Comparative mitochondrial genomics of endemic Mexican vesper yellow bats genus Rhogeessa (Chiroptera: Vespertilionidae) and insights into internal relationships in the family Vespertilionidae

In the species-rich family Vespertilionidae, vesper yellow bats in the genus Rhogeessa include eleven species, three of them endemic to Mexico. These insectivorous bats provide important ecosystem services, including pest control. Even though some aspects of their biology are well- known, only a few genomic resources are available for these species, which limits our understanding of their biology. In this study, we assembled and annotated the mitochondrial genome of four species: R. aenea, R. genowaysi, R. mira, and R. parvula. We generated a phylomitogenomic hypothesis based on translated protein-coding genes for a total of 52 species in the family Vespertilionidae and examined the phylogenetic position of the genus Rhogeessa and species within the family. The AT-rich mitogenomes of R. aenea, R. genowaysi, R. mira, and R. parvula are 16,763, 16,781, 16,807, and 16,794 pb in length, respectively. Each studied mitogenome encodes 13 Protein Coding Genes (PCGs), 22 transfer RNA genes, and 2 rRNA genes, and contains a putative control region (CR). All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that lacked the DHU arm in all studied mitogenomes. Selective pressure analyses indicated that all protein-coding genes are exposed to purifying selection. The phylomitogenomic analysis supported the monophyletic status of the family Vespertilionidae, confirmed the placement of Rhogeessa within the tribe Antrozoini, and clarified phylogenetic relationships within and among subfamilies and tribes in this family. Our results indicate that phylomitogenomics are useful to explore the evolutionary history of vesper bats. The assembly and comprehensive analysis of mitochondrial genomes offer the potential to generate molecular references and resources beneficial for genetic analyses aimed at understanding the ecology and evolution of these remarkable bats.

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.

De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing

The plant family Balsaminaceae comprises only two genera, and they are a study in contrasts. While Impatiens is an impressively prolific genus, with over 1,000 species and more being discovered each year, its sister genus, Hydrocera, has one solitary species, H. triflora. The two genera also differ in geographic distribution and habitat type (Impatiens species are widely distributed in much of the Old World and N. America, while H. triflora is confined to wetlands specific to S. India, Sri Lanka, and SE Asia). Other contrasting features include plant habit, habitat, floral architecture, mode of seed dispersal, and a host of other traits. The family Balsaminaceae is therefore an excellent model for studying speciation and character evolution as well as understanding the proximal and evolutionary forces that have driven the two genera to adopt such contrasting evolutionary paths. Various species of the Impatiens genus are also commercially important in the ornamental flower industry and as sources of phytochemicals that are of medicinal and other commercial value. As a preliminary step towards studying the genomic basis of the contrasting features of the two genera, we have sequenced and assembled, de novo, the genome of an iconic Impatiens species from N. America, namely I. capensis, and report our findings here.

The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates

BACKGROUND

The harsh conditions of high-altitude environments are known to drive the evolution of physiological and morphological traits in endothermic animals. These conditions are expected to result in the adaptive evolution of protein coding genes encoded in mitochondrial genomes that are vital for the oxidative phosphorylation pathway. In this study, we formally tested for signatures of adaptive evolution on mitochondrial protein coding genes in Tapirus pinchaque and other odd-toed ungulates inhabiting high-elevation environments.

RESULTS

The AT-rich mitochondrial genome of T. pinchaque is 16,750 bp long. A phylomitogenomic analysis supports the monophyly of the genus Tapirus and families in the Perissodactyla. The ratio of non-synonymous to synonymous substitutions demonstrated that all mitochondrial genes undergo purifying selection in T. pinchaque and other odd ungulates living at high elevations. Over this negative background selection, Branch Models suggested that cox3 and nad6 might be undergoing stronger purifying selection than other mitochondrial protein coding genes. Furthermore, Site Models suggested that one and four sites in nad2 and nad5, respectively, could be experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation of selection strength in nad6, evidence of episodic diversifying selection in cob, and revealed episodic positive/diversifying selection signatures for two sites in nad1, and one site each in nad2 and nad4.

CONCLUSION

The mitochondrial genome of T. pinchaque is an important genomic resource for conservation of this species and this study contributes to the understanding of adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates inhabiting high-altitude environments.

