Malay, M. C. D. | bioRxiv Science

bioRxiv2025

Draft Genome of the Endangered Visayan Spotted Deer (Rusa alfredi)

The Visayan Spotted Deer (Rusa alfredi) is an endangered and endemic species in the Philippines facing significant threats from habitat loss and hunting. It is considered as the worlds most threatened deer species by the International Union for Conservation of Nature (IUCN) thus its conservation has been a top priority. Despite its status, there is a notable lack of genomic information available for R. alfredi and the genus Rusa in general. This study presents the first draft genome assembly of the Visayan Spotted Deer (VSD), Rusa alfredi, using Illumina short-read sequencing technology. The RusAlf_1.1 assembly has a 2.52 Gb total length with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genomes completeness, and includes the annotation of 24,531 genes. Phylogenetic analysis based on single-copy orthologs reveals a close evolutionary relationship between the R. alfredi and the genus Cervus. The availability of the RusAlf_1.1 genome assembly represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, which could contribute to more effective conservation and management strategies for this endangered species. This genomic resource can help in assuring the survival of Rusa alfredi in the country.

genomics↗

bioRxiv2023

Intra- and interspecific variations in genome sizes of Agaricia corals from Curacao

Genome size is a fundamental biological trait that is known to exhibit high diversity among eukaryotic species, but its intraspecific diversity has only scarcely been studied to date. In scleractinian corals, genome size data are only available for a few species. In this study, intra- and interspecific variations in genome size of the coral genus Agaricia collected from Curacao were investigated. Morphology was congruent with genetic analyses of the nuclear markers internal transcribed spacer 2 (ITS2) and L-threonine 3-dehydrogenase (TDH) in delimiting three Agaricia species among our samples. A refined Feulgen Image Analysis Densitometry (FIAD) protocol yielded genome sizes that ranged from 0.359 pg to 0.593 pg within this genus (a 1.7-fold range). The highest intraspecific variation in genome size was recorded in the depth-generalist A. lamarcki (1.5-fold range), followed by the depth specialist A. humilis (1.4-fold range) and A. agaricites (1.3-fold range), the species with an intermediate depth distribution. The mean genome size of A. agaricites (0.495 pg) was significantly larger than that of A. lamarcki (0.448 pg) and A. humilis (0.434 pg). No correlation between average genome size and nucleotide polymorphism{pi} was detected, but we found an almost linear correlation between intraspecific variance of genome size and{pi} of ITS2 (Pearsons r = 0.984, p = 0.113). Genome size and collection depths of both A. lamarcki (Pearsons r = 0.328, p = 0.058) and A. agaricites (Pearsons r = -0.270, p = 0.221) were also not significantly associated. To our knowledge, this study provides the first account of intraspecific variation in corals; the apparent correlation detected between the nucleotide polymorphism of a species and the variance of its genome size will have to be tested using a larger taxonomic spectrum of scleractinian corals as well as in other groups of animals.

evolutionary biology↗