A Second-Generation Integrated Map of the Silkworm Reveals Synteny and Conserved Gene Order Between Lepidopteran Insects

Yasukochi, Yuji; Ashakumary, Laksmikutty A.; Baba, Kohtaro; Yoshido, Atsuo; Sahara, Ken

doi:10.1534/genetics.106.055541

Cited by 67 publications

(85 citation statements)

References 23 publications

(35 reference statements)

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“…The development of nine H. armigera Z-linked markers in this study (Supplementary Table S2) was informed by previous reports of synteny in lepidopterans (Jiggins et al, 2005;Yasukochi et al, 2006;d'Alencon et al, 2010). Apt and Tpi have been established as Z-linked loci in multiple species, whereas the other loci were chosen because they were single-copy sequences that had 1:1 orthologs on B. mori Z-linked genes.…”

Section: Development Of Z-linked Epic Markersmentioning

confidence: 86%

“…Loci were chosen according to the following criteria: they were likely to be located on the Z chromosome, likely to be dispersed across the Z chromosome, we were confident in their gene models, their introns were of a size appropriate for reliable PCR amplification, and had flanking exon sequence conservation. We chose to examine Apt and Tpi because they had been reported to be Z-linked in Lepidoptera species (Jiggins et al, 2005;Yasukochi et al, 2006;d'Alencon et al, 2010). Two P450 genes were chosen but neither were expected to have a role in insecticide resistance as their orthologs have roles in development (Willingham and Keil, 2004;Feyereisen, 2005).…”

Section: Methodsmentioning

confidence: 99%

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High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Song¹,

Downes²,

Parker³

et al. 2015

Heredity

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Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of 'selective sweeps'. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci in three Australian H. armigera populations. We find that estimates of π are in the higher range among other insects and linkage disequilibrium decays over short distances. One of the surveyed loci, a cytochrome P450, shows an unusual haplotype configuration with a divergent allele at high frequency that led us to investigate the possibility of an adaptive introgression around this locus.

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Section: Development Of Z-linked Epic Markersmentioning

confidence: 86%

Section: Methodsmentioning

confidence: 99%

High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Song¹,

Downes²,

Parker³

et al. 2015

Heredity

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show abstract

“…Bacterial artificial chromosomes (BACs) used for FISH analysis were described by Yasukochi et al (2006) (Table 1). We selected additional 4D3C and 3C11C BACs for the present study (Table 1).…”

Section: Fish Analysismentioning

confidence: 99%

Mapping and recombination analysis of two moth colour mutations, Black moth and Wild wing spot, in the silkworm Bombyx mori

et al. 2015

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Many lepidopteran insects exhibit body colour variations, where the high phenotypic diversity observed in the wings and bodies of adults provides opportunities for studying adaptive morphological evolution. In the silkworm Bombyx mori, two genes responsible for moth colour mutation, Bm and Ws, have been mapped to 0.0 and 14.7 cM of the B. mori genetic linkage group 17; however, these genes have not been identified at the molecular level. We performed positional cloning of both genes to elucidate the molecular mechanisms that underlie the moth wing-and body-colour patterns in B. mori. We successfully narrowed down Bm and Ws to~2-Mb-long and 100-kb-long regions on the same scaffold Bm_scaf33. Gene prediction analysis of this region identified 77 candidate genes in the Bm region, whereas there were no candidate genes in the Ws region. Fluorescence in-situ hybridisation analysis in Bm mutant detected chromosome inversion, which explains why there are no recombination in the corresponding region. The comparative genomic analysis demonstrated that the candidate regions of both genes shared synteny with a region associated with wing-and body-colour variations in other lepidopteran species including Biston betularia and Heliconius butterflies. These results suggest that the genes responsible for wing and body colour in B. mori may be associated with similar genes in other Lepidoptera.

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“…This sample is concentrated on species within the Papilionoidea (Heliconius spp. (Jiggins et al, 2005;Kapan et al, 2006;The Heliconius Genome Consortium, 2012), Bicyclus anynana ( Van't Hof et al, 2008;Beldade et al, 2009), Colias hybrid (Wang and Porter, 2004), Papilio hybrid (Winter and Porter, 2010)) and one other macrolepidopteran, Bombyx mori (Bombycoidea) (Yasukochi et al, 2006;Yamamoto et al, 2008). Linkage maps are also available for two other distantly related superfamilies, Pyraloidea (Ostrinia nubilalis; Dopman et al, 2004) and Yponomeutoidea (Plutella xylostella (Heckel et al, 1999;Baxter et al, 2011)).…”

Section: Introductionmentioning

confidence: 99%

Linkage map of the peppered moth, Biston betularia (Lepidoptera, Geometridae): a model of industrial melanism

et al. 2012

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We have constructed a linkage map for the peppered moth (Biston betularia), the classical ecological genetics model of industrial melanism, aimed both at localizing the network of loci controlling melanism and making inferences about chromosome dynamics. The linkage map, which is based primarily on amplified fragment length polymorphisms (AFLPs) and genes, consists of 31 linkage groups (LGs; consistent with the karyotype). Comparison with the evolutionarily distant Bombyx mori suggests that the gene content of chromosomes is highly conserved. Gene order is conserved on the autosomes, but noticeably less so on the Z chromosome, as confirmed by physical mapping using bacterial artificial chromosome fluorescence in situ hybridization (BAC-FISH). Synteny mapping identified three pairs of B. betularia LGs (11/29, 23/30 and 24/31) as being orthologous to three B. mori chromosomes (11, 23 and 24, respectively). A similar finding in an outgroup moth (Plutella xylostella) indicates that the B. mori karyotype (n ¼ 28) is a phylogenetically derived state resulting from three chromosome fusions. As with other Lepidoptera, the B. betularia W chromosome consists largely of repetitive sequence, but exceptionally we found a W homolog of a Z-linked gene (laminin A), possibly resulting from ectopic recombination between the sex chromosomes. The B. betularia linkage map, featuring the network of known melanization genes, serves as a resource for melanism research in Lepidoptera. Moreover, its close resemblance to the ancestral lepidopteran karyotype (n ¼ 31) makes it a useful reference point for reconstructing chromosome dynamic events and ancestral genome architectures. Our study highlights the unusual evolutionary stability of lepidopteran autosomes; in contrast, higher rates of intrachromosomal rearrangements support a special role of the Z chromosome in adaptive evolution and speciation.

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A Second-Generation Integrated Map of the Silkworm Reveals Synteny and Conserved Gene Order Between Lepidopteran Insects

Cited by 67 publications

References 23 publications

High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Mapping and recombination analysis of two moth colour mutations, Black moth and Wild wing spot, in the silkworm Bombyx mori

Linkage map of the peppered moth, Biston betularia (Lepidoptera, Geometridae): a model of industrial melanism

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