Lab of Richard ffrench-Constant

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato.

PLoS Genet. 2010;6(2):e1000796

Authors: Counterman BA, Araujo-Perez F, Hines HM, Baxter SW, Morrison CM, Lindstrom DP, Papa R, Ferguson L, Joron M, Ffrench-Constant RH, Smith CP, Nielsen DM, Chen R, Jiggins CD, Reed RD, Halder G, Mallet J, McMillan WO

Wing pattern evolution in Heliconius butterflies provides some of the most striking examples of adaptation by natural selection. The genes controlling pattern variation are classic examples of Mendelian loci of large effect, where allelic variation causes large and discrete phenotypic changes and is responsible for both convergent and highly divergent wing pattern evolution across the genus. We characterize nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium (LD), and candidate gene expression patterns across two unlinked genomic intervals that control yellow and red wing pattern variation among mimetic forms of Heliconius erato. Despite very strong natural selection on color pattern, we see neither a strong reduction in genetic diversity nor evidence for extended LD across either patterning interval. This observation highlights the extent that recombination can erase the signature of selection in natural populations and is consistent with the hypothesis that either the adaptive radiation or the alleles controlling it are quite old. However, across both patterning intervals we identified SNPs clustered in several coding regions that were strongly associated with color pattern phenotype. Interestingly, coding regions with associated SNPs were widely separated, suggesting that color pattern alleles may be composed of multiple functional sites, conforming to previous descriptions of these loci as "supergenes." Examination of gene expression levels of genes flanking these regions in both H. erato and its co-mimic, H. melpomene, implicate a gene with high sequence similarity to a kinesin as playing a key role in modulating pattern and provides convincing evidence for parallel changes in gene regulation across co-mimetic lineages. The complex genetic architecture at these color pattern loci stands in marked contrast to the single casual mutations often identified in genetic studies of adaptation, but may be more indicative of the type of genetic changes responsible for much of the adaptive variation found in natural populations.

PMID: 20140239 [PubMed - in process]

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade.

PLoS Genet. 2010;6(2):e1000794

Authors: Baxter SW, Nadeau NJ, Maroja LS, Wilkinson P, Counterman BA, Dawson A, Beltran M, Perez-Espona S, Chamberlain N, Ferguson L, Clark R, Davidson C, Glithero R, Mallet J, McMillan WO, Kronforst M, Joron M, Ffrench-Constant RH, Jiggins CD

Wing patterning in Heliconius butterflies is a longstanding example of both Müllerian mimicry and phenotypic radiation under strong natural selection. The loci controlling such patterns are "hotspots" for adaptive evolution with great allelic diversity across different species in the genus. We characterise nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium, and candidate gene expression at two loci and across multiple hybrid zones in Heliconius melpomene and relatives. Alleles at HmB control the presence or absence of the red forewing band, while alleles at HmYb control the yellow hindwing bar. Across HmYb two regions, separated by approximately 100 kb, show significant genotype-by-phenotype associations that are replicated across independent hybrid zones. In contrast, at HmB a single peak of association indicates the likely position of functional sites at three genes, encoding a kinesin, a G-protein coupled receptor, and an mRNA splicing factor. At both HmYb and HmB there is evidence for enhanced linkage disequilibrium (LD) between associated sites separated by up to 14 kb, suggesting that multiple sites are under selection. However, there was no evidence for reduced variation or deviations from neutrality that might indicate a recent selective sweep, consistent with these alleles being relatively old. Of the three genes showing an association with the HmB locus, the kinesin shows differences in wing disc expression between races that are replicated in the co-mimic, Heliconius erato, providing striking evidence for parallel changes in gene expression between Müllerian co-mimics. Wing patterning loci in Heliconius melpomene therefore show a haplotype structure maintained by selection, but no evidence for a recent selective sweep. The complex genetic pattern contrasts with the simple genetic basis of many adaptive traits studied previously, but may provide a better model for most adaptation in natural populations that has arisen over millions rather than tens of years.

PMID: 20140188 [PubMed - in process]

Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence.

