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 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.

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.

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 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).

'Candidatus Tisiphia' is a widespread Rickettsiaceae symbiont in the mosquito Anopheles plumbeus (Diptera: Culicidae)

Symbiotic bacteria can alter host biology by providing protection from natural enemies, or alter reproduction or vectoral competence. Symbiont-linked control of vector-borne disease in Anopheles has been hampered by a lack of symbioses that can establish stable vertical transmission in the host. Previous screening found the symbiont 'Candidatus Tisiphia' in Anopheles plumbeus, an aggressive biter and potential secondary vector of malaria parasites and West Nile virus. We screened samples collected over 10-years across Germany and used climate databases to assess environmental influence on incidence. We observed a 95% infection rate, and that the frequency of infection did not fluctuate with broad environmental factors. Maternal inheritance is indicated by presence in the ovaries through FISH microscopy. Finally, we assembled a high-quality 1.6 Mbp draft genome of 'Ca. Tisiphia' to explore its phylogeny and potential metabolic competence. The infection is closely related to strains found in Culicoides biting midges and shows similar patterns of metabolism, providing no evidence of the capacity to synthesize B-vitamins. This infection offers avenues for onward research in anopheline mosquito symbioses. Additionally, it provides future opportunity to study the impact of 'Ca. Tisiphia' on natural and transinfected hosts, especially in relation to reproductive fitness and vectorial competence and capacity.

The Complete Genome Sequences of 5 Species of Sardinella (Clupeidae, Clupeiformes)

We present the complete genome sequences of 5 species of Sardinella. Illumina sequencing was performed on genetic material 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.

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.

The Complete Genome Sequences of 2 Species of Geukensia (Brachidontinae, Mytilidae)

We present the complete genome sequences of Geukensia demissa and Geukensia granosissima. 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 available via Genbank.

Genomic Assessment of the Contribution of the Wolbachia Endosymbiont of Eurosta solidaginis to Gall Induction

We explored the genome of the Wolbachia strain, wEsol, symbiotic with the plant-gall-inducing fly Eurosta solidaginis with the goal of determining if wEsol contributes to gall induction by its insect host. Gall induction by insects has been hypothesized to involve the secretion of the phytohormones cytokinin and auxin and/or proteinaceous effectors to stimulate cell division and growth in the host plant. We sequenced the metagenome of E. solidaginis and wEsol and assembled and annotated the genome of wEsol. The wEsol genome has an assembled length of 1.66 Mbp and contains 1878 protein-coding genes. The wEsol genome is replete with proteins encoded by mobile genetic elements and shows evidence of seven different prophages. We also detected evidence of multiple small insertions of wEsol genes into the genome of the host insect. Our characterization of the genome of wEsol indicates that it is compromised in the synthesis of dimethylallyl pyrophosphate (DMAPP) and S-adenosyl L-methionine (SAM), which are precursors required for the synthesis of cytokinins and methylthiolated cytokinins. wEsol is also incapable of synthesizing tryptophan, and its genome contains no enzymes in any of the known pathways for the synthesis of indole-3-acetic acid (IAA) from tryptophan. wEsol must steal DMAPP and L-methionine from its host and therefore is unlikely to provide cytokinin and auxin to its insect host for use in gall induction. Furthermore, in spite of its large repertoire of predicted Type IV secreted effector proteins, these effectors are more likely to contribute to the acquisition of nutrients and the manipulation of the host's cellular environment to contribute to growth and reproduction of wEsol than to aid E. solidaginis in manipulating its host plant. Combined with earlier work that shows that wEsol is absent from the salivary glands of E. solidaginis, our results suggest that wEsol does not contribute to gall induction by its host.

The Complete Genome Sequences of 19 Species of Snipes (Scolopacidae, Charadriiformes, Aves)

We present the complete genome sequences of 19 species of snipes from 7 genera. 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.

The Complete Genome Sequences of 9 Species of Swallowtail Butterflies (Papilionidae, Lepidoptera)

We present the complete genome sequences of 9 species of Papilionidae from 3 genera (Graphium, Ornithoptera, Papilio). Illumina sequencing was performed on genetic material from individual 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.

The Complete Genome Sequence of Chrysina resplendens (Scarabaeidae, Coleoptera) the Golden Jewel Scarab

Chrysina resplendens is a scarab beetle endemic to Central America. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR5170512) and Assembly (JAADJY000000000).

The Complete Genome Sequences of 7 Species of Epizoanthus (Epizoanthidae, Zoantharia, Hexacorallia, Cnidaria)

We present the complete genome sequences of 7 species of the zoantharian genus Epizoanthus. Illumina sequencing was performed on genetic material from single 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 Complete Genome Sequence of Adansonia digitata (Malvaceae, Malvales), the African Baobab

Adansonia digitata, the African Baobab, is a long-lived tree species found in sub-Saharan Africa. 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 (SRR23340274) and assembled genome (JAQSVH000000000).

The Complete Genome Sequences of 13 Species of Brachycnemina (Cnidaria, Hexacorallia, Anthozoa, Zoantharia)

We present the complete genome sequences of 13 species of the zoantharian suborder Brachycnemina (Haddon, and Shackleton, 1891; Poliseno et al., 2020). Genome sequencing was performed on genetic material from single wild-collected individuals. For each species the sequence reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank.

