Search for: All records

We present the complete genome sequences of 64 species of amphibians (61 Anurans, 2 Caudates and 1 Caecilian) including complete genomes from four type specimens. Illumina sequencing was performed on DNA extracted from wild-caught specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank. 

We present complete genome sequences of 12 species of Percopsiformes. 

We present the complete genome sequences of 101 species of reptiles (four testudines, one crocodilian and 96 squamates) including the complete genome of one type specimen. Illumina sequencing was performed on DNA extracted from wild-caught specimens. The reads were assembled using ade novomethod followed by a finishing step. The raw and assembled data are publicly available via Genbank. 

We present the complete genome sequences of 11 species of kingbirds. Illumina sequencing was performed on genetic material from wild-caught and museum specimens. The reads were assembled using ade novomethod followed by a finishing step. The raw and assembled data are publicly available via Genbank. 

We present the complete genome sequences of 22 species of owls. Illumina sequencing was performed on DNA extracted from wild-caught specimens. The reads were assembled using ade novomethod followed by a finishing step. The raw and assembled data are publicly available via Genbank. 

We present the complete genome sequences of 31 species of hawks. Illumina sequencing was performed on genetic material from wild-caught specimens. The reads were assembled using ade novomethod followed by a finishing step. The raw and assembled data are publicly available via Genbank. 

Abstract Hawks, eagles, and their relatives (Accipitriformes: Accipitridae) are a diverse and charismatic clade of modern birds, with many members that are instantly recognized by the general public. However, surprisingly little is known about the relationships among genera within Accipitridae, and several studies have suggested that some genera (in particular, the megadiverse genus Accipiter) are not monophyletic. Here, we combine a large new dataset obtained from ultraconserved elements, generated from whole genome sequencing of 134 species, with publicly available legacy markers (i.e. a suite of commonly sequenced mitochondrial and nuclear genes) to infer a well-supported, time-calibrated phylogeny of 237 extant or recently extinct species. Our densely sampled phylogeny, which includes 90% of recognized species, confirms the non-monophyly of Accipiter and provides a sufficient basis to revise the genus-level taxonomy, such that all genera in Accipitridae represent monophyletic groups. 

Abstract Habitat transitions have shaped the evolutionary trajectory of many clades. Sea catfishes (Ariidae) have repeatedly undergone ecological transitions, including colonizing freshwaters from marine environments, leading to an adaptive radiation in Australia and New Guinea alongside non-radiating freshwater lineages elsewhere. Here, we generate and analyze one long-read reference genome and 66 short-read whole genome assemblies, in conjunction with genomic data for 54 additional species. We investigate how three major ecological transitions have shaped genomic variation among ariids over their ~ 50 million-year evolutionary history. Our results show that relatively younger freshwater lineages exhibit a higher incidence of positive selection than their more ancient marine counterparts. They also display a larger disparity in body shapes, a trend that correlates with a heightened occurrence of positive selection on genes associated with body size and elongation. Although positive selection in the Australia and New Guinea radiation does not stand out compared to non-radiating lineages overall, selection across the prolactin gene family during the marine-to-freshwater transition suggests that strong osmoregulatory adaptations may have facilitated their colonization and radiation. Our findings underscore the significant role of selection in shaping the genome and organismal traits in response to habitat shifts across macroevolutionary scales. 

Many molluscan genomes have been published to date, however only three are from representatives of the subphylum Aculifera (Polyplacophora, Caudofoveata, and Solenogastres), the sister taxon to all other molluscs. Currently, genomic resources are completely lacking for Solenogastres. This gap in knowledge hinders comparative and evolutionary studies. Here, we sequenced the genomes of the solenogaster aplacophoransEpimenia babaiSalvini-Plawen, 1997 andNeomenia megatrapezataSalvini-Plawen & Paar-Gausch, 2004 using a hybrid approach combining Oxford Nanopore and Illumina reads. ForE. babai, we produced a 628 Mbp haploid assembly (N50 = 413 Kbp, L50 = 370) that is rather complete with a BUSCO completeness score of 90.1% (82.0% single, 8.1% duplicated, 6.0% fragmented, and 3.9% missing). ForN. megatrapezata, we produced a 412 Mbp haploid assembly (N50 = 132 Kbp, L50 = 881) that is also rather complete with a BUSCO completeness score of 85.1% (81.7% single, 3.4% duplicated, 8.1% fragmented, and 6.8% missing). Our annotation pipeline predicted 25,393 gene models forE. babaiwith a BUSCO score of 92.4% (80.5% single, 11.9% duplicated, 4.9% fragmented, and 2.7% missing) and 22,463 gene models forN. megatrapezatawith a BUSCO score of 90.2% (81.0% single, 9.2% duplicated, 4.7% fragmented, and 5.1% missing). Phylogenomic analysis recovered Solenogastres as the sister taxon to Polyplacophora and Aculifera as the sister taxon to all other sampled molluscs with maximal support. These represent the first whole-genome resources for Solenogastres and will be valuable for future studies investigating this understudied group and molluscan evolution as a whole. 

Abstract We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of ultraconserved elements (UCEs) and anchored hybrid enriched loci (AHEs), as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other and strongly congruent with previously published snake phylogenies. To show the additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (S. admiraltiensis and T. doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus australis and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high-coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.