Insect Mol Biol. 2009 Nov 10;

Authors: Pauchet Y, Wilkinson P, Vogel H, Nelson DR, Reynolds SE, Heckel DG, Ffrench-Constant RH

Abstract The tobacco hornworm Manduca sexta is an important model for insect physiology but genomic and transcriptomic data are currently lacking. Following a recent pyrosequencing study generating immune related expressed sequence tags (ESTs), here we use this new technology to define the M. sexta larval midgut transcriptome. We generated over 387 000 midgut ESTs, using a combination of Sanger and 454 sequencing, and classified predicted proteins into those involved in digestion, detoxification and immunity. In many cases the depth of 454 pyrosequencing coverage allowed us to define the entire cDNA sequence of a particular gene. Many new M. sexta genes are described including up to 36 new cytochrome P450s, some of which have been implicated in the metabolism of host plant-derived nicotine. New lepidopteran gene families such as the beta-fructofuranosidases, previously thought to be restricted to Bombyx mori, are also described. An unexpectedly high number of ESTs were involved in immunity, for example 39 contigs encoding serpins, and the increasingly appreciated role of the midgut in insect immunity is discussed. Similar studies of other tissues will allow for a tissue by tissue description of the M. sexta transcriptome and will form an essential complimentary step on the road to genome sequencing and annotation.

PMID: 19909380 [PubMed - as supplied by publisher]

Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence.

Insect Mol Biol. 2009 Nov 10;

Authors: Pauchet Y, Wilkinson P, Vogel H, Nelson DR, Reynolds SE, Heckel DG, Ffrench-Constant RH

Abstract The tobacco hornworm Manduca sexta is an important model for insect physiology but genomic and transcriptomic data are currently lacking. Following a recent pyrosequencing study generating immune related expressed sequence tags (ESTs), here we use this new technology to define the M. sexta larval midgut transcriptome. We generated over 387 000 midgut ESTs, using a combination of Sanger and 454 sequencing, and classified predicted proteins into those involved in digestion, detoxification and immunity. In many cases the depth of 454 pyrosequencing coverage allowed us to define the entire cDNA sequence of a particular gene. Many new M. sexta genes are described including up to 36 new cytochrome P450s, some of which have been implicated in the metabolism of host plant-derived nicotine. New lepidopteran gene families such as the beta-fructofuranosidases, previously thought to be restricted to Bombyx mori, are also described. An unexpectedly high number of ESTs were involved in immunity, for example 39 contigs encoding serpins, and the increasingly appreciated role of the midgut in insect immunity is discussed. Similar studies of other tissues will allow for a tissue by tissue description of the M. sexta transcriptome and will form an essential complimentary step on the road to genome sequencing and annotation.

PMID: 19909380 [PubMed - as supplied by publisher]

Sex chromosome evolution in cotton stainers of the genus Dysdercus (Heteroptera: Pyrrhocoridae).

Cytogenet Genome Res. 2009;125(4):292-305

Authors: Bressa MJ, Papeschi AG, Vítková M, Kubícková S, Fuková I, Pigozzi MI, Marec F

The neo-X and neo-Y sex chromosomes of Dysdercus albofasciatus represent a unique model for the study of early stages of sex chromosome evolution since they retained the ability to pair and recombine, in contrast to sex chromosomes in most Heteroptera. Here we examined structure, molecular differentiation, and meiotic behaviour of the D. albofasciatus neo-sex chromosomes. Two related species with the ancestral X0 system, D. chaquensis and D. ruficollis, were used for a comparison. In D. albofasciatus, 2 nucleolar organizer regions (NORs) were identified on the neo-X chromosome using fluorescence in situ hybridization (FISH) with an rDNA probe, whereas a single NOR was found on an autosomal pair in the other 2 species. Genomic in situ hybridization (GISH) differentiated a part of the original X in the neo-X chromosome but not the neo-Y chromosome. The same segment of the neo-X chromosome was identified by Zoo-FISH with a chromosome painting probe derived from the X chromosome of D. ruficollis, indicating that this part is conserved between the species. Immunostaining against the cohesin subunit SMC3 revealed that only terminal regions of the D. albofasciatus neo-Xneo-Y bivalent pair and form a synaptonemal complex, which is in keeping with the occurrence of terminal chiasmata, whereas the interstitial region forms a large loop indicating the absence of homology. These results support the hypothesis that the neo-X chromosome evolved by insertion of the original X chromosome into 1 NOR-bearing autosome in an ancestor carrying the X0 system. As a consequence, the homologue of this NOR-autosome became the neo-Y chromosome. A subsequent inversion followed by transposition of the NOR located on the neo-Y onto the neo-X chromosome resulted in the present neo-sex chromosome system in D. albofasciatus.

PMID: 19864893 [PubMed - in process]

The insect toxin complex of Yersinia.

