligate intracellular symbiont Buchnera aphidicola does not contribute to the adaptation of Myzus persicae to feeding on tobacco.

Functional and evolutionary analysis of the genome of an obligate fungal symbiont

Nutritional symbionts of insects include some of the most bizarre genomes studied to date, with extremely reduced size, biased base composition, and limited metabolic abilities. A monophyletic group of aphids within the subfamily Cerataphidinae have lost the bacterial symbiont common to all other Aphididae (Buchnera aphidicola), which have been replaced by a eukaryotic one, the yeast-like symbiont (YLS). As symbionts are expected to experience reduced effective population size (Ne) and largely clonal life cycles, we used this system as a model to test the hypothesis that chronically high levels of genetic drift will result in an increase in size of a eukaryotic genome. We sequenced the genome of the YLS of the aphid Cerataphis brasiliensis and observed elevated rates of protein sequence evolution and intron proliferation in YLS orthologs relative to those of its closest-sequenced relative, consistent with predictions. A moderate amount of repetitive DNA was found along with evidence of directed mutation to prevent proliferation of repetitive elements. Despite increased intron numbers, the overall genome structure appears not to have undergone massive expansion and is around 25 Mb in size. Compared with Buchnera, the YLS appears to have a much broader metabolic repertoire, though many gene families have been reduced in the YLS relative to related fungi. The patterns observed in the YLS genome suggest that its symbiotic lifestyle is permissive to intron proliferation and accelerated sequence evolution, though other factors appear to limit its overall genome expansion.

Deep sequencing of the transcriptomes of soybean aphid and associated endosymbionts

BACKGROUND

The soybean aphid has significantly impacted soybean production in the U.S. Transcriptomic analyses were conducted for further insight into leads for potential novel management strategies.

METHODOLOGY/PRINCIPAL FINDINGS

Transcriptomic data were generated from whole aphids and from 2,000 aphid guts using an Illumina GAII sequencer. The sequence data were assembled de novo using the Velvet assembler. In addition to providing a general overview, we demonstrate (i) the use of the Multiple-k/Multiple-C method for de novo assembly of short read sequences, followed by BLAST annotation of contigs for increased transcript identification: From 400,000 contigs analyzed, 16,257 non-redundant BLAST hits were identified; (ii) analysis of species distributions of top non-redundant hits: 80% of BLAST hits (minimum e-value of 1.0-E3) were to the pea aphid or other aphid species, representing about half of the pea aphid genes; (iii) comparison of relative depth of sequence coverage to relative transcript abundance for genes with high (membrane alanyl aminopeptidase N) or low transcript abundance; (iv) analysis of the Buchnera transcriptome: Transcripts from 57.6% of the genes from Buchnera aphidicola were identified; (v) identification of Arsenophonus and Wolbachia as potential secondary endosymbionts; (vi) alignment of full length sequences from RNA-seq data for the putative salivary gland protein C002, the silencing of which has potential for aphid management, and the putative Bacillus thuringiensis Cry toxin receptors, aminopeptidase N and alkaline phosphatase.

CONCLUSIONS/SIGNIFICANCE

THIS STUDY PROVIDES THE MOST COMPREHENSIVE DATA SET TO DATE FOR SOYBEAN APHID GENE EXPRESSION: This work also illustrates the utility of short-read transcriptome sequencing and the Multiple-k/Multiple-C method followed by BLAST annotation for rapid identification of target genes for organisms for which reference genome sequences are not available, and extends the utility to include the transcriptomes of endosymbionts.

