@article {22984, title = {Chromosomal-level genome assembly of the Coffee Bee Hawk Moth reveals the evolution of chromosomes and the molecular basis of distinct phenotypes}, journal = {Genome Biology and Evolution}, volume = {15}, year = {2023}, month = {09/2023}, pages = {evad141}, chapter = {evad141}, abstract = {

\"Cephonodes hylas, the coffee bee hawk moth is a hawk moth species with unique characteristics, such as larvae feeding on gardenia, overcoming the toxicity of its iridoid glycosides, diurnal adults, and transparent wings. Although C. hylas is a fascinating model for molecular biological research, genome sequence analysis-based genetic approaches to elucidate these peculiarities have not yet been undertaken. We successfully achieved de novo genome assembly at the chromosome level of C. hylas comparable to the Lepidoptera model organism, silkworm. Additionally, 16,854 protein-coding genes were annotated, and the constructed genome sequence and annotated genes were of the highest quality BUSCO completion compared to closely related species. Comparative genome analysis revealed the process of chromosomal evolution from the Bombycoidea ancestral (n = 31) genome and changes in turnover at the chromosome level associated with chromosomal fusion events, such as the rate of repetitive sequence insertion. These analyses were only possible because the genome was constructed at the chromosome level. Additionally, increased the nonsynonymous/synonymous rate (dN/dS) ratios were observed in multiple photoreceptor-related genes that were strongly associated with the acquisition of diurnal activity. Furthermore, tandemly duplicated expanded genes containing many digestive and other enzymes and larval midgut-specific expression were also confirmed. These genes may be involved in the metabolism of genipin, a toxin found in gardenias. Using the genome sequence of C. hylas determined at the chromosome level, we have successfully identified new insights into the chromosomal evolution of Bombycoidea, as well as the relationship between the genome sequence and its characteristic traits.\"

}, keywords = {CEPHONODES, CHROMOSOME ASSEMBLY, CHROMOSOMES, DETOXIFICATION, DIURNALISM, EVOLUTION, FOODPLANT CHEMISTRY, FOODPLANT SPECIFICITY, GENOME ASSEMBLY, HYLES, MANDUCA, OPSIN, SPHINGIDAE, WING TRANSPARENCY}, url = {https://doi.org/10.1093/gbe/evad141}, author = {Yamabe, T. and Kajitani, R. and Toyoda, A. and Itoh, T.} } @unpublished {22556, title = {High quality genomes corroborate 29 chromosomes of the haploid Hyles (Lepidoptera: Sphingidae) karyotype}, year = {2022}, pages = {1-47}, type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 {22519, title = {The genome sequence of the small elephant hawk moth, Deilephila porcellus (Linnaeus, 1758) [version 1; peer review: 2 approved]}, journal = {Wellcome Open Research 2021}, volume = {7}, year = {2021}, month = {03/2022}, pages = {80}, chapter = {80}, abstract = {

\"We present a genome assembly from an individual male Deilephila porcellus (the small elephant hawk moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 402 megabases in span. The majority of the assembly (99.99\%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled.\"

}, keywords = {CHROMOSOME ASSEMBLY, DARWIN TREE OF LIFE, DEILEPHILA, GENOME ASSEMBLY, SPHINGIDAE, WORLDMAP1}, doi = {10.12688/wellcomeopenres.17740.1}, url = {https://wellcomeopenresearch.org/articles/7-80/v1}, author = {Boyes, D. and et al.} } @article {22519, title = {The genome sequence of the lime hawk-moth, Mimas tiliae (Linnaeus, 1758) [version 1; peer review: 2 approved]}, journal = {Wellcome Open Research 2021}, volume = {6}, year = {2021}, month = {12/2021}, pages = {357}, chapter = {357}, abstract = {

\"We present a genome assembly from an individual male Mimas tiliae (the lime hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 478 megabases in span. The complete assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled.\"

}, keywords = {CHROMOSOME ASSEMBLY, DARWIN TREE OF LIFE, GENOME ASSEMBLY, MIMAS, SPHINGIDAE, WORLDMAP1}, doi = {10.12688/wellcomeopenres.17485.1}, url = {https://wellcomeopenresearch.org/articles/6-357/v1}, author = {Boyes, D. and Holland, P.W.H. and et al.} } @unpublished {22213, title = {De novo genome assembly of the Tobacco Hornworm moth ( Manduca sexta)}, year = {2020}, month = {08/2020}, pages = {1-18}, type = {Unpublished preprint}, abstract = {

\"The Tobacco hornworm, Manduca sexta, is a lepidopteran insect that is used extensively as a model system for studying insect biology, development, neuroscience and immunity. However, current studies rely on the highly fragmented reference genome Msex_1.0, which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present the new reference genome for M. sexta , JHU_Msex_v1.0, applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly is 470 Mb and is ~20x more continuous than the original assembly, with scaffold N50 \>14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of the M. sexta genome improves resequencing studies and benefits future research on M. sexta as a model organism.\"

}, keywords = {CHROMOSOME ASSEMBLY, GENE ANNOTATION, GENOME ASSEMBLY, MANDUCA, METAMORPHOSIS, MIDGUT, MINION, NOVASEQ, SPHINGIDAE}, url = {https://doi.org/10.1101/2020.08.29.270983}, author = {Gershman, A. and Romer, T.G. and Fan, Y. and Razaghi, R. and Smith, W.A. and Timp, W.} }