Adv Exp Med Biol. 2007;603:247-57

Authors: Waterfield N, Hares M, Hinchliffe S, Wren B, ffrench-Constant R

Many members of the Yersinia genus encode homologues of insect toxins first observed in bacteria that are insect pathogens such as Photorhabdus, Xenorhabdus and Serratia entomophila. These bacteria secrete high molecular weight insecticidal toxins comprised of multiple protein subunits, termed the Toxin Complexes or Tc's. In Photorhabdus three distinct Tc subunits are required for full oral toxicity in insects, that include the [A], [B] and [C] types, although the exact stochiometry remains unclear. The genomes of Photorhabdus strains encode multiple tc loci, although only two have been shown to exhibit oral and injectable activity against the Hawk Moth, Manduca sexta. The exact role of the remaining homologues is unclear. The availability of bacterial genome sequences has revealed the presence of tc gene homologues in many different species. In this chapter we review the tc gene homologues in Yersinia genus. We discuss what is known about the activity of the Yersinia Tc protein homologues and attempt to relate this to the evolution of the genus and of the tca gene family.

PMID: 17966421 [PubMed - indexed for MEDLINE]

Analysis of varicella zoster virus attenuation by evaluation of chimeric parent Oka/vaccine Oka recombinant viruses in skin xenografts in the SCIDhu mouse model.

Virology. 2005 Feb 5;332(1):337-46

Authors: Zerboni L, Hinchliffe S, Sommer MH, Ito H, Besser J, Stamatis S, Cheng J, Distefano D, Kraiouchkine N, Shaw A, Arvin AM

Varicella-zoster virus (VZV) is the only human herpes virus for which a vaccine has been licensed. A clinical VZV isolate, designated the parent Oka (pOka) strain was passed in human and non-human fibroblasts to produce vaccine Oka (vOka). The pOka and vOka viruses exhibit similar infectivity in cultured cells but healthy susceptible individuals given vaccines derived from vOka rarely develop the cutaneous vesicular lesions characteristic of varicella. Inoculation of skin xenografts in the SCIDhu mouse model of VZV pathogenesis demonstrated that vOka had a reduced capacity to replicate in differentiated human epidermal cells in vivo (Moffat, J.F., Zerboni, L., Kinchington, P.R., Grose, C., Kaneshima, H., Arvin A.M., 1998a. Attenuation of the vaccine Oka strain of varicella-zoster virus and role of glycoprotein C in alphaherpesvirus virulence demonstrated in the SCID-hu mouse. J Virol. 72:965-74). In order to investigate the attenuation of vOka in skin, we made chimeric pOka and vOka recombinant viruses from VZV cosmids. Six chimeric pOka/vOka viruses were generated using cosmid sets that incorporate linear overlapping fragments of VZV DNA from cells infected with pOka or vOka. The cosmid sets consist of pOka and vOka DNA segments that have identical restriction sites. As expected, the growth kinetics and plaque morphologies of the six chimeric pOka/vOka viruses were indistinguishable in vitro. However, the chimeric viruses exhibited varying capacities to replicate when evaluated in skin xenografts in vivo. The presence of ORFs 30-55 from the pOka genome was sufficient to maintain wild-type infectivity in skin. Chimeric viruses containing different vOka components retained the attenuation phenotype, suggesting that vOka attenuation is multi-factorial and can be produced by genes from different regions of the vOka genome.

PMID: 15661165 [PubMed - indexed for MEDLINE]

Construction of a Yersinia pestis microarray.

Adv Exp Med Biol. 2003;529:47-9

Authors: Stabler RA, Hinds J, Witney AA, Isherwood K, Oyston P, Titball R, Wren B, Hinchliffe S, Prentice M, Mangan JA, Butcher PD

PMID: 12756727 [PubMed - indexed for MEDLINE]

Construction of varicella-zoster virus recombinants from parent Oka cosmids and demonstration that ORF65 protein is dispensable for infection of human skin and T cells in the SCID-hu mouse model.

J Virol. 2003 May;77(10):6062-5

Authors: Niizuma T, Zerboni L, Sommer MH, Ito H, Hinchliffe S, Arvin AM

We generated an ORF65 deletion mutant by using a cosmid system constructed from the genome of a low-passage clinical isolate (P-Oka). Using the SCID-hu mouse model, we demonstrated that the ORF65 protein is dispensable for viral replication in skin and T cells, which are critical host cell targets during primary varicella-zoster virus infection.

