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1. The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids

   https://doi.org/10.1073/pnas.2310763120  

   Yuan, Jiaqing ; Kitchener, Andrew C. ; Lackey, Laurie Bingaman ; Sun, Ting ; Jiangzuo, Qigao ; Tuohetahong, Yilamujiang ; Zhao, Le ; Yang, Peng ; Wang, Guiqiang ; Huang, Chen ; et al ( January 2024 , Proceedings of the National Academy of Sciences)

   Habitat degradation and loss of genetic diversity are common threats faced by almost all of today’s wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat,Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.

    

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2. Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus

   https://doi.org/10.1093/g3journal/jkac339  

   Roberts, May B. ; Schultz, Darrin T. ; Gatins, Remy ; Escalona, Merly ; Bernardi, Giacomo ; de Koning, ed., D. J. ( March 2023 , G3 Genes|Genomes|Genetics)

   Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure, and speciation (Dascyllus). The genus Dascyllus includes a group of small-bodied species, and a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex that is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus, is a widespread and common coral reef fish species found across the tropical Indo-Pacific. Here, we present the first-genome assembly of this species. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the Benchmarking Universal Single-Copy Orthologs score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. We also find that the D. trimaculatus chromosomes are each homologous with single chromosomes of the closely related clownfish species, Amphiprion percula. This assembly will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade.

    

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3. Chromosome-level genome of the wood stork ( Mycteria americana ) provides insight into avian chromosome evolution

   https://doi.org/10.1093/jhered/esad077  

   Flamio, Jr, Richard ; Ramstad, Kristina M. ; Suh, ed., Alexander ( December 2023 , Journal of Heredity)

   Despite being quite specious (~10,000 extant species), birds have a fairly uniform genome size and karyotype (including the common occurrence of microchromosomes) relative to other vertebrate lineages. Storks (Family Ciconiidae) are a charismatic and distinct group of large wading birds with nearly worldwide distribution but few genomic resources. Here we present an annotated chromosome-level reference genome and chromosome orthology analysis for the wood stork (Mycteria americana), a species that has been federally protected under the Endangered Species Act since 1984. The annotated chromosome-level reference assembly was produced using the blood of a wild female wood stork chick, has a length of 1.35 Gb, a contig N50 of 37 Mb, a scaffold N50 of 80 Mb, and a BUSCO score of 98.8%. We identified 31 autosomal pairs and two sex chromosomes in the wood stork genome, but failed to identify four additional autosomal microchromosomes previously found via karyotyping. Orthology analyses confirmed reported synapomorphies unique to storks and identified the chromosomes participating in these fusions. This study highlights the difficulty and potential problems associated with delineating microchromosomes in reference genome assemblies. It also provides a foundation for studying karyotype evolution in the core water bird clade that includes penguins, albatrosses, storks, cormorants, herons, and ibises. Finally, our reference genome will allow for numerous genomic studies, such as genome-wide association studies of local adaptation, that will aid in wood stork conservation.

    

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4. Chromosome-Level Genome Assembly for the Angiosperm Silene conica

   https://doi.org/10.1093/gbe/evad192  

   Fields, Peter D. ; Weber, Melody M. ; Waneka, Gus ; Broz, Amanda K. ; Sloan, Daniel B. ; Castric, ed., Vincent ( October 2023 , Genome Biology and Evolution)

   The angiosperm genus Silene has been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome of Silene conica based on Pacific Bioscience HiFi, Hi-C, and Bionano technologies. The assembly produced 10 scaffolds (1 per chromosome) with a total length of 862 Mb and only ∼1% gap content. These results confirm previous observations that S. conica and its relatives have a reduced base chromosome number relative to the genus's ancestral state of 12. Silene conica has an exceptionally large mitochondrial genome (>11 Mb), predominantly consisting of sequence of unknown origins. Analysis of shared sequence content suggests that it is unlikely that transfer of nuclear DNA is the primary driver of this mitochondrial genome expansion. More generally, this assembly should provide a valuable resource for future genomic studies in Silene, including comparative analyses with related species that recently evolved sex chromosomes.

    

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5. A chromosomal-scale reference genome of the New World Screwworm, Cochliomyia hominivorax

   https://doi.org/10.1093/dnares/dsac042  

   Tandonnet, Sophie ; Krsticevic, Flavia ; Basika, Tatiana ; Papathanos, Philippos A ; Torres, Tatiana T ; Scott, Maxwell J ( February 2023 , DNA Research)

   The New World Screwworm, Cochliomyia hominivorax (Calliphoridae), is the most important myiasis-causing species in America. Screwworm myiasis is a zoonosis that can cause severe lesions in livestock, domesticated and wild animals, and occasionally in people. Beyond the sanitary problems associated with this species, these infestations negatively impact economic sectors, such as the cattle industry. Here, we present a chromosome-scale assembly of C. hominivorax’s genome, organized in 6 chromosome-length and 515 unplaced scaffolds spanning 534 Mb. There was a clear correspondence between the D. melanogaster linkage groups A–E and the chromosomal-scale scaffolds. Chromosome quotient (CQ) analysis identified a single scaffold from the X chromosome that contains most of the orthologs of genes that are on the D. melanogaster fourth chromosome (linkage group F or dot chromosome). CQ analysis also identified potential X and Y unplaced scaffolds and genes. Y-linkage for selected regions was confirmed by PCR with male and female DNA. Some of the long chromosome-scale scaffolds include Y-linked sequences, suggesting misassembly of these regions. These resources will provide a basis for future studies aiming at understanding the biology and evolution of this devastating obligate parasite.

    

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