@article {22966, title = {High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)}, journal = {BMC Genomics}, volume = {24}, year = {2023}, month = {08/2023}, pages = {443}, chapter = {443}, abstract = {

\"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).\"

}, keywords = {CHROMOSOMES, DNA, HEMARIS, HI-C, HYLES, KARYOLOGY, LAOTHOE, MACROGLOSSUM, MANDUCA, MERIAN ELEMENTS, MIMAS, MITOGENOME, PACBIO LONG READS, SPHINGIDAE, SYNTENY}, doi = {10.1186/s12864-023-09506-y}, url = {https://doi.org/10.1186/s12864-023-09506-y}, author = {Hundsdoerfer, A.K. and Schell, T. and Patzold, F. and Wright, C.J. and Yoshido, A. and Marec, F. and Danek, H. and Winkler, S. and Greve, C. and Podsiadlowski, L. and Hiller, M. and Pippel, M.} } @article {22915, title = {Rediscovery of Hyles svetlana Shovkoon, 2010 (Lepidoptera: Sphingidae) from Kyzyl-Kum desert, Uzbekistan}, journal = {Bonn Zoological Bulletin}, volume = {72}, year = {2023}, pages = {63-66}, chapter = {63}, abstract = {

\"Thirty-six years after the last published record of Hyles svetlana in Uzbekistan, we found the species at multiple locations in the Kyzl-Kum desert in 2022. Furthermore, we discovered larvae feeding on Eremurus anisopterus pointing to a possible oligophagous nature of H. svetlana, as described in early days, when it was still considered a desert population of H. centralasiae. We found phenotypes in both larva and imago of H. svetlana which appeared to be more similar to Hyles euphorbiae, giving rise to more questions regarding the relationships within the genus Hyles and the genetic identity of H. svetlana.\"

}, keywords = {FOODPLANT, HYLES, IMMATURE STAGES, LARVAL POLYMORPHISM, SPHINGIDAE, UZBEKISTAN, WING PATTERN}, url = {https://doi.org/10.20363/BZB-2023.72.1.063}, author = {Patzold, F. and Amirov, I. and Turg{\textquoteright}unboye, O. and Kholmatov, B. and Hundsdoerfer, A.K.} } @unpublished {22556, title = {High quality genomes corroborate 29 chromosomes of the haploid Hyles (Lepidoptera: Sphingidae) karyotype}, year = {2022}, pages = {1-47}, type = {Unpublished bioRxiv preprint}, abstract = {

\"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.

}, keywords = {CHROMOSOME ASSEMBLY, CHROMOSOMES, FISH ANALYSIS, GENOME ASSEMBLY, HYLES, SPHINGIDAE}, doi = {10.1101/2022.04.08.487644}, url = {https://doi.org/10.1101/2022.04.08.487644}, author = {Hundsdoerfer, A.K. and Schell, T. and Patzold, F. and Yoshido, A. and Marec, F. and Daneck, H. and Winkler, S. and Greve, C. and Hiller, M. and Pippel, M.} } @article {22271, title = {The phylogenetics and biogeography of the Central Asian hawkmoths, Hyles hippophaes and H. chamyla: Can mitogenomics and machine learning bring clarity?}, journal = {Diversity}, volume = {13}, year = {2021}, month = {05/2021}, pages = {213}, chapter = {213}, abstract = {

\"The western Palaearctic species of the hawkmoth genus Hyles (Lepidoptera: Sphingidae) have long been the subject of molecular phylogenetic research. However, much less attention has been paid to the taxa inhabiting the central and eastern Palaearctic, particularly Central Asia, where almost 50\% of the species diversity of the genus occurs. Yet, many taxonomic conundrums hinder a proper assessment of the true diversity in these moths. One still unresolved group of species includes Hyles hippophaes and Hyles chamyla. Despite a largely overlapping morphology and ecology, a plethora of infraspecific taxa display some unique divergent characters over a wide geographical area. In this study, we undertook a taxonomic assessment of each population and resolved this species complex using an integrative approach. A combination of new computational techniques (DAISY-II) in comparative morphology and recent advances in DNA extraction methods and sequencing of museum specimens (WISC) alongside more traditional genetic approaches allowed testing of the three main phenotypes\—bienerti, chamyla and apocyni\—in terms of their morphological, mitochondrial and biogeographical integrity, and to elucidate their evolutionary relationships. Our results support the existence of two closely related species, Hyles chamyla and H. hippophaes, but \“H. chamyla apocyni\” is best regarded as a hybrid between H. chamyla and H. h. bienerti. The results indicate that the evolutionary relationship between H. chamyla and H. hippophaes is one of admixture in the context of ongoing ecological differentiation, which has led to shared morphological characters and a blurring of the species boundaries. These results clarify the evolutionary relationships of this species complex and open future research lines, including the analysis of nuclear markers and denser sampling, particularly of H. hippophaes and H. vespertilio in western Europe.\"

}, keywords = {BIOGEOGRAPHY, CATALOGUE, CENTRAL ASIA, DAISY-II, DISTRIBUTION, DNA, HYBRIDS, HYLES, INTROGRESSION, MACHINE LEARNING; ARTIFICAL NEURAL NETWORKS, MAXIMUM LIKELIHOOD, MITOGENOME, MTDNA, PHYLOGENOMICS, PRINCIPAL COMPONENTS ANALYSIS, SPHINGIDAE, TCS NETWORKS, TYPES, WING PATTERN}, doi = {10.3390/d13050213}, url = {https://doi.org/10.3390/d13050213}, author = {Patzold, F. and Marabuto, E. and Daneck, H. and O{\textquoteright}Neill, M.A. and Kitching, I.J. and Hundsdoerfer, A.K.} } @article {22186, title = {Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens}, journal = {PLoS ONE}, volume = {17}, year = {2020}, month = {07/2020}, pages = {e0235222}, chapter = {e0235222}, abstract = {

\"Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch\® PCR \& DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.\"

}, keywords = {ADNA, COI, COII, DNA, EXTRACTION PROTOCOLS, HYLES, MAXIMUM LIKELIHOOD, METHODOLOGY, MTDNA, MUSEUM, NEXTGEN SEQUENCING, SAMPLING, SPHINGIDAE, TRNA(LEU), TYPES}, url = {https://doi.org/10.1371/journal.pone.0235222}, author = {Patzold, F. and Zilli, A. and Hundsdoerfer, A.K.} } @article {22089, title = {A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)}, journal = {GigaScience}, volume = {9}, year = {2020}, month = {01/2020}, pages = {giaa001 [10 pp.]}, chapter = {giaa001}, abstract = {

\"Background: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged \∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. Results: Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51\× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3\%) than other Bombycoidea species such as Bombyx mori (45.7\%) and Manduca sexta (27.5\%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5\% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2\%) and M. sexta (90\%) annotations. Conclusions: Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.\"

}, keywords = {BOMBYX, GENE ANNOTATION, GENOME ASSEMBLY, HYLES, ITALY, MANDUCA, PACBIO LONG READS, SPHINGIDAE, WORLDMAP1}, doi = {10.1093/gigascience/giaa001}, author = {Pippel, M. and Jebb, D. and Patzold, F. and Winkler, S. and Vogel, H. and Myers, G. and Hiller, M. and Hundsdoerfer, A.K.} }