The Genome Sequences of 118 Taxonomically Diverse Eukaryotes of the Salish Sea.

We present the complete genome sequences of 118 taxonomically diverse eukaryotes from the Salish Sea. Illumina sequencing was performed on genetic material from wild-collected individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.

The genomic and cellular basis of biosynthetic innovation in rove beetles.

How evolution at the cellular level potentiates macroevolutionary change is central to understanding biological diversification. The >66,000 rove beetle species (Staphylinidae) form the largest metazoan family. Combining genomic and cell type transcriptomic insights spanning the largest clade, Aleocharinae, we retrace evolution of two cell types comprising a defensive gland-a putative catalyst behind staphylinid megadiversity. We identify molecular evolutionary steps leading to benzoquinone production by one cell type via a mechanism convergent with plant toxin release systems, and synthesis by the second cell type of a solvent that weaponizes the total secretion. This cooperative system has been conserved since the Early Cretaceous as Aleocharinae radiated into tens of thousands of lineages. Reprogramming each cell type yielded biochemical novelties enabling ecological specialization-most dramatically in symbionts that infiltrate social insect colonies via host-manipulating secretions. Our findings uncover cell type evolutionary processes underlying the origin and evolvability of a beetle chemical innovation.

The Complete Genome Sequence of Ajuga reptans (Lamiaceae, Lamiales), Bugleweed.

We present the whole genome sequence of Ajuga reptans. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR24502601) and assembled genome (JAUEKW000000000).

The Complete Genome Sequences of 37 Bird Species from the Ecuadorian Andes.

We present the complete genome sequences of 37 Ecuadorian bird species widespread throughout the tropical Andes.

The Complete Genome Sequences of 23 Finch Species (Fringillidae, Passeriformes).

We present complete genome sequences of 23 species of finches from 6 genera.

The Draft Genome Sequences of 63 Species of Catfish (Ariidae, Siluriformes).

We present genome sequences of 63 species of catfish from the Ariidae family. Illumina sequencing was performed on tissue from wild-collected museum 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.

The Complete Genome Sequences of 7 Hypoplectrus species (Serranidae, Perciformes).

Species in the genus Hypoplectrus are found primarily in coral reefs in the Caribbean Sea and the Gulf of Mexico, particularly around Florida and the Bahamas. They are a popular choice for hobbyist saltwater aquariums. Members of this genus are simultaneous hermaphrodites, as they have both male and female sexual organs at the same time as an adult. We present the genome sequences of 7 species of Hypoplectrus. Raw read data and assembled genomes are available in Genbank.

The complete genome sequences of two species of seventeen-year cicadas: Magicicada septendecim and Magicicada septendecula.

The genus Magicicada (Hemiptera: Cicadidae) includes the periodical cicadas of Eastern North America. Spending the majority of their long lives underground, the adult cicadas emerge every 13 or 17 years to spend 4-6 weeks as adult to mate. We present the whole genome sequences of two species of 17-year cicadas, Magicicada septendecim and Magicicada septendecula. The reads were assembled by a de novo method followed by alignments to related species. Annotation was performed by GeneMark-ES. The raw and assembled data is available via NCBI Short Read Archive and Assembly databases.

The complete genome sequence of the protogynous hermaphrodite North American annual killifish Millerichthys robustus (Rivulidae, Cyprinodontiformes).

The Mexican Rivulus, Millerichthys robustus, is an enigmatic species of seasonal killifish endemic of the Southeast Mexico that has changed paradigms on the evolution of annualism in killifishes. This species survives in ephemeral environments that experience a period of seasonal drought that causes the death of all adult fish. However, populations persist due to their drought-resistant embryos capable of arresting their development in diapause until the next the rainy season. Millerichthys evolved unique characteristics within annual killifishes as a functional sequential hermaphroditism, in which females change to males (protogynous) under perceived conditions of mate competition. Also, M. robustus express different color phenotypes in both sexes: five-color phenotypes continuously distributed in various perceptual units between yellow and red in males, and different number of ocelli disposed in caudal peduncle in females. The phylogenetic relationships of M. robustus revealed that it is a sister clade to two non-annual species found exclusively in Cuba (Rivulus cylindraceus and Rivulus berovidesi), indicating that the annual life cycle, through the acquisition of embryonic diapause, has evolved independently in this species. Here, we present the complete genome sequences for the North American annual killifish Millerichthys robustus. The raw data and assembled genome are available in GeneBank.