The effect of the egg-predator Carcinonemertes conanobrieni on the reproductive performance of the Caribbean spiny lobster Panulirus argus

BACKGROUND

The Caribbean spiny lobster Panulirus argus is heavily fished throughout its Greater Caribbean and Gulf of Mexico distribution, suggesting a heightened susceptibility to a fisheries collapse. In 2017, a nemertean worm, Carcinonemertes conanobrieni was described from ovigerous females of P. argus in Florida, USA. A year later, the presence of the same egg predator was recorded along the southern Caribbean coast (Colombia). The effect of this egg predator on the reproductive performance, including fecundity, embryo mortality, and reproductive output, of its host is unknown. This study tested whether C. conanobrieni affects embryo mortality, fecundity, and reproductive output in brooding females of P. argus.

RESULTS

Artisan fishers caught 90 ovigerous lobsters near Pueblo Viejo, Magdalena, Colombia. Each ovigerous female was examined for the presence/absence of the egg predator. Lobster egg mortality (%), fecundity (nº eggs female^-1), and reproductive output (%) were estimated. Prevalence of C. conanobrieni in the studied population was 87.78%. The mean intensity of C. conanobrieni (all life stages) in the population was 11.68 (± 1.98) egg predators per brood mass sample. Infected females brooding late-stage embryos exhibited lower fecundity, lower reproductive performance values, and higher embryo mortality compared to infected females brooding early-stage embryos. Embryo stage and worm infection level negatively impacted fecundity and reproductive output. Worm infection level and the number of adult nemertean worms also negatively affected embryo mortality.

CONCLUSIONS

These results demonstrate an adverse effect of C. conanobrieni on the reproductive performance of P. argus. The interactive impact of this egg predator, natural stressors, and anthropogenic stressors on individual P. argus reproductive performance could facilitate losses at large-scale fisheries levels.

Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae

Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as 'vulnerable', 'endangered', and 'near threatened', respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.

Low coverage sequencing provides insights into the key features of the nuclear and mitochondrial genomes of the Alligator Snapping Turtle Macrochelys temminckii

The alligator snapping turtle Macrochelys temminckii is a culturally, ecologically, and evolutionary relevant species of conservation concern. In this study, we conducted a genome survey of M. temminckii. Using a low-coverage short read sequencing strategy, this study estimated the genome size, repetitive genome content, annotated and quantified repetitive elements, assembled the 45S rRNA DNA operon, and characterized in detail the mitochondrial genome of M. temminckii. Using a k-mer strategy, the estimated haploid genome size varied between 3.77 and 3.19 Gbp, which is within the range previously reported for other representatives of the family Chelydridae. Repetitive genome content estimates using different k-mers (21 to 51) indicated that more than 75% of the genome of M. temminckii comprised repetitive elements. Taking into account only annotated repetitive elements, the most common repetitive elements were classified as Class I - Long Interspersed Nuclear Element (LINE) which were more abundant than Class I - Penelope and Class I - Long Terminal Repeat (LTR) Ty3-gypsy mobile elements. Less abundant repeat element families in the nuclear genome of M. temminckii included Class I - DIRS mobile elements and Satellite DNA. The nuclear ribosomal operon was partially assembled into two contigs, one encoding the complete ssrDNA and a second comprising the full lsrDNA. The AT-rich complete mitochondrial genome was 16,570 bp long. These new genomic resources are of utmost importance to aid in the development of conservation plans for this freshwater turtle.

Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica

The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered 'endangered' by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.

The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes

The roosterfish Nematistius pectoralis is considered as one of the most magnificent sportfishes worldwide. This study developed the first genomic resource for this trophy-fish that is heavily targeted by the fly-fishing industry. The complete mitochondrial genome of N. pectoralis was assembled using short read sequences and analyzed in detail. The mitochondrial genome of N. pectoralis is 16,537 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S and 16S), and 22 transfer RNA genes. A long intergenic space 770 bp in length was assumed to be the D-loop or Control Region (CR). Most of the PCGs and tRNA genes are encoded in the L-strand. All PCGs are under purifying selection and atp8 and nad6 experienced the least selective pressure. All tRNAs exhibit a cloverleaf secondary structure except tRNA-Serine 1 that lacked the D-arm loop. The D-loop of N. pectoralis exhibits three domains commonly described in other fishes; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the newly recognized order Carangiformes based on all 13 mitochondrial PCGs did not support the monophyly of this clade but recognized several families as monophyletic, including Bothidae, Carangidae, Istiophoridae, Latidae, Paralichthyidae, Polynemidae, and Rhombosoleidae. Nematistius pectoralis was sister to a clade composed of Toxotes chatareus (fam. Toxotidae) + Lactarius lactarius (fam. Lactariidae). This genomic resource developed for N. pectoralis will aid in improving our understanding of the population genomics of and strengthen conservation and management strategies in this remarkable trophy-fish.