PMID: 12719598 [PubMed - indexed for MEDLINE]

Mutational analysis of open reading frames 62 and 71, encoding the varicella-zoster virus immediate-early transactivating protein, IE62, and effects on replication in vitro and in skin xenografts in the SCID-hu mouse in vivo.

J Virol. 2003 May;77(10):5607-20

Authors: Sato B, Ito H, Hinchliffe S, Sommer MH, Zerboni L, Arvin AM

The varicella-zoster virus (VZV) genome has unique long (U(L)) and unique short (U(S)) segments which are flanked by internal repeat (IR) and terminal repeat (TR) sequences. The immediate-early 62 (IE62) protein, encoded by open reading frame 62 (ORF62) and ORF71 in these repeats, is the major VZV transactivating protein. Mutational analyses were done with VZV cosmids generated from parent Oka (pOka), a low-passage clinical isolate, and repair experiments were done with ORF62 from pOka and vaccine Oka (vOka), which is derived from pOka. Transfections using VZV cosmids from which ORF62, ORF71, or the ORF62/71 gene pair was deleted showed that VZV replication required at least one copy of ORF62. The insertion of ORF62 from pOka or vOka into a nonnative site in U(S) allowed VZV replication in cell culture in vitro, although the plaque size and yields of infectious virus were decreased. Targeted mutations in binding sites reported to affect interaction with IE4 protein and a putative ORF9 protein binding site were not lethal. Single deletions of ORF62 or ORF71 from cosmids permitted recovery of infectious virus, but recombination events repaired the defective repeat region in some progeny viruses, as verified by PCR and Southern hybridization. VZV infectivity in skin xenografts in the SCID-hu model required ORF62 expression; mixtures of single-copy recombinant Oka Delta 62 (rOka Delta 62) or rOka Delta 71 and repaired rOka generated by recombination of the single-copy deletion mutants were detected in some skin implants. Although insertion of ORF62 into the nonnative site permitted replication in cell culture, ORF62 expression from its native site was necessary for cell-cell spread in differentiated human skin tissues in vivo.

PMID: 12719553 [PubMed - indexed for MEDLINE]

ButterflyBase: a platform for lepidopteran genomics.

Nucleic Acids Res. 2008 Jan;36(Database issue):D582-7

Authors: Papanicolaou A, Gebauer-Jung S, Blaxter ML, Owen McMillan W, Jiggins CD

With over 100 000 species and a large community of evolutionary biologists, population ecologists, pest biologists and genome researchers, the Lepidoptera are an important insect group. Genomic resources [expressed sequence tags (ESTs), genome sequence, genetic and physical maps, proteomic and microarray datasets] are growing, but there has up to now been no single access and analysis portal for this group. Here we present ButterflyBase (http://www.butterflybase.org), a unified resource for lepidopteran genomics. A total of 273 077 ESTs from more than 30 different species have been clustered to generate stable unigene sets, and robust protein translations derived from each unigene cluster. Clusters and their protein translations are annotated with BLAST-based similarity, gene ontology (GO), enzyme classification (EC) and Kyoto encyclopaedia of genes and genomes (KEGG) terms, and are also searchable using similarity tools such as BLAST and MS-BLAST. The database supports many needs of the lepidopteran research community, including molecular marker development, orthologue prediction for deep phylogenetics, and detection of rapidly evolving proteins likely involved in host-pathogen or other evolutionary processes. ButterflyBase is expanding to include additional genomic sequence, ecological and mapping data for key species.

PMID: 17933781 [PubMed - indexed for MEDLINE]

Synteny and chromosome evolution in the lepidoptera: evidence from mapping in Heliconius melpomene.

Genetics. 2007 Sep;177(1):417-26

Authors: Pringle EG, Baxter SW, Webster CL, Papanicolaou A, Lee SF, Jiggins CD

The extent of conservation of synteny and gene order in the Lepidoptera has been investigated previously only by comparing a small subset of linkage groups between the moth Bombyx mori and the butterfly Heliconius melpomene. Here we report the mapping of 64 additional conserved genes in H. melpomene, which contributed 47 markers to a comparative framework of 72 orthologous loci spanning all 21 H. melpomene chromosomes and 27 of the 28 B. mori chromosomes. Comparison of the maps revealed conserved synteny across all chromosomes for the 72 loci, as well as evidence for six cases of chromosome fusion in the Heliconius lineage that contributed to the derived 21-chromosome karyotype. Comparisons of gene order on these fused chromosomes revealed two instances of colinearity between H. melpomene and B. mori, but also one instance of likely chromosomal rearrangement. B. mori is the first lepidopteran species to have its genome sequenced, and the finding that there is conserved synteny and gene order among Lepidoptera indicates that the genomic tools developed in B. mori will be broadly useful in other species.

