The first complete genomes of Metalmarks and the classification of butterfly families

Abstract

Sequencing complete genomes of all major phylogenetic groups of organisms opens unprecedented opportunities to study evolution and genetics. We report draft genomes of Calephelis nemesis and Calephelis virginiensis, representatives of the family Riodinidae. They complete the genomic coverage of butterflies at the family level. At 809 and 855 Mbp, respectively, they become the largest available Lepidoptera genomes. Comparison of butterfly genomes shows that the divergence between Riodinidae and Lycaenidae dates to the time when other families started to diverge into subfamilies. Thus, Riodinidae may be considered a subfamily of Lycaenidae. Calephelis species exhibit unique gene expansions in actin-disassembling factor, cofilin, and chitinase. The functional implications of these gene expansions are not clear, but they may aid molting of caterpillars covered in extensive setae. The two Calephelis species diverged about 5 million years ago and they differ in proteins involved in metabolism, circadian clock, regulation of development, and immune responses.

Molecular Phylogeny and Historical Biogeography of the Butterfly Tribe Aeromachini Tutt (Lepidoptera: Hesperiidae) from China

“…Butterfly fossils are very rare and only 48 fossil butterfly species are named so far [31], making up a very low proportion of the total fossil record. The ages of butterflies and butterfly divergence time inferred in most previous studies are very different based on their calibrations on these few fossils [29,53,54,55,56]. The results of this study indicate that, although the first divergence time of the tribe Aeromachini (43 Mya) is earlier than the previously estimated times at 34 Mya, the ages of major evolutionary events in the taxa are consistent with previous studies [18].…”

Genomics of a complete butterfly continent

“…We sequenced and annotated 23 reference genomes of butterflies from the United States. Combined with the 13 genomes published previously (3)(4)(5)(6)(7)(8)(9)(10)(11)(20)(21)(22)(23)) (8 by our group), a total of 36 reference genomes are used in this study. The N50 of the new genomic assemblies ranges from 50 to 3,700 kb, and they are over 95% complete in essential genes (24) ( Table 1).…”

“…We annotated protein-coding genes using three approaches: homology-based, transcript-based, and de novo gene prediction. We used protein sets from Papilio machaon (21), Pieris rapae (9), Calycopis cecrops (10), Calephelis nemesis (8), Danaus plexippus (4), Cecropterus lyciades (7), Bombyx mori (87), and Drosophila melanogaster (88) as references for homology-based annotation. These references include one species from each of the 6 butterfly families and the established model organisms, silkworm and fruit fly with expected high quality of gene models.…”

“…Therefore, we replaced the clades for each family in these trees with the trees constructed for each individual butterfly family using python ETE3 module (109) to generate the USC butterfly trees used in this study. These trees were rescaled as previously described (39,110) and the time axis was added to the tree constructed from all nuclear genes based on our published calibration (8) to match the ages of common nodes between the current and previous trees.…”

Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae)

“…Armed with these new methods, researchers can obtain nearly complete genomes of butterflies at a price they paid for only a dozen gene markers a decade ago [6][7][8][9][10][11][12]. Half a billion base pairs of genomic sequence dwarf several thousand base pairs of gene markers, and are more successful at distillation of phylogenetic signal from the noise of homoplasies [13].…”