| 1. |
- Ahola, Virpi, et al.
(author)
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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
- 2014
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4737-
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Journal article (peer-reviewed)abstract
- Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
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| 2. |
- Neethiraj, Ramprasad, et al.
(author)
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Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach : New insights into the genetics underlying colour variation in diverse taxa
- 2017
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 26:19, s. 4990-5002
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Journal article (peer-reviewed)abstract
- While large-scale genomic approaches are increasingly revealing the genetic basis of polymorphic phenotypes such as colour morphs, such approaches are almost exclusively conducted in species with high-quality genomes and annotations. Here, we use Pool-Seq data for both genome assembly and SNP frequency estimation, followed by scanning for F-ST outliers to identify divergent genomic regions. Using paired-end, short-read sequencing data from two groups of individuals expressing divergent phenotypes, we generate a de novo rough-draft genome, identify SNPs and calculate genomewide F-ST differences between phenotypic groups. As genomes generated by Pool-Seq data are highly fragmented, we also present an approach for super-scaffolding contigs using existing protein-coding data sets. Using this approach, we reanalysed genomic data from two recent studies of birds and butterflies investigating colour pattern variation and replicated their core findings, demonstrating the accuracy and power of a Pool-Seq-only approach. Additionally, we discovered new regions of high divergence and new annotations that together suggest novel parallels between birds and butterflies in the origins of their colour pattern variation.
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| 3. |
- Hill, Jason, et al.
(author)
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Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution
- 2019
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In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:6
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Journal article (peer-reviewed)abstract
- Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.
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