First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird's) tapir (Tapirus bairdii)

Baird's tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America, and is categorized as 'endangered' on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG's). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length consisting of 13 protein-coding genes (PCG's), two ribosomal RNA genes (rrnS (12s ribosomal RNA and rrnL (16s ribosomal RNA)), and 22 transfer RNA (tRNA) genes. A 33 bp long region was identified to be the origin of replication for the light strand (O_L), and a 1,247 bp long control region (CR) contains the origin of replication for the heavy strand (O_H). A majority of the PCG's and tRNA genes are encoded on the positive, or heavy, strand. The gene order in T. baiirdi is identical to that of T. indicus and T. terrestris, the only two other species of extant tapirs with assembled mitochondrial genomes. An analysis of Ka/Ks ratios for all the PCG's show values <1, suggesting that all these PCGs experience strong purifying selection. A maximum-likelihood phylogenetic analysis supports the monophyly of the genus Tapirus and the order Perissodactyla. The complete annotation and analysis of the mitochondrial genome of T. bairdii will contribute to a better understanding of the population genomic diversity and structure of this species, and it will assist in the conservation and protection of its dwindling populations.

Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis

Background

Whole mitochondrial genomes are quickly becoming markers of choice for the exploration of within-species genealogical and among-species phylogenetic relationships. Most often, ‘primer walking’ or ‘long PCR’ strategies plus Sanger sequencing or low-pass whole genome sequencing using Illumina short reads are used for the assembling of mitochondrial chromosomes. In this study, we first confirmed that mitochondrial genomes can be sequenced from long reads using nanopore sequencing data exclusively. Next, we examined the accuracy of the long-reads assembled mitochondrial chromosomes when comparing them to a ‘gold’ standard reference mitochondrial chromosome assembled using Illumina short-reads sequencing.

Results

Using a specialized bioinformatics tool, we first produced a short-reads mitochondrial genome assembly for the silky shark C. falciformis with an average base coverage of 9.8x. The complete mitochondrial genome of C. falciformis was 16,705 bp in length and 934 bp shorter than a previously assembled genome (17,639 bp in length) that used bioinformatics tools not specialized for the assembly of mitochondrial chromosomes. Next, low-pass whole genome sequencing using a MinION ONT pocket-sized platform plus customized de-novo and reference-based workflows assembled and circularized a highly accurate mitochondrial genome in the silky shark Carcharhinus falciformis. Indels at the flanks of homopolymer regions explained most of the dissimilarities observed between the ‘gold’ standard reference mitochondrial genome (assembled using Illumina short reads) and each of the long-reads mitochondrial genome assemblies. Although not completely accurate, mitophylogenomics and barcoding analyses (using entire mitogenomes and the D-Loop/Control Region, respectively) suggest that long-reads assembled mitochondrial genomes are reliable for identifying a sequenced individual, such as C. falciformis, and separating the same individual from others belonging to closely related congeneric species.

Conclusions

This study confirms that mitochondrial genomes can be sequenced from long-reads nanopore sequencing data exclusively. With further development, nanopore technology can be used to quickly test in situ mislabeling in the shark fin fishing industry and thus, improve surveillance protocols, law enforcement, and the regulation of this fishery. This study will also assist with the transferring of high-throughput sequencing technology to middle- and low-income countries so that international scientists can explore population genomics in sharks using inclusive research strategies. Lastly, we recommend assembling mitochondrial genomes using specialized assemblers instead of other assemblers developed for bacterial and/or nuclear genomes.

Observations on the Population Genetic Structure of the Leaf Galling Nematode, Ditylenchus gallaeformans

Ditylenchus gallaeformans is a plant parasitic nematode that induces galls on aboveground parts of Melastomataceae plants. It differs from most gall-inducing nematodes in that it is not an endoparasite and has been considered as a possible biological control agent against invasive species of Miconia. Little is known about D. gallaeformans biology, genetic differences among populations, and host preferences. This study examined the genetic differences among D. gallaeformans populations from different locations and host species and the phylogenetic relationships among them. Nematodes were collected from galls in plants from Costa Rica, Dominica, and Trinidad. The Cytochrome c oxidase 1 (cox1) region was sequenced from a total of 33 individual nematodes isolated from 33 different plant individuals, representing 21 species of Melastomataceae. Phylogenetic reconstructions, haplotype networks, and analysis of molecular variance showed that the species is monophyletic and has three major clades, which were mostly consistent with geographic location but not with host species. The first clade was composed by two subclades, one with individuals from Costa Rica and one with individuals from Dominica. The second and third clades comprised nematodes only from Trinidad. Overall, there is no evidence of host-species specialization in D. gallaeformans. Biocontrol efforts using the nematode against invasive Miconia could focus on geographical location matching but likely will not need to match host species.

