Abstract The dramatic transition to parthenogenetic reproduction is often accompanied by similarly dramatic changes in genome organisation. Genomic changes may precede or succeed the onset of parthenogenesis and may directly or indirectly contribute to the success of this reproductive transition and fitness of parthenogenetic animals. To gain greater understanding of these changes, we combined cytogenetic and comparative analyses to document variation in heterochromatin and large-scale rearrangements among 18 strains of Drosophila mercatorum capable of varying degrees of parthenogenetic reproduction. This revealed that element F is 4.4-fold larger (95% confidence interval 4.0–4.8) in strains capable of parthenogenesis but that multiple large chromosomal inversions (2.8–9 megabases) on element B likely arose earlier. We combined phylogenetic analysis with comparisons of these genomic changes and parthenogenetic ability in D. mercatorum strains collected in South America, North America, Hawaii, and Africa. This indicated that the heterochromatin expansion has arisen once and appears to gradually increase with the rate of parthenogenetic ability. However, since this increase was also present in obligate sexually reproducing strains, heterochromatin expansion was not a consequence of parthenogenesis. It is therefore possible that heterochromatin expansion and parthenogenetic ability are unrelated but are carried together; that a shared underlying mechanism promotes both; or that heterochromatin expansion itself drives the capacity for parthenogenetic reproduction.
Abstract Evaluation of genome size has been extensively used in different fields. In many studies, it has been employed to test correlation with other parameters such as metabolic rates, longevity, and ecological/geographical distribution. Moreover, genome size assessed with cytometrical methods can be useful to evaluate the completeness of genome assemblies. In this latter case, knowledge of the accuracy of cytometry-based genome size measurement is fundamental, and a pivotal factor is the internal standard used during measurement. In the present article, I tested the correlation between cytometry-measured genome sizes and assembly sizes, finding a probable systemic error. Indeed, the two most widely used internal standard, i.e., human and chicken, are traditionally set equal to 3.5 and 1.25 pg, respectively. With the advent of telomere-to-telomere genome assemblies, we can now know the real genome size for several species, being actually 3.19 pg for human and 1.12 pg for chicken. Recalculating the genome size for 912 vertebrate species, I assessed the level of genome assembly completeness, explored the influence of factors such as sequencing platform, and gave some suggestions for future studies.
Abstract High-quality genome assemblies are essential for robust research across biological and medical fields. Assembly errors can have far-reaching consequences for downstream analyses, including gene annotation and the inference of synteny. In contrast to the rapid growth of genomic data volume, there is a notable lag in the integration of chromosome-level assemblies with cytogenetic data. We conducted the first direct genome-to-genome comparison, integrating comparative chromosome painting, the alignment of chromosome-specific probes to available genome assemblies, and a synteny-based comparison of independent chromosome-level assemblies of the loggerhead sea turtle (Caretta caretta, 2n = 56) and the red-eared slider (Trachemys scripta elegans, 2n = 50). Using two independent sets of flow-sorted chromosome-specific probes in cross-species hybridizations, together with the sequencing and mapping of chromosome-derived DNA libraries, we assigned assembled scaffolds to all physical chromosomes of both species. In C. caretta, chromosomal assignments and genome-wide synteny were fully consistent with the published assembly, except for the reduced sizes of two microchromosome scaffolds, which we attribute to the under-representation of repetitive DNA. In contrast, in T. s. elegans, cytogenetic validation of the assemblies revealed a false rearrangement compared with a missed one. Our results show that even highly contiguous vertebrate genome assemblies can misrepresent chromosome structure. When cytogenetic analyses reveal such inaccuracies, updated reference genomes should be generated for widely studied species to enable accurate inference of karyotype evolution and downstream comparative genomic analyses.
We established primary fibroblast cultures from a Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica) and generated highly contiguous reference genome assemblies using Oxford Nanopore Technologies PromethION long-read sequencing. The Japanese raccoon dog assembly spanned 2.69 Gb in 813 scaffolds, with a scaffold N50 of 52 Mb and a Benchmarking Universal Single-Copy Orthologs completeness score of 98.2%. The Japanese red fox assembly spanned 2.47 Gb in 903 scaffolds, with a scaffold N50 of 139 Mb and a Benchmarking Universal Single-Copy Orthologs completeness score of 97.5%. Phylogenomic analysis placed the Japanese raccoon dog in a lineage distinct from the continental raccoon dog, supporting its evolutionary differentiation within Nyctereutes. The Japanese red fox formed a distinct lineage within the red fox clade, consistent with its recognized regional differentiation. These genome assemblies and associated fibroblast cultures provide resources for studies of canid systematics, population history, local adaptation, comparative genome evolution, and conservation genetics.
