03721nas a2200445 4500008004100000245014500041210007100186260001200257300000800269490000700277520254300284653001602827653000802843653001202851653000902863653001002872653001402882653001202896653001702908653001202925653002002937653001002957653001502967653002202982653001503004653001203019100002303031700001503054700001603069700001703085700001603102700001403118700001403132700001603146700001403162700002203176700001503198700001503213856004703228 2023 eng d00aHigh‑quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)0 aHigh‑quality haploid genomes corroborate 29 chromosomes and high c08/2023 a4430 v243 a

"Background

Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics.

Results

The genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function.
 

Conclusions

Our two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae)."

10aCHROMOSOMES10aDNA10aHEMARIS10aHI-C10aHYLES10aKARYOLOGY10aLAOTHOE10aMACROGLOSSUM10aMANDUCA10aMERIAN ELEMENTS10aMIMAS10aMITOGENOME10aPACBIO LONG READS10aSPHINGIDAE10aSYNTENY1 aHundsdoerfer, A.K.1 aSchell, T.1 aPatzold, F.1 aWright, C.J.1 aYoshido, A.1 aMarec, F.1 aDanek, H.1 aWinkler, S.1 aGreve, C.1 aPodsiadlowski, L.1 aHiller, M.1 aPippel, M. uhttps://doi.org/10.1186/s12864-023-09506-y02107nas a2200289 4500008004100000245010900041210006900150300000900219520128100228653002401509653001601533653001801549653002001567653001001587653001501597100002301612700001501635700001601650700001601666700001401682700001501696700001601711700001401727700001501741700001501756856004601771 2022 eng d00aHigh quality genomes corroborate 29 chromosomes of the haploid Hyles (Lepidoptera: Sphingidae) karyotype0 aHigh quality genomes corroborate 29 chromosomes of the haploid H a1-473 a

"FISH analysis of the karyotype revealed n = 29 chromosomes in Hyles euphorbiae. The measured genome sizes of H. euphorbiae and H. vespertilio are estimated to have average 1C DNA values of 472 and 562 Mb respectively. The H. euphorbiae genome was PacBio sequenced and amended by Hi-C Illumina data yielding a 504Mb assembly with a scaffold N50 of 18.2 Mb and 99.9% of the data being represented by the 29 largest scaffolds, corroborating the haploid karyotype. Chromosome length estimations based on karyotype image data provide an additional quality metric of the assembled chromosome sizes. Hi-C data was also used for chromosome-level scaffolding of the published H. vespertilio genome, leading to a second assembly (651 Mb) with scaffold N50 of 22 Mb, 98% in the 29 largest scaffolds representing the chromosomes. The larger H. vespertilio genome size was accompanied by a proportional increase of repeats from 45% in H. euphorbiae to nearly 55% in H. vespertilio.
In both Hyles species, the three wing pattern genes, optix, wingless/wint-1 and cortex, were found on chromosomes 23, 4 and 17, respectively. Peaks of divergence surrounding wingless/wnt-1 and cortex provide candidate genomic areas in which wing patterns are determined in this genus.

10aCHROMOSOME ASSEMBLY10aCHROMOSOMES10aFISH ANALYSIS10aGENOME ASSEMBLY10aHYLES10aSPHINGIDAE1 aHundsdoerfer, A.K.1 aSchell, T.1 aPatzold, F.1 aYoshido, A.1 aMarec, F.1 aDaneck, H.1 aWinkler, S.1 aGreve, C.1 aHiller, M.1 aPippel, M. uhttps://doi.org/10.1101/2022.04.08.487644