Genome survey sequencing of the phyto-parasitic nematode Hoplolaimus galeatus

BACKGROUND

Hoplolaimus galeatus is a plant-parasite nematode with a broad range of hosts. This nematode is known to damage cotton, corn, and soybean crops. Hoplolaimus galeatus is also an economically important pest of turfgrasses. Despite its economical importance, no genomic resources exist for this parasite.

METHODS

Using 300 bp paired-end short read sequencing, this study estimated genome size, analyzed a nearly complete mitochondrial chromosome, and explored nuclear repetitive elements, including microsatellites, in H. galeatus for the first time. The phylogenetic placement of H. galeatus in the superfamily Tylenchoidea was also examined.

RESULTS

The average haploid genome size estimated using a k-mer approach was 517.69 Mbp. The partially assembled mitochondrial genome of H. galeatus is 16,578 bp in length and comprised of 11 protein-coding genes, two ribosomal RNA genes, and 16 transfer RNA genes. A maximum likelihood phylogenetic analysis confirmed the monophyly of the genus Hoplolaimus and the superfamily Tylenchoidea. Repetitive elements constituted  50% of the nuclear genome while half of the genome represented single- or low-copy sequences. A large portion of repetitive sequences could not be assigned to known repeat element families. Considering only annotated repetitive elements, the most ubiquitous belonged to Class II- Subclass 2-Maverick elements, Class I-LTR-Ty-3/Bel-Pao elements, and satellites. 45S ribosomal DNA was also abundant and a total of 36 SSRs were identified.This study developed genomic resources for the plant-parasitic nematode Hoplolaimus galeatus that will contribute to the better understanding of meta-population connectivity and putative genomic mechanisms involved in the exploitation of the broad range of host plants used by H. galeatus.

First Genomic Resource of the Columbia Lance Nematode Hoplolaimus columbus

The Columbia lance nematode Hoplolaimus columbus has been reported frequently from North America due to its negative impact on agricultural production. In this study, for the first time, we sequenced the whole genome of a female specimen by using whole-genome amplification and Illumina MiSeq. Data were de novo assembled to form scaffolds of 205.75 Mbp consisting of 118,374 contigs. The largest scaffold was 636,881 bp. Benchmarking Universal Single-Copy Orthologs completeness was 66.6% (eukaryotic dataset), and >8,000 unique genes were predicted by GeneMark-ES. In total, 61,855 protein sequences were predicted by AUGUSTUS, and 10,085 of them were annotated by PANNZER2 with at least one function. These data will provide valuable resources for studies focusing on pathogenicity and phylogenomics of plant-parasitic nematodes.

A genomic portrait of Sturnira parvidens: mitochondrial chromosome, repetitive elements, and microsatellite discovery

The yellow-shouldered bat, Sturnira parvidens (Phyllostomidae), is an abundant and widespread species in southern North America and Mesoamerica. Despite its important ecological role, no genomic resources exist for this species. Using low-coverage short Illumina 150 bp pair-end reads sequencing, this study reports the mitochondrial chromosome and nuclear repetitive elements, including microsatellites, in S. parvidens. The mitochondrial genome of S. parvidens is 16,612 bp in length and is comprised of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Repetitive elements constituted ~67% of the nuclear genome while ~33% of the genome represented single- or low-copy sequences. A moderate proportion of repetitive sequences (31% putative families) could not be assigned to known repeat element families. Considering only annotated repetitive elements, the most ubiquitous repetitive elements belonged to Class I-LINE and Satellite DNA, which were considerably more abundant than Class I-LTR elements and Class II-DNA transposons (TcMar-Mariner and hAT-Charlie). A total of 193 microsatellites were identified.

The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico

BACKGROUND

The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species.

METHODS AND RESULTS

This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150 bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400 bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs.

CONCLUSIONS

This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species.

