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Abstract As one of just a handful of nonbilaterian animal phyla, Cnidaria are key to understanding genome evolution across Metazoa. Despite their importance and diversity, the genomes of most species in the phylum are unsequenced, due in large part to difficulties cultivating them in a laboratory. Here, we present a genome sequence of Bougainvillia cf. muscus, a hydrozoan with 4 marginal bulbs each containing 7 simple eyes (ocelli). This species appeared in our tanks from contamination. While we lacked sufficient samples for transcriptomic or functional studies, we were able to expand our knowledge of how the genome of this species compares to the few, better studied members of hydrozoans by investigating synteny to other cnidarians, repetitive element content, and phylogenetics and synteny of vision-related genes in this eyed species compared to eyeless relatives. The genome sequence consists of 350 contigs with an N50 of 10 Mb, a total genome length of 375.328 Mb, a BUSCO score of 90.1%, and predicted protein coding genes totaling 46,431. We found a high degree of macrosynteny conservation with Hydra vulgaris, Hydractinia symbiolongicarpus, and Turritopsis rubra. Repetitive elements make up 62% of this Bougainvillia genome. For vision-related genes, we identified 20 cnidarian opsins (cnidops) in Bougainvillia and found instances of gene duplication and loss in families associated with bilaterian eye development, phototransduction, and visual cycling. This high-quality, contiguous genome in an eyed hydrozoan will be a valuable resource for additional comparative genomic studies. 

The Mountain bongo (Tragelaphus eurycerus isaaci), a critically endangered tragelaphine antelope native to the montane forests of Kenya, faces significant threats from habitat loss and hunting. Although the Mountain bongo is a flagship species in Kenya, the majority are found in small, isolated populations of less than 100 animals total, making it a species of high conservation concern. In this report, we present a chromosome-length draft genome assembly for the Mountain bongo, generated using a combination of linked-read and proximity ligation (Hi-C) sequencing techniques. The assembly resulted in a 2.96 Gb sized genome with a contig N50 of 79.5 kb and a scaffold N50 of 192 Mb. Assembly completeness was 95.1% based on 12,234 Benchmarking Universal Single-Copy Orthologs (BUSCO) and annotation revealed 29,820 protein-coding genes, of which 27,761 were functionally annotated, and a repetitive content of 47.31%. Synteny analysis against the domestic cattle (Bos taurus) genome assembly revealed numerous chromosomal rearrangements between the 2 species. Our analysis also revealed insights into the evolutionary and demographic history of the Mountain bongo, offering valuable information for conservation management. We also assembled and annotated the mitochondrial genome which showed <1% differences from the Lowland bongo subspecies, T. e. eurycerus. By integrating genomic data with traditional conservation methods, this reference lays the foundation to evaluate and preserve genetic diversity of both in situ and ex situ populations of the Mountain bongo amidst growing environmental pressures. 

The aye-aye (Daubentonia madagascariensis) is the only extant member of the Daubentoniidae primate family. Although several reference genomes exist for this endangered strepsirrhine primate, the predominant usage of short-read sequencing has resulted in limited assembly contiguity and completeness, and no protein-coding gene annotations have yet been released. Here, we present a novel, fully annotated, chromosome-level hybrid de novo assembly for the species based on a combination of Oxford Nanopore Technologies long reads and Illumina short reads and scaffolded using genome-wide chromatin interaction data—a community resource that will improve future conservation efforts as well as primate comparative analyses. 

Abstract Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts from the algae they consume. These “photosynthetic animals” incorporate stolen chloroplasts, called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the sacoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys that can retain photosynthetically active kleptoplasts for several months without feeding. We used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to produce a 786-Mb assembly (N50 = 0.459 Mb) containing 68,514 predicted protein-coding genes. A phylogenetic analysis found no evidence of horizontal acquisition of genes from algae. We performed gene family and gene expression analyses to identify E. crispata genes unique to kleptoplast-containing slugs that were more highly expressed in fed versus unfed developmental life stages. Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four polyketide synthase genes that could potentially encode proteins producing UV- and oxidation-blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource that provides potential targets for functional analyses and enables further investigation into the evolution and mechanisms of kleptoplasty in animals.