Whole Snake Genomes from Eighteen Families of Snakes (Serpentes: Caenophidia) and Their Applications to Systematics.

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 UCEs and 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 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 (Stegonotus admiraltiensis and Tropidonophis 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 cucullatus 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.

The Draft Genome Sequences of 50 Salamander species (Caudata, Amphibia).

We present partial genome sequences of 50 salamander species (Urodela) from 10 genera and 4 families. These span nearly the entire range of genome sizes in salamanders, from ~14-130GB, the latter of which is among the largest of all animal genomes. Only three salamander genomes were available to this point, from Ambystomatidae (one species) and Salamandridae (two species from two genera), to which we have added Amphiumidae (one species), Plethodontidae (45 species from 6 genera), Proteidae (one species), and Sirenidae (three species from two genera). These span ~140 million years of evolutionary divergence, leaving only Cryptobranchidae, Hynobiidae, and Rhyacotritonidae as salamander families without genome assemblies. These data should facilitate additional future work on speciation and genome evolution, both within Urodela and across Animalia.

The Complete Genome Sequences of 12 Species of Enteromius (Cyprinidae, Cypriniformes, Actinopteri).

We present the complete genome sequences of 12 species of Enteromius. Illumina sequencing was performed on genetic material from museum 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.

Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement.

The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.

The Complete Genome Sequences of 12 Species of Plants from the Yucatan Peninsula, Mexico.

We present the complete genome sequences of 12 species of plants from Campeche, Mexico and the greater Yucatan Peninsula: Agave americana, Agave angustifolia, Agave fourcroydes, Agave karwinskii, Agave potatorum, Agave tequiliana, Annona squamosa, Cedrela odorata, Pouteria campechiana, Pouteria glomerata, Trichilia hirta and Trichilia minutiflora.

Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family.

Asian mock vipers of the genus Psammodynastes and African forest snakes of the genus Buhoma are two genera belonging to the snake superfamily Elapoidea. The phylogenetic placements of Psammodynastes and Buhoma within Elapoidea has been extremely unstable which has resulted in their uncertain and debated taxonomy. We used ultraconserved elements and traditional nuclear and mitochondrial markers to infer the phylogenetic relationships of these two genera with other elapoids. Psammodynastes, for which a reference genome has been sequenced, were found, with strong branch support, to be a relatively early diverging split within Elapoidea that is sister to a clade consisting of Elapidae, Micrelapidae and Lamprophiidae. Hence, we allocate Psammodynastes to its own family, Psammodynastidae new family. However, the phylogenetic position of Buhoma could not be resolved with a high degree of confidence. Attempts to identify the possible sources of conflict in the rapid radiation of elapoid snakes suggest that both hybridisation/introgression during the rapid diversification, including possible ghost introgression, as well as incomplete lineage sorting likely have had a confounding role. The usual practice of combining mitochondrial loci with nuclear genomic data appears to mislead phylogeny reconstructions in rapid radiation scenarios, especially in the absence of genome scale data.

The Complete Genome Sequences of seven species of sea slugs (Nudibranchia, Gastropoda, Mollusca).

We present the complete genome sequences of seven species of sea slugs. Illumina sequencing was performed on tissue from wild-collected museum 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.

The Complete Genome Sequence of Ceratonia siliqua L. (Fabaceae, Fabales), Carob.

We present the whole genome sequence of Ceratonia siliqua L. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR24502586) and assembled genome (JASKGM000000000).

Insights into the genome of the 'Loco' Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae.

BACKGROUND: The Peruvian 'chanque' or Chilean 'loco' Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes. RESULTS: Using a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs. CONCLUSION: The information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.

The Complete Genome Sequence of Portunus pelagicus (Portunidae, Decapoda), the Blue Swimming Crab.

Portunus pelagicus is a large crab found in the Indo-Pacific. We present the whole genome sequence of this species. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR25655135) and assembled genome (JAWWMC000000000).

The Genome Sequences of 17 Species of Carnivorous Plants.

We present the genome sequences of 17 species of carnivorous plants. Illumina sequencing was performed on genetic material from cultivated individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are available via Genbank.