Genome Survey Sequencing of an Iconic 'Trophy' Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery

The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation of Nature, N. pectoralis is assessed globally as Data Deficient. Using low-coverage short Illumina 300 bp pair-end reads sequencing, this study reports, for the first time, the genome size, single/low-copy genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon and microsatellites, in N. pectoralis. The haploid genome size estimated using a k-mer approach was 816.04 Mbp, which is within the range previously reported for other representatives of the Carangiformes order. Single/low-copy genome content (63%) was relatively high. A large portion of repetitive sequences could not be assigned to the known repeat element families. Considering only annotated repetitive elements, the most common were classified as Satellite DNA which were considerably more abundant than Class I-Long Interspersed Nuclear Elements and Class I-LTR Retroviral elements. The nuclear ribosomal operon in N. pectoralis consists of, in the following order: a 5′ ETS (length = 948 bp), ssrDNA (1835 bp), ITS1 (724 bp), a 5.8S rDNA (158 bp), ITS2 (508 bp), lsrDNA (3924 bp), and a 3′ ETS (32 bp). A total of 44 SSRs were identified. These newly developed genomic resources are most relevant for improving the understanding of biology, developing conservation plans, and managing the fishery of the iconic N. pectoralis.

Continuous aqueous phase reforming of a synthetic brewery wastewater with Pt/C and PtRe/C catalysts for biohydrogen production

This work investigates H₂ production through aqueous phase reforming (APR) of synthetic brewery wastewater in a continuous fixed bed reactor with Pt and PtRe (3 wt %) catalysts supported on activated carbon. The influence of weight hourly space velocity (WHSV) and superficial Ar gas flow velocity (V_Ar) was assessed for the sake of optimisation, while reaction temperature and pressure were maintained at 225 °C and 28 bar, respectively. H₂ production was found to be higher using the PtRe catalyst at the lowest WHSV (0.03 h^-1) and highest V_Ar (0.8 cm s^-1). The comparison of the maximum H₂ production obtained in this work (27.9 μmol min^-1) with other treatment processes shows the potential of the application of APR process for H₂ production from brewery wastewater. Despite the different reaction conditions tested, the catalysts showed deactivation with time on stream, which was related to the formation of solid deposits on the surface of the catalysts. Therefore, future research should be related to the development of more stable catalysts, strategies that avoid deactivation by coking and regeneration processes.

Thor dicaprio sp. nov., a new, conspicuously coloured shrimp from the tropical western Atlantic, with taxonomic remarks on the T. amboinensis (De Man, 1888) complex (Decapoda: Caridea: Thoridae)

Thor amboinensis (De Man, 1888), known as sexy shrimp or anemone squat shrimp and popular among divers and aquarists, was previously believed to have a worldwide distribution, with populations throughout the tropical parts of the Indo-Pacific and Atlantic Ocean. However, consistent differences in some details of the colour pattern strongly suggest that T. amboinensis does not represent a single species, but a pantropical species complex. A recent phylogeographic analysis of T. amboinensis based on molecular data confirmed that this taxon is composed of at least five putative cryptic or pseudocryptic species. In the present study, a new cryptic species, Thor dicaprio sp. nov., is established for the western Atlantic populations previously referred to as T. amboinensis. The new species can be distinguished from all other members of the T. amboinensis complex by two differences in the colour pattern and a subtle difference in the size and setation of the appendix masculina, the latter yet to be confirmed. The conspicuous red-white banding of the antennal flagella appears to be the most diagnostic feature of the new species. In addition, T. dicaprio sp. nov. forms a genetically distinctive, homogeneous, tropical western Atlantic (TWA) clade, with the COI pairwise genetic distances from other clades ranging from 8.8% to 19.2%. The distribution of T. dicaprio sp. nov. includes the entire Caribbean Sea, parts of the Gulf of Mexico, Florida, Bahamas, Bermuda, as well as some offshore localities off northern and eastern Brazil. The main aspects and biology and ecological variability of T. dicaprio sp. nov. are discussed in the light of phylogeographic data presently available for the T. amboinensis complex.

The complete mitochondrial genome of the Honduran white bat Ectophylla alba (Allen 1982) (Chiroptera: Phyllostomidae)

