Research ArticleEVOLUTIONARY BIOLOGY

Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution

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Science Advances  12 Jun 2019:
Vol. 5, no. 6, eaau3648
DOI: 10.1126/sciadv.aau3648
  • Fig. 1 Chromosomal mapping of the moth B. mori (Bombycoidea) to the butterflies P. napi (Pieridae), H. melpomene, and M. cinxia (Nymphalidae).

    (A) SCOs connecting B. mori to P. napi (n = 2354), M. cinxia (n = 2086), and H. melpomene (n = 2771). The Z chromosome is chromosome 1 in B. mori and P. napi and chromosome 21 in H. melpomene. Links between orthologs originate from B. mori and are colored by their chromosome of origin, and then extend to P. napi (colored green), M. cinxia (colored orange), and H. melpomene chromosomes (colored blue). Links are clustered into blocks of synteny, forming colored ribbons that represent a contiguous block of genes spanning a region in both species. Chromosomes 2 to 25 in P. napi are ordered in size from largest to smallest. (B) SCOs between the two largest autosomes of P. napi and the other Lepidoptera highlight the former’s derived chromosomal translocation events. Here, band width for each species is proportional to the length of the inferred chromosomal region of orthology with white space indicating regions with homology to other chromosomes not shown. Individual chromosomes are not to scale.

  • Fig. 2 Validation of the largest four P. napi chromosomes.

    Within each, the x axis indicates physical distance in megabase. (A) Mate pair spanning depth (MPSD) is shown across each chromosome, summed from the 3-, 7-, and 40-kb libraries (genome average = 1356). Of the scaffold join positions, 74 of 97 were each spanned by >50 properly paired reads (mean = 117.8; SD = 298.7), while the remaining 23 scaffold joins had 0 MP spans. (B) Black dots represent the linkage map markers [restriction site-associated DNA sequencing (RAD-seq) data] and their recombination distance in centimorgans (cM) along chromosomes (i.e., this is the linkage map). (C) Results from the female marker map of maternally inherited markers (RNA sequencing and whole-genome data), where all markers within a chromosome are completely linked owing to suppressed recombination in females (thus, recombination distance is not shown in the y axis). (D) B. mori collinear blocks, colored and labeled by their chromosomal origin, as in Fig. 1A, along with orientation in B. mori indicated by an arrow with its head toward the nearest telomere. (E) P. napi scaffolds comprising each chromosome, labeled to indicate scaffold number and orientation. (F) To the right of each P. napi chromosome is a Circos plot showing the location and orientation of the collinear blocks from each B. mori donor chromosome that comprise a given P. napi chromosome, colored as in Fig. 1A. A twist in the ribbon indicates a reversal of the 5′ to 3′ orientation of the B. mori relative to the P. napi chromosomes. Ribbon width on the P. napi chromosome is relative to the size of the collinear block. The remaining chromosomes are shown in fig. S1.

  • Fig. 3 Comparative assessment of genome assemblies and chromosomal evolution across the Lepidoptera.

    (A) A time-calibrated phylogeny of the currently available lepidopteran genomes (n = 24), with branches colored by the N50 of their assemblies and time in million years ago. (B) Table of the genome assembly N50 for each species, followed by estimates of their chromosomal similarity relative to B. mori versus P. napi. In each scaffold of each genome, SCOs were identified that were shared with B. mori and P. napi. Then, we quantified the number of times a scaffold contained SCOs derived from >1 chromosome of B. mori, but from a single P. napi chromosome (Pnapi-like scaffold), or vice versa (Bmori-like scaffold), or both from one chromosome (similar) (fig. S3 and note S9). Three additional P. napi genomes are included, representing the original Allpaths assembly that used only 3- and 7-kb MP libraries [Pieris napi (3, 7 kb)], the Allpaths assembly after an additional round of scaffolding with 40-kb MP libraries [Pieris napi (3, 7, and 40 kb)], and then the 40-kb scaffolded assembly scaffolded a third time and error-corrected with HiC libraries and the HiRise pipeline [Pieris napi (3, 7, and 40 kb)]. Higher Pn-like values indicate support for a P. napi–like chromosomal structure (see note S11 for more details). For a complementary BLAST-like approach, see fig. S9.

  • Fig. 4 Haploid chromosomal evolution across Pieridae.

    Shown in the center is a genus-level phylogeny for Pieridae, colored by the ancestral state reconstruction of the chromosomal fusion and fission events giving rise to the haploid chromosome counts of the taxa, whose values are represented as a bar plot (n = 201 species). As only a time-calibrated genus-level phylogeny exists for Pieridae, all genera with >1 species were set to an arbitrary polytomy at 5 million years ago, while deeper branches reflect calibrated nodes. The outgroup is set to n = 31, reflecting the butterfly chromosomal mode. Note that while the color scale stops at 50, members of the Leptidea clade exceed this value.