The central role of the host cell in symbiotic nitrogen metabolism

Symbiotic nitrogen recycling enables animals to thrive on nitrogen-poor diets and environments. It traditionally refers to the utilization of animal waste nitrogen by symbiotic micro-organisms to synthesize essential amino acids (EAAs), which are translocated back to the animal host. We applied metabolic modelling and complementary metabolite profiling to investigate nitrogen recycling in the symbiosis between the pea aphid and the intracellular bacterium Buchnera, which synthesizes EAAs. The results differ from traditional notions of nitrogen recycling in two important respects. First, aphid waste ammonia is recycled predominantly by the host cell (bacteriocyte) and not Buchnera. Host cell recycling is mediated by shared biosynthetic pathways for four EAAs, in which aphid transaminases incorporate ammonia-derived nitrogen into carbon skeletons synthesized by Buchnera to generate EAAs. Second, the ammonia substrate for nitrogen recycling is derived from bacteriocyte metabolism, such that the symbiosis is not a sink for nitrogenous waste from other aphid organs. Host cell-mediated nitrogen recycling may be general among insect symbioses with shared EAA biosynthetic pathways generated by the loss of symbiont genes mediating terminal reactions in EAA synthesis.

Comparative genomics of Serratia spp.: two paths towards endosymbiotic life

Symbiosis is a widespread phenomenon in nature, in which insects show a great number of these associations. Buchnera aphidicola, the obligate endosymbiont of aphids, coexists in some species with another intracellular bacterium, Serratia symbiotica. Of particular interest is the case of the cedar aphid Cinara cedri, where B. aphidicola BCc and S. symbiotica SCc need each other to fulfil their symbiotic role with the insect. Moreover, various features seem to indicate that S. symbiotica SCc is closer to an obligate endosymbiont than to other facultative S. symbiotica, such as the one described for the aphid Acirthosyphon pisum (S. symbiotica SAp). This work is based on the comparative genomics of five strains of Serratia, three free-living and two endosymbiotic ones (one facultative and one obligate) which should allow us to dissect the genome reduction taking place in the adaptive process to an intracellular life-style. Using a pan-genome approach, we have identified shared and strain-specific genes from both endosymbiotic strains and gained insight into the different genetic reduction both S. symbiotica have undergone. We have identified both retained and reduced functional categories in S. symbiotica compared to the Free-Living Serratia (FLS) that seem to be related with its endosymbiotic role in their specific host-symbiont systems. By means of a phylogenomic reconstruction we have solved the position of both endosymbionts with confidence, established the probable insect-pathogen origin of the symbiotic clade as well as the high amino-acid substitution rate in S. symbiotica SCc. Finally, we were able to quantify the minimal number of rearrangements suffered in the endosymbiotic lineages and reconstruct a minimal rearrangement phylogeny. All these findings provide important evidence for the existence of at least two distinctive S. symbiotica lineages that are characterized by different rearrangements, gene content, genome size and branch lengths.

Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches

BACKGROUND

The bacterial family Enterobacteriaceae gave rise to a variety of symbiotic forms, from the loosely associated commensals, often designated as secondary (S) symbionts, to obligate mutualists, called primary (P) symbionts. Determination of the evolutionary processes behind this phenomenon has long been hampered by the unreliability of phylogenetic reconstructions within this group of bacteria. The main reasons have been the absence of sufficient data, the highly derived nature of the symbiont genomes and lack of appropriate phylogenetic methods. Due to the extremely aberrant nature of their DNA, the symbiotic lineages within Enterobacteriaceae form long branches and tend to cluster as a monophyletic group. This state of phylogenetic uncertainty is now improving with an increasing number of complete bacterial genomes and development of new methods. In this study, we address the monophyly versus polyphyly of enterobacterial symbionts by exploring a multigene matrix within a complex phylogenetic framework.