A Draft Genome Sequence of Dorometra sesokonis (Antedonidae, Comatulida, Crinoidea, Echinodermata)

We present the complete genome sequence of Dorometra sesokonis. Genome sequencing was performed on genetic material from a single wild-collected individual. The sequence 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 Iris sibirica and Iris virginica (Iridaceae, Asparagales)

We present the complete genome sequences of Iris sibirica and Iris virginica. Illumina sequencing was performed on genetic material from individual cultivated 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 Conuropsis carolinensis, the Carolina Parakeet

The Carolina Parakeet (Conuropsis carolinensis) is an extinct species of parrot that was native to the eastern, midwest, and plains regions of the United States. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR21023482) and assembled genome (JAOBYI000000000).

The Complete Genome Sequences of 94 Species of Parrots (Psittaciformes, Aves)

We present the complete genome sequences of 94 species of parrots from 40 genera. Illumina sequencing was performed on genetic material from single individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.

The Complete Genome Sequence of Cyanopsitta spixii, the Spix's Macaw

The Spix's Macaw (Cyanopsitta spixii) is a critically endangered parrot that was once endemic to Brazil. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR15037507) and Assembly (GCA_024336845).

The complete genome sequences of Erythroxylum coca and Erythroxylum novogranatense

The flowering plant genus Erythroxylum contains approximately 300 species, including the economically and socially consequential crops called coca. We present the genome sequences of Erythroxylum coca and E. novogranatense, two cultigens produced for medicinal and quotidian use in the Andes and Amazon regions of South America, as well as the international cocaine industry. Sequencing was performed on an Illumina X-Ten platform, and reads were assembled by a de novo method followed by finishing via comparison with several species from the same genus. The BioProject, raw and assembled data can be accessed in GenBank for E. coca (PRJNA676123; JAJMLV000000000) and E. novogranatense (PRJNA675212; JAJKBF000000000).

The Complete Genome Sequence of Protonotaria citrea, the Prothonotary Warbler

The Prothonotary Warbler (Protonotaria citrea) is a nearctic-neotropical migratory songbird that breeds in forested swamps and riparian areas in the eastern-central United States and southern Ontario. It is the sole eastern North American wood-warbler that nests in cavities, the only species in the genus Protonotaria, and is one of the few hole-nesting hosts of the Brown-headed Cowbird (Molothrus ater), an obligate brood parasite. We present the whole genome sequence of this wood-warbler species. Illumina sequencing was performed on a genetic sample from a single female individual. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR19579445) and Assembly (JAOYNP000000000).

The Complete Genome Sequence of Chlorophytum comosum (Asparagaceae, Asparagales), the Spider Plant

Chlorophytum comosum is a species of evergreen perennial flowering plant native to tropical and southern Africa but has become naturalized in other parts of the world, including western Australia and Bangladesh. We present the whole genome sequence of Chlorophytum comosum. 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 (SRR11638255) and assembled genome (GCA_025212335).

The Complete Genome Sequence of Lythrypnus dalli, the Bluebanded Goby

The Bluebanded goby (Lythrypnus dalli) is a small, highly social marine goby. We present the whole genome sequence of this species. A total of 118,266,160 paired end reads consisting of 17.9G bases were obtained by sequencing tissue from a single individual. The reads were assembled by a de novo method followed by alignment to related species. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR5170315) and Assembly (GCA_011763505).

The Complete Genome Sequence of Erigeron philadelphicus, the Philadelphia Fleabane

The Philadelphia Fleabane (Erigeron philadelphicus) is a common flower across North America, growing along roadsides and in fields and woodlands. Each plant has 3 to 35 small daisy-like flowers at the top of the plant. Flowers are 0.5 - 0.8" across, with 150 or more pink to white thread-like petals and a yellow center disk. We present the whole genome sequence of this species. Illumina sequencing was performed on a single leaf from a wild-collected plant. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR13004263) and Assembly (GCA_024320915).

The complete genome sequence of Androctonus mauritanicus, the Moroccan black thick-tailed scorpion

Androctonus mauritanicus is a large scorpion indigenous to North Africa. Notable for its extremely potent venom, it is responsible for several human deaths a year. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single wild-caught individual. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR10738938) and Assembly (GCA_011317285).

The Complete Genome Sequence of the Simalia boeleni, the Boelen's Python

The Boelen's Python (Simalia boeleni) is a python endemic to the mountains of New Guinea. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR19167501) and assembled genome (JANKYG000000000).

The Complete Genome Sequence of Amorphophallus titanum, the Corpse Flower

The Corpse Flower, or Titan Arum (Amorphophallus titanum) is a flowering plant in the family Araceae. endemic to a limited range in the rainforests of Sumatra, Indonesia. It is notable for two reasons: it produces the world's largest known unbranched flower, and it produces a strong odor of rotting meat to attract pollinators. We present the whole genome sequence of this species. A total of 335,712,220 paired-end Illumina reads consisting of 100.7G bases were obtained by Illumina sequencing the leaf tissue of a single individual. The reads were assembled by a de novo method followed by contig extension using related species as references. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR11565159) and genome assembly (GCA_024336825).

The Complete Genome Sequence of Telfairia occidentalis, the African Fluted Pumpkin

Telfairia occidentalis is a tropical vine grown in West Africa as a leaf vegetable and for its edible seeds. We present the whole genome sequence of this species. Illumina sequencing was performed on a leaf tissue sample from a single cultivated plant. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR14834394) and Genome Assembly (JAOANK000000000).

The Complete Genome Sequences of 18 Species of Gadiformes (Actinopterygii, Chordata)

We present the complete genome sequences of 18 species of Gadiformes from 9 genera. Illumina sequencing was performed on genetic material from single wild-caught individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.

The Complete Genome Sequences of 38 Species of Elephantfishes (Mormyridae, Osteoglossiformes)

We present the complete genome sequences of 38 species of elephantfishes from 20 genera. Illumina sequencing was performed on genetic material from single wild-caught individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.