  • Fig. 5 Comparison of gene content and chromosomal location of collinear blocks between P. napi and B. mori in observed and randomly permuted genomes.

    (A) Observed pattern of conserved collinear block location within P. napi chromosome 9, wherein telomere-facing and interior origins of the syntenic blocks are conserved between species despite their reshuffling. (B) Percentage distance from the end (DFE) of SCOs in P. napi versus B. mori chromosomes. Counts binned on the color axis. (C) Comparisons of the number of collinear blocks that are terminal in both P. napi and B. mori chromosomes (n = 18, red line), compared to 10,000 simulated genomes composed of randomly joined collinear blocks that would be expected in a fission/fusion scenario (histogram: average = 10.7; SD = 6.8). (D) Distribution of number of syntenic blocks with GO term enrichment in 10,000 simulated genomes. Simulated syntenic blocks were constructed by breaking the P. napi genome into blocks of the same size as observed but in a random order. The mean number of GO-enriched fragments in each of the simulated 10,000 genomes was 38.8 with a variance of 46.6 and maximum of 52. This is significantly lower than the observed 57 enriched regions in P. napi (P < 0.0001).

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/6/eaau3648/DC1

    Note S1. Genome assembly, mtDNA assembly, HaploMerger results, and BUSCO analysis.

    Note S2. HiRise scaffolding and misassembly correction.

    Note S3. Linkage group correction of misassemblies.

    Note S4. Functional annotation summary.

    Note S5. RBH of orthologs.

    Note S6. Whole-genome sequencing and RNA-based linkage map.

    Note S7. MP spanning.

    Note S8. Alignment between P. napi and P. rapae.

    Note S9. Syntenic block support of scaffold joins.

    Note S10. SNP generation from nextRAD library sequence.

    Note S11. Comparison of P. napi versus B. mori collinear blocks within Lepidoptera genomes.

    Note S12. Estimation of genomic rearrangements.

    Note S13. Lepidopteran synteny cutoff selection.

    Table S1. Read data used in assembly and analysis.

    Table S2. Genomic data from Lepbase used in the comparative assessment of genome assemblies.

    Table S3. Lepidopteran phylogeny calibrations.

    Table S4. GO term enrichment in syntenic blocks.

    Fig. S1. Chromosomal assembly validation figures.

    Fig. S2. Alignment of P. rapae scaffolds to P. napi chromosomes.

    Fig. S3. Example of criteria used to determine napi-like and mori-like joins.

    Fig. S4. Permutation analysis of chromosomal terminal ends.

    Fig. S5. Repetitive element distribution across chromosomes.

    Fig. S6. Insert size distribution.

    Fig. S7. The mtDNA of P. napi.

    Fig. S8. Chronogram of lepidopteran genomes with node labels.

    Fig. S9. Comparative assessment of genome assemblies and chromosomal evolution across, using a BLAST-like approach.

    References (6985)

  • Supplementary Materials

    The PDF file includes:

    • Note S1. Genome assembly, mtDNA assembly, HaploMerger results, and BUSCO analysis.
    • Note S2. HiRise scaffolding and misassembly correction.
    • Note S3. Linkage group correction of misassemblies.
    • Legend for note S4
    • Note S5. RBH of orthologs.
    • Note S6. Whole-genome sequencing and RNA-based linkage map.
    • Note S7. MP spanning.
    • Note S8. Alignment between P. napi and P. rapae.
    • Note S9. Syntenic block support of scaffold joins.
    • Note S10. SNP generation from nextRAD library sequence.
    • Note S11. Comparison of P. napi versus B. mori collinear blocks within Lepidoptera genomes.
    • Note S12. Estimation of genomic rearrangements.
    • Note S13. Lepidopteran synteny cutoff selection.
    • Table S1. Read data used in assembly and analysis.
    • Legend for table S2
    • Table S3. Lepidopteran phylogeny calibrations.
    • Legend for table S4
    • Fig. S1. Chromosomal assembly validation figures.
    • Fig. S2. Alignment of P. rapae scaffolds to P. napi chromosomes.
    • Fig. S3. Example of criteria used to determine napi-like and mori-like joins.
    • Fig. S4. Permutation analysis of chromosomal terminal ends.
    • Fig. S5. Repetitive element distribution across chromosomes.
    • Fig. S6. Insert size distribution.
    • Fig. S7. The mtDNA of P. napi.
    • Fig. S8. Chronogram of lepidopteran genomes with node labels.
    • Fig. S9. Comparative assessment of genome assemblies and chromosomal evolution across, using a BLAST-like approach.
    • References (6985)

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • Note S4 (.zip format). Functional annotation summary.
    • Table S2 (Microsoft Excel format). Genomic data from Lepbase used in the comparative assessment of genome assemblies.
    • Table S4 (.tsv format). GO term enrichment in syntenic blocks.

    Files in this Data Supplement:

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