PMID: 17603110 [PubMed - indexed for MEDLINE]

Genomic tools and cDNA derived markers for butterflies.

Mol Ecol. 2005 Aug;14(9):2883-97

Authors: Papanicolaou A, Joron M, McMillan WO, Blaxter ML, Jiggins CD

The Lepidoptera have long been used as examples in the study of evolution, but some questions remain difficult to resolve due to a lack of molecular genetic data. However, as technology improves, genomic tools are becoming increasingly available to tackle unanswered evolutionary questions. Here we have used expressed sequence tags (ESTs) to develop genetic markers for two Müllerian mimic species, Heliconius melpomene and Heliconius erato. In total 1363 ESTs were generated, representing 330 gene objects in H. melpomene and 431 in H. erato. User-friendly bioinformatic tools were used to construct a nonredundant database of these putative genes (available at http://www.heliconius.org), and annotate them with blast similarity searches, InterPro matches and Gene Ontology terms. This database will be continually updated with EST sequences for the Papilionideae as they become publicly available, providing a tool for gene finding in the butterflies. Alignments of the Heliconius sequences with putative homologues derived from Bombyx mori or other public data sets were used to identify conserved PCR priming sites, and develop 55 markers that can be amplified from genomic DNA in both H. erato and H. melpomene. These markers will be used for comparative linkage mapping in Heliconius and will have applications in other phylogenetic and genomic studies in the Lepidoptera.

PMID: 16029486 [PubMed - indexed for MEDLINE]

The insect toxin complex of Yersinia.

Adv Exp Med Biol. 2007;603:247-57

Authors: Waterfield N, Hares M, Hinchliffe S, Wren B, ffrench-Constant R

Many members of the Yersinia genus encode homologues of insect toxins first observed in bacteria that are insect pathogens such as Photorhabdus, Xenorhabdus and Serratia entomophila. These bacteria secrete high molecular weight insecticidal toxins comprised of multiple protein subunits, termed the Toxin Complexes or Tc's. In Photorhabdus three distinct Tc subunits are required for full oral toxicity in insects, that include the [A], [B] and [C] types, although the exact stochiometry remains unclear. The genomes of Photorhabdus strains encode multiple tc loci, although only two have been shown to exhibit oral and injectable activity against the Hawk Moth, Manduca sexta. The exact role of the remaining homologues is unclear. The availability of bacterial genome sequences has revealed the presence of tc gene homologues in many different species. In this chapter we review the tc gene homologues in Yersinia genus. We discuss what is known about the activity of the Yersinia Tc protein homologues and attempt to relate this to the evolution of the genus and of the tca gene family.

PMID: 17966421 [PubMed - indexed for MEDLINE]

The insecticidal toxin makes caterpillars floppy 2 (Mcf2) shows similarity to HrmA, an avirulence protein from a plant pathogen.

FEMS Microbiol Lett. 2003 Dec 12;229(2):265-70

Authors: Waterfield NR, Daborn PJ, Dowling AJ, Yang G, Hares M, ffrench-Constant RH

The Photorhabdus luminescens W14 toxin encoding gene makes caterpillars floppy (mcf) was discovered due to its ability to kill caterpillars when expressed in Escherichia coli. Here we describe a homologue of mcf (renamed as mcf1), termed mcf2, discovered in the same genome. The mcf2 gene predicts another large toxin whose central domain, like Mcf1, also shows limited homology to Clostridium cytotoxin B. However, the N-terminus of Mcf2 shows significant similarity to the type-III secreted effector HrmA from the plant pathogen Pseudomonas syringae and no similarity to the N-terminus of Mcf1. HrmA is a plant avirulence gene whose transient expression in tobacco cells results in cell death. Here we show that E. coli expressing Mcf2 can, like E. coli expressing Mcf1, kill insects. Further, expression of the c-Myc tagged N-terminus of Mcf2, the region showing similarity to HrmA, results in nuclear localisation of the fusion protein and subsequent destruction of transfected mammalian cells. The Mcf1 and Mcf2 toxins therefore belong to a family of high molecular mass toxins, differing at their N-termini, which encode different effector domains.

PMID: 14680709 [PubMed - indexed for MEDLINE]