RESULTS

We assembled the richest taxon sampling of Enterobacteriaceae to date (50 taxa, 69 orthologous genes with no missing data) and analyzed both nucleic and amino acid data sets using several probabilistic methods. We particularly focused on the long-branch attraction-reducing methods, such as a nucleotide and amino acid data recoding and exclusion (including our new approach and slow-fast analysis), taxa exclusion and usage of complex evolutionary models, such as nonhomogeneous model and models accounting for site-specific features of protein evolution (CAT and CAT+GTR). Our data strongly suggest independent origins of four symbiotic clusters; the first is formed by Hamiltonella and Regiella (S-symbionts) placed as a sister clade to Yersinia, the second comprises Arsenophonus and Riesia (S- and P-symbionts) as a sister clade to Proteus, the third Sodalis, Baumannia, Blochmannia and Wigglesworthia (S- and P-symbionts) as a sister or paraphyletic clade to the Pectobacterium and Dickeya clade and, finally, Buchnera species and Ishikawaella (P-symbionts) clustering with the Erwinia and Pantoea clade.

CONCLUSIONS

The results of this study confirm the efficiency of several artifact-reducing methods and strongly point towards the polyphyly of P-symbionts within Enterobacteriaceae. Interestingly, the model species of symbiotic bacteria research, Buchnera and Wigglesworthia, originated from closely related, but different, ancestors. The possible origins of intracellular symbiotic bacteria from gut-associated or pathogenic bacteria are suggested, as well as the role of facultative secondary symbionts as a source of bacteria that can gradually become obligate maternally transferred symbionts.

Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide

As predicted by the nearly neutral model of evolution, numerous studies have shown that reduced N(e) accelerates the accumulation of slightly deleterious changes under genetic drift. While such studies have mostly focused on eukaryotes, bacteria also offer excellent models to explore the effects of N(e). Most notably, the genomes of host-dependent bacteria with small N(e) show signatures of genetic drift, including elevated K(a)/K(s). Here, I explore the utility of an alternative measure of selective constraint: the per-site rate of radical and conservative amino acid substitutions (D(r)/D(c)). I test the hypothesis that purifying selection against radical amino acid changes is less effective in two insect endosymbiont groups (Blochmannia of ants and Buchnera of aphids), compared to related gamma-Proteobacteria. Genome comparisons demonstrate a significant elevation in D(r)/D(c) in endosymbionts that affects the majority (66-79%) of shared orthologs examined. The elevation of D(r)/D(c) in endosymbionts affects all functional categories examined. Simulations indicate that D(r)/D(c) estimates are sensitive to codon frequencies and mutational parameters; however, estimation biases occur in the opposite direction as the patterns observed in genome comparisons, thereby making the inference of elevated D(r)/D(c) more conservative. Increased D(r)/D(c) and other signatures of genome degradation in endosymbionts are consistent with strong effects of genetic drift in their small populations, as well as linkage to selected sites in these asexual bacteria. While relaxed selection against radical substitutions may contribute, genome-wide processes such as genetic drift and linkage best explain the pervasive elevation in D(r)/D(c) across diverse functional categories that include basic cellular processes. Although the current study focuses on a few bacterial lineages, it suggests D(r)/D(c) is a useful gauge of selective constraint and may provide a valuable alternative to K(a)/K(s) when high sequence divergences preclude estimates of K(s). Broader application of D(r)/D(c) will benefit from approaches less prone to estimation biases.

Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont

The genome sequencing of Buchnera aphidicola BCc from the aphid Cinara cedri, which is the smallest known Buchnera genome, revealed that this bacterium had lost its symbiotic role, as it was not able to synthesize tryptophan and riboflavin. Moreover, the biosynthesis of tryptophan is shared with the endosymbiont Serratia symbiotica SCc, which coexists with B. aphidicola in this aphid. The whole-genome sequencing of S. symbiotica SCc reveals an endosymbiont in a stage of genome reduction that is closer to an obligate endosymbiont, such as B. aphidicola from Acyrthosiphon pisum, than to another S. symbiotica, which is a facultative endosymbiont in this aphid, and presents much less gene decay. The comparison between both S. symbiotica enables us to propose an evolutionary scenario of the transition from facultative to obligate endosymbiont. Metabolic inferences of B. aphidicola BCc and S. symbiotica SCc reveal that most of the functions carried out by B. aphidicola in A. pisum are now either conserved in B. aphidicola BCc or taken over by S. symbiotica. In addition, there are several cases of metabolic complementation giving functional stability to the whole consortium and evolutionary preservation of the actors involved.

Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera

Analyses of genome reduction in obligate bacterial symbionts typically focus on the removal and retention of protein-coding regions, which are subject to ongoing inactivation and deletion. However, these same forces operate on intergenic spacers (IGSs) and affect their contents, maintenance, and rates of evolution. IGSs comprise both non-coding, non-functional regions, including decaying pseudogenes at varying stages of recognizability, as well as functional elements, such as genes for sRNAs and regulatory control elements. The genomes of Buchnera and other small genome symbionts display biased nucleotide compositions and high rates of sequence evolution and contain few recognizable regulatory elements. However, IGS lengths are highly correlated across divergent Buchnera genomes, suggesting the presence of functional elements. To identify functional regions within the IGSs, we sequenced two Buchnera genomes (from aphid species Uroleucon ambrosiae and Acyrthosiphon kondoi) and applied a phylogenetic footprinting approach to alignments of orthologous IGSs from a total of eight Buchnera genomes corresponding to six aphid species. Inclusion of these new genomes allowed comparative analyses at intermediate levels of divergence, enabling the detection of both conserved elements and previously unrecognized pseudogenes. Analyses of these genomes revealed that 232 of 336 IGS alignments over 50 nucleotides in length displayed substantial sequence conservation. Conserved alignment blocks within these IGSs encompassed 88 Shine-Dalgarno sequences, 55 transcriptional terminators, 5 Sigma-32 binding sites, and 12 novel small RNAs. Although pseudogene formation, and thus IGS formation, are ongoing processes in these genomes, a large proportion of intergenic spacers contain functional sequences.

New clues about the evolutionary history of metabolic losses in bacterial endosymbionts, provided by the genome of Buchnera aphidicola from the aphid Cinara tujafilina

The symbiotic association between aphids (Homoptera) and Buchnera aphidicola (Gammaproteobacteria) started about 100 to 200 million years ago. As a consequence of this relationship, the bacterial genome has undergone a prominent size reduction. The downsize genome process starts when the bacterium enters the host and will probably end with its extinction and replacement by another healthier bacterium or with the establishment of metabolic complementation between two or more bacteria. Nowadays, several complete genomes of Buchnera aphidicola from four different aphid species (Acyrthosiphon pisum, Schizaphis graminum, Baizongia pistacea, and Cinara cedri) have been fully sequenced. C. cedri belongs to the subfamily Lachninae and harbors two coprimary bacteria that fulfill the metabolic needs of the whole consortium: B. aphidicola with the smallest genome reported so far and "Candidatus Serratia symbiotica." In addition, Cinara tujafilina, another member of the subfamily Lachninae, closely related to C. cedri, also harbors "Ca. Serratia symbiotica" but with a different phylogenetic status than the one from C. cedri. In this study, we present the complete genome sequence of B. aphidicola from C. tujafilina and the phylogenetic analysis and comparative genomics with the other Buchnera genomes. Furthermore, the gene repertoire of the last common ancestor has been inferred, and the evolutionary history of the metabolic losses that occurred in the different lineages has been analyzed. Although stochastic gene loss plays a role in the genome reduction process, it is also clear that metabolism, as a functional constraint, is also a powerful evolutionary force in insect endosymbionts.

Structure and dynamics of the operon map of Buchnera aphidicola sp. strain APS

BACKGROUND

Gene expression regulation is still poorly documented in bacteria with highly reduced genomes. Understanding the evolution and mechanisms underlying the regulation of gene transcription in Buchnera aphidicola, the primary endosymbiont of aphids, is expected both to enhance our understanding of this nutritionally based association and to provide an intriguing case-study of the evolution of gene expression regulation in a reduced bacterial genome.