The Honduran white bat, Ectophylla alba (Allen 1982), is one of eight species belonging to the family Phyllostomidae that exclusively roosts in tents. Due to its restricted distribution, habitat specificity, and diet requirements, E. alba has been strongly affected by habitat loss and fragmentation during the last decade. In this study, we developed the first genomic resource for this species; we assembled and analyzed in detail the complete mitochondrial genome of E. alba. The mitogenome of E. alba is 16,664 bp in length and is comprised of 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes (tRNAs), and a putative Control Region (CR) 1,232 bp in length. Gene arrangement in the mitochondrial chromosome of E. alba is identical to that reported before in other species of co-familiar bats. All PCGs are under purifying selection, with atp8 experiencing the least selective pressure. In all PCGs, codons ending with adenine are preferred over others ending in thymine and cytosine. Except tRNA-Serine 1, all tRNAs exhibit a cloverleaf secondary structure. The CR of E. alba exhibits three domains commonly described in other mammals, including bats; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the family Phyllostomidae based on all 13 mitochondrial PCGs confirms the monophyletic status of the subfamily Sternodermatinae and indicates the close relationship between E. alba and the genus Artibeus. This is the first genomic resource developed for E. alba and represents the first step to improving our understanding of the genomic underpinnings involved in the evolution of specialization as well as acclimatization and adaptation to local and global change of specialist bats.

The mitochondrial genome of the endangered Spiny Butterfly Ray Gymnura altavela (Linnaeus 1758) (Myliobatiformes: Gymnuridae) provides insights into cryptic lineages

The Spiny Butterfly Ray, Gymnura altavela, is found in tropical and temperate coastal waters with a discontinuous distribution: it occurs along the east coast of the United States of America, Brazil, and Uruguay in the western Atlantic Ocean, from Portugal to Angola in the eastern Atlantic, and also in the Mediterranean Sea. Globally, Gymnura altavela is considered endangered by the International Union for Conservation of Nature (IUCN). Our study analyzed the complete mitochondrial genome of G. altavela sequenced from an individual captured in the western Atlantic and compared it with a mitochondrial genome from a conspecific collected in the Mediterranean to explore if G. altavela comprises cryptic species. The newly assembled mitochondrial genome of G. altavela is 19,361bp in length and has 13 protein-coding genes (PCGs), two ribosomal RNA genes (12s ribosomal RNA and 16s ribosomal RNA), 22 transfer RNA (tRNA) genes, and a 3,659 bp control region. The gene order is identical to that reported for the specimen collected in the Mediterranean and that of the congeneric Long-tailed Butterfly Ray, G. poecilura. A phylomitogenomic analysis based on translated PCGs supported the monophyly of the genus Gymnura and indicated that genetic dissimilarity between G. altavela from the western Atlantic Ocean and the Mediterranean Sea was greater than that calculated among congeneric species belonging to the genera Mobula and Neotrygon, similar to that calculated among congeneric stingrays in the genus Hemitrygon, but lower than that calculated among congeneric species in the genera Pateobatis and Urogymnus. Overall, our comparisons suggest that G. altavela comprises cryptic species or at least indicates considerable genetic structure between populations in the western Atlantic and Mediterranean. We present these findings in a phylomitogenomic analysis of other Myliobatiformes and Rhinopristiformes. Additional phylogeographic and taxonomic studies of G. altavela are needed to support conservation efforts for this endangered ray that may comprise cryptic evolutionary units.

Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation

Background

The complex life cycle of the coconut crab, Birgus latro, begins when an obligate terrestrial adult female visits the intertidal to hatch zoea larvae into the surf. After drifting for several weeks in the ocean, the post-larval glaucothoes settle in the shallow subtidal zone, undergo metamorphosis, and the early juveniles then subsequently make their way to land where they undergo further physiological changes that prevent them from ever entering the sea again. Here, we sequenced, assembled and analyzed the coconut crab genome to shed light on its adaptation to terrestrial life. For comparison, we also assembled the genomes of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus, and the short-tailed marine-living red king crab, Paralithodes camtschaticus. Our selection of the latter two organisms furthermore allowed us to explore parallel evolution of the crab-like form in anomurans.

Results

All three assembled genomes are large, repeat-rich and AT-rich. Functional analysis reveals that the coconut crab has undergone proliferation of genes involved in the visual, respiratory, olfactory and cytoskeletal systems. Given that the coconut crab has atypical mitochondrial DNA compared to other anomurans, we argue that an abundance of kif22 and other significantly proliferated genes annotated with mitochondrial and microtubule functions, point to unique mechanisms involved in providing cellular energy via nuclear protein-coding genes supplementing mitochondrial and microtubule function. We furthermore detected in the coconut crab a significantly proliferated HOX gene, caudal, that has been associated with posterior development in Drosophila, but we could not definitively associate this gene with carcinization in the Anomura since it is also significantly proliferated in the ornate spiny lobster. However, a cuticle-associated coatomer gene, gammacop, that is significantly proliferated in the coconut crab, may play a role in hardening of the adult coconut crab abdomen in order to mitigate desiccation in terrestrial environments.

