Cryptic, extensive and non-random chromosome reorganization revealed by a butterfly chromonome

Abstract

Taxonomic orders vary in their degree of chromosomal conservation with some having high rates of chromosome number turnover despite maintaining some core sets of ordered genes (e.g. Mammalia) and others exhibiting rapid rates of gene-order reshuffling without changing chromosomal count (e.g. Diptera). However few clades exhibit as much conservation as the Lepidoptera for which both chromosomal count and gene colinearity (synteny) are very high over the past 140 MY. In contrast, here we report extensive chromosomal rearrangements in the genome of the green-veined white butterfly (Pieris napi, Pieridae, Linnaeus, 1758). This unprecedented reshuffling is cryptic: microsynteny and chromosome number do not indicate the extensive rearrangement revealed by a chromosome level assembly and high-resolution linkage map.Furthermore, the rearrangement blocks themselves appear to be non-random, as they are significantly enriched for clustered groups of functionally annotated genes revealing that the evolutionary dynamics acting on Lepidopteran genome structure are more complex than previously envisioned.

The molecular genetic basis of herbivory between butterflies and their host plants

“…We began our butterfly GWAS by assembling a high-quality reference genome sequence for the Cabbage White butterfly, Pieris rapae . For the reference genome, we combined next-generation DNA sequencing data from one PCR-free paired-end Illumina library, three mate-pair libraries (3 kbp, 7 kbp, 40 kbp), a Dovetail Chicago library, and information from the genome assembly of a closely related species, Pieris napi 22 , to generate an assembly of 323 Mbp, with a N50 of 11.5 Mbp, spanning the 25 P. rapae chromosomes 23 (Supplementary Figs. 1 and 2).…”

“…If there was a partial overlap, the smaller scaffold was broken and the unique fragment was placed adjacent to the larger scaffold (details in Supplementary Material finalPrapae.agp). Chromosomal relationships of scaffolds were inferred from alignment using LAST (version 714) 61 to the chromosomal structure of a closely related species Pieris napi 22 (Supplementary Fig. 1), and validated with scaffold junction spanning mate pair and syntenic blocks (Supplementary Fig.…”

The determinants of genetic diversity in butterflies – Lewontin’s paradox revisited

“…However, what is cause and effect is far from clear and chromosome number may itself depend on the efficacy of selection. Recently Hill et al [40] found that chromosomes in Pieris napi are derived from multiple ancestral syntenic blocks, suggesting a series of fission events that was followed by the creation of a novel chromosome organisation through fusions. Because P. napi returned to a karyotype close to the ancestral n c = 31 of butterflies, there appears to be some selective advantage in organising the genome this way, and chromosome rearrangements that produce karyotypes distant from n c = 31 may only be tolerated when N e s < 1.…”