RESULTS

A Bayesian predictor was defined to infer the B. aphidicola transcription units, which were further validated using transcriptomic data and RT-PCR experiments. The characteristics of B. aphidicola predicted transcription units (TUs) were analyzed in order to evaluate the impact of operon map organization on the regulation of gene transcription.On average, B. aphidicola TUs contain more genes than those of E. coli. The global layout of B. aphidicola operon map was mainly shaped by the big reduction and the rearrangements events, which occurred at the early stage of the symbiosis. Our analysis suggests that this operon map may evolve further only by small reorganizations around the frontiers of B. aphidicola TUs, through promoter and/or terminator sequence modifications and/or by pseudogenization events. We also found that the need for specific transcription regulation exerts some pressure on gene conservation, but not on gene assembling in the operon map in Buchnera. Our analysis of the TUs spacing pointed out that a selection pressure is maintained on the length of the intergenic regions between divergent adjacent gene pairs.

CONCLUSIONS

B. aphidicola can seemingly only evolve towards a more polycistronic operon map. This implies that gene transcription regulation is probably subject to weak selection pressure in Buchnera conserving operons composed of genes with unrelated functions.

Insecticidal activity of recombinant avidin produced in yeast

An expression construct encoding chicken (Gallus gallus) avidin was assembled from amplified fragments of genomic DNA. Recombinant, functional avidin was produced in Pichia pastoris, with yields of up to 80 mg/l of culture supernatant. The recombinant avidin had similar insecticidal activity to egg white avidin when assayed against larvae of a lepidopteran crop pest, cabbage moth (Mamestra brassicae), causing >90% reduction in growth and 100% mortality when fed in optimised diets at levels of 1.5 microM and 15 microM (100 ppm and 1000 ppm wet weight of recombinant protein). The recombinant protein was also highly toxic to a hemipteran pest, the pea aphid (Acyrthosiphon pisum), when fed in liquid artificial diet, causing 100% mortality after 4 days when present at concentrations > or = 3.8 microM (0.25 mg/ml, 250 ppm). Mortality was dose-dependent, with an estimated LC(50) of 2.1 microM. Toxicity to A. pisum was prevented by biotin supplementation of diet. In contrast, avidin had no significant effects on the survival of cereal aphid (Sitobion avenae) at concentrations up to 30 microM in liquid diet. Analysis of genomic DNA showed that symbionts from both aphid species lack the ability to synthesise biotin de novo. Cereal aphids appear to be less sensitive to recombinant avidin in the diet through proteolysis of the ingested protein, which would allow recovery of bound biotin.

Limited endosymbiont variation in Diuraphis noxia (Hemiptera: Aphididae) biotypes from the United States and South Africa

Symbiosis allows an insect access to imbalanced food sources on which other organisms cannot survive. A bacterial endosymbiont, Buchnera aphidicola, gives aphids the ability to feed on phloem depleted of certain essential amino acids by producing those required. Pseudogenes and lower plasmid copy numbers of essential amino acid genes in B. aphidicola, endosymbiont of the Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae), suggest that this symbiotic relationship is degenerating. The complete endosymbiont assemblages, copy numbers of plasmids (important in essential amino acid production), and sequence variation in B. aphidicola, from 10 Russian wheat aphid biotypes, were investigated. B. aphidicola was found to be monosymbiotic in the Russian wheat aphid biotypes and other Diuraphis species examined. An insert, occurring in an inverted repeat region on the leucine plasmid, was the only variation found in the approximately 10-kb B. aphidicola sequence analyzed from each Russian wheat aphid biotype. This inverted repeat was shown previously to be conserved within the family Aphididae. The insert occurred in B. aphidicola sequences isolated from four Russian wheat aphid biotypes. Copy numbers of the leucine plasmid differ between the South African and U.S. biotypes and were similar to previously reported values for biotypes from the same geographic regions. These results suggest that B. aphidicola may still contribute to Russian wheat aphid fitness when the aphid feeds on a variety of hosts.

Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host

Genome reduction is typical of obligate symbionts. In cellular organelles, this reduction partly reflects transfer of ancestral bacterial genes to the host genome, but little is known about gene transfer in other obligate symbioses. Aphids harbor anciently acquired obligate mutualists, Buchnera aphidicola (Gammaproteobacteria), which have highly reduced genomes (420–650 kb), raising the possibility of gene transfer from ancestral Buchnera to the aphid genome. In addition, aphids often harbor other bacteria that also are potential sources of transferred genes. Previous limited sampling of genes expressed in bacteriocytes, the specialized cells that harbor Buchnera, revealed that aphids acquired at least two genes from bacteria. The newly sequenced genome of the pea aphid, Acyrthosiphon pisum, presents the first opportunity for a complete inventory of genes transferred from bacteria to the host genome in the context of an ancient obligate symbiosis. Computational screening of the entire A. pisum genome, followed by phylogenetic and experimental analyses, provided strong support for the transfer of 12 genes or gene fragments from bacteria to the aphid genome: three LD–carboxypeptidases (LdcA1, LdcA2,ψLdcA), five rare lipoprotein As (RlpA1-5), N-acetylmuramoyl-L-alanine amidase (AmiD), 1,4-beta-N-acetylmuramidase (bLys), DNA polymerase III alpha chain (ψDnaE), and ATP synthase delta chain (ψAtpH). Buchnera was the apparent source of two highly truncated pseudogenes (ψDnaE and ψAtpH). Most other transferred genes were closely related to genes from relatives of Wolbachia (Alphaproteobacteria). At least eight of the transferred genes (LdcA1, AmiD, RlpA1-5, bLys) appear to be functional, and expression of seven (LdcA1, AmiD, RlpA1-5) are highly upregulated in bacteriocytes. The LdcAs and RlpAs appear to have been duplicated after transfer. Our results excluded the hypothesis that genome reduction in Buchnera has been accompanied by gene transfer to the host nuclear genome, but suggest that aphids utilize a set of duplicated genes acquired from other bacteria in the context of the Buchnera–aphid mutualism.

Bacterial lineages have repeatedly evolved intimate symbioses with eukaryotic hosts, the most famous cases being those of the cell organelles, mitochondria, and plastids. Symbiont genomes typically lose many ancestral genes, raising the question of how they function with so few genes. In organelles, part of the answer involves gene transfer to the host genome, allowing maintenance of essential functions. So far, the extent of gene transfer to hosts has not been assessed for other cases of intimate, obligate symbiosis. Aphids harbor an ancient coevolved intracellular symbiont, called Buchnera. We used the newly available sequence of the pea aphid genome to conduct an exhaustive computational search for genes of bacterial ancestry. We found that no functional genes have been transferred from Buchnera, ruling out such transfer as a driving force in genome reduction in this symbiont. However, the aphid genome does contain eight transcribed genes of apparent bacterial origin, some of which have been duplicated after transfer. Based on their expression patterns, most of these appear to function specifically in the aphid-Buchnera symbiosis, presenting the possibility that the maintenance of obligate intracellular symbioses can be affected by the acquisition and duplication of genes transferred from unrelated bacterial lineages.

International Aphid Genomics Consortium. Genome sequence of the pea aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Genome sequence of the pea aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum

Buchnera aphidicola is the primary obligate intracellular symbiont of most aphid species. B. aphidicola and aphids have been evolving in parallel since their association started, about 150 Myr ago. Both partners have lost their autonomy, and aphid diversification has been confined to smaller ecological niches by this co-evolution. B. aphidicola has undergone major genomic and biochemical changes as a result of adapting to intracellular life. Several genomes of B. aphidicola from different aphid species have been sequenced in the last decade, making it possible to carry out analyses and comparative studies using system-level in silico methods. This review attempts to provide a systemic description of the symbiotic function of aphid endosymbionts, particularly of B. aphidicola from the pea aphid Acyrthosiphon pisum, by analyzing their structural genomic properties, as well as their genetic and metabolic networks.