Conclusion

The abundance of genomic features in the three assembled genomes serve as a source of hypotheses for future studies of anomuran environmental adaptations such as shell-utilization, perception of visual and olfactory cues in terrestrial environments, and cuticle sclerotization. We hypothesize that the coconut crab exhibits gene proliferation in lieu of alternative splicing as a terrestrial adaptation mechanism and propose life-stage transcriptomic assays to test this hypothesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07636-9.

Comparative mitochondrial genomics of sponge-dwelling snapping shrimps in the genus Synalpheus: Exploring differences between eusocial and non-eusocial species and insights into phylogenetic relationships in caridean shrimps

The genus Synalpheus is a cosmopolitan clade of marine shrimps found in most tropical regions. Species in this genus exhibit a range of social organizations, including pair-forming, communal breeding, and eusociality, the latter only known to have evolved within this genus in the marine realm. This study examines the complete mitochondrial genomes of seven species of Synalpheus and explores differences between eusocial and non-eusocial species considering that eusociality has been shown before to affect the strength of purifying selection in mitochondrial protein coding genes. The AT-rich mitochondrial genomes of Synalpheus range from 15,421 bp to 15,782 bp in length and comprise, invariably, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 648 bp to 994 bp long intergenic space is assumed to be the D-loop. Mitochondrial gene synteny is identical among the studied shrimps. No major differences occur between eusocial and non-eusocial species in nucleotide composition and codon usage profiles of PCGs and in the secondary structure of tRNA genes. Maximum likelihood phylogenetic analysis of the complete concatenated PCG complement of 90 species supports the monophyly of the genus Synalpheus and its family Alpheidae. Moreover, the monophyletic status of the caridean families Alvinocaridae, Atyidae, Thoridae, Lysmatidae, Palaemonidae, and Pandalidae within caridean shrimps are fully or highly supported by the analysis. We therefore conclude that mitochondrial genomes contain sufficient phylogenetic information to resolve relationships at high taxonomic levels within the Caridea. Our analysis of mitochondrial genomes in the genus Synalpheus contributes to the understanding of the coevolution between genomic architecture and sociality in caridean shrimps and other marine organisms.

A first look at the 'repeatome' of Benedenia humboldti, a major pathogen in yellowtail aquaculture: Repetitive element characterization, nuclear rRNA operon assembly, and microsatellite discovery

The monogenean Benedenia humboldti is a pathogen of the yellowtail Seriola lalandi in the South-Eastern Pacific ocean. Using low-coverage short Illumina 150bp pair-end reads sequencing, this study examines, for the first time, the 'repeatome' (= repetitive genomic elements), including the 45S ribosomal RNA DNA operon and microsatellites, in B. humboldti. Repetitive elements comprised a large fraction of the nuclear genome and a considerable proportion of them could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to the 45S ribosomal RNA operon or were classified as satellite DNA and Class I - Long Interspersed Nuclear Elements (LINEs) which were considerably more abundant than Class I - LTR elements. The ribosomal RNA gene operon in B. humboldti is comprised of, in the following order, a 5' ETS (length = 233 bp), ssrDNA (2082 bp), ITS1 (346 bp), 5.8S rDNA (150 bp), ITS2 (572 bp), lsrDNA (3887 bp), and a 3' ETS (1097 bp). A total of 15 SSRs were identified. These newly developed genomic resources will contribute to the better understanding of meta-population connectivity in this species, cryptic species in the genus, and will advance pest management strategies.

Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery

BACKGROUND

Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region.

METHODS

This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus.

RESULTS

Using a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5' ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3' ETS (287 bp). A total of 1,281 SSRs were identified.

Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus

Background

Whole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ‘primer walking’ or ‘long PCR’ followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a ‘gold’ standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobster Panulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region.

Results

LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not ‘perfect’, phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other related species in the same genus, family, and superorder.

Conclusions

This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.

Aqueous phase reforming coupled to catalytic wet air oxidation for the removal and valorisation of phenolic compounds in wastewater

Aqueous phase reforming (APR) coupled to catalytic wet air oxidation (CWAO) has been investigated as an approach to remove phenolic compounds from wastewater, converting them into valuable gases. Partial oxidation of phenol was achieved in the first CWAO stage trying to minimize mineralization so to allow a high yield to valuable gases in the second APR stage. APR runs were carried out with different mixtures of compounds corresponding to phenol oxidation pathway (phenol, quinones, long and short chain acids) and representing different degrees of oxidation in CWAO stage. A range of TOC and COD removal (74-90%) was observed in APR stage for the single compounds, with higher removal for long chain acids. Likewise, long chain acids provided with the highest conversion to gases. APR of mixtures rich in acids gave the highest yield to CH₄ (11.0 mmol CH₄/g TOC_initial). H₂ production was low in all cases, due to competing direct conversion of long and short chain acids into CH₄. TOC and COD removal from wastewater was similar in APR-CWAO and APR, however the conversion to gases and the yield to CH₄ were markedly higher for APR-CWAO, thus overcoming the difficulties previously observed in the direct APR of phenol.

The complete mitochondrial genome of the red-jointed brackish-water fiddler crab Minuca minax (LeConte 1855) (Brachyura: Ocypodidae): New family gene order, and purifying selection and phylogenetic informativeness of protein coding genes

Minuca minax is a semi-terrestrial crustacean that commonly lives in low salinity, riverine habitats along the shores of the eastern United States. This study reports, for the first time, the complete mitochondrial genome of M. minax. The AT-rich mitochondrial genome of M. minax is 15,937 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 737 bp long intergenic space is assumed to be the D-loop. Most of the PCGs and tRNA genes are encoded in the L-strand. The gene order observed in the mitochondrial genome of M. minax is new although almost identical to that reported in confamiliar species. In all other confamiliar species to which M. minax is compared, the positions of the trnQ gene and the trnI gene are switched. K_A/K_S ratios calculated for all mitochondrial PCGs show values of <1, indicating that these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n = 13], 15 species) supports the monophyly of the subfamilies Ocypodinae and Gelaminidae. Mitochondrial PCGs have enough phylogenetic information to reveal relationships supporting higher taxonomic levels within this family. The knowledge of a complete mitochondrial genome from the red-jointed brackish-water fiddler crab M. minax contributes to the better understanding of meta-population connectivity and the mechanisms involved in the adaptation of marine organisms to near-limnic conditions.

The complete mitochondrial genome of the Columbia lance nematode, Hoplolaimus columbus, a major agricultural pathogen in North America

BACKGROUND

The plant-parasitic nematode Hoplolaimus columbus is a pathogen that uses a wide range of hosts and causes substantial yield loss in agricultural fields in North America. This study describes, for the first time, the complete mitochondrial genome of H. columbus from South Carolina, USA.

METHODS

The mitogenome of H. columbus was assembled from Illumina 300 bp pair-end reads. It was annotated and compared to other published mitogenomes of plant-parasitic nematodes in the superfamily Tylenchoidea. The phylogenetic relationships between H. columbus and other 6 genera of plant-parasitic nematodes were examined using protein-coding genes (PCGs).

RESULTS

The mitogenome of H. columbus is a circular AT-rich DNA molecule 25,228 bp in length. The annotation result comprises 12 PCGs, 2 ribosomal RNA genes, and 19 transfer RNA genes. No atp8 gene was found in the mitogenome of H. columbus but long non-coding regions were observed in agreement to that reported for other plant-parasitic nematodes. The mitogenomic phylogeny of plant-parasitic nematodes in the superfamily Tylenchoidea agreed with previous molecular phylogenies. Mitochondrial gene synteny in H. columbus was unique but similar to that reported for other closely related species.

CONCLUSIONS

The mitogenome of H. columbus is unique within the superfamily Tylenchoidea but exhibits similarities in both gene content and synteny to other closely related nematodes. Among others, this new resource will facilitate population genomic studies in lance nematodes from North America and beyond.

The complete mitochondrial genome of the eusocial sponge-dwelling snapping shrimp Synalpheus microneptunus

In the marine realm, eusociality is only known to have evolved within a clade of sponge-dwelling snapping shrimps in the genus Synalpheus. Deciphering the genomic underpinnings of eusociality in these marine shrimps has been limited by the sparse genomic resources in this genus. Here, we report, for a eusocial shrimp Synalpheus microneptunus, a complete mitochondrial genome (22X coverage) assembled from short Illumina 150 bp paired-end reads. The 15,603 bp long mitochondrial genome of S. microneptunus is AT-rich and includes 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and an 834 bp intergenic region assumed to be the D-loop. The gene order is identical to that reported for most caridean shrimps and corresponds to the presumed Pancrustacean ground pattern. All PCGs showed signs of purifying selection, with K_A/K_S <<1 across the whole PCGs and most sliding windows within PCGs. Maximum-likelihood and Bayesian inference phylogenetic analyses of 13 PCGs and 68 terminals supports the monophyly of the Caridea and the family Alpheidae. The complete mitochondrial genome of the eusocial shrimp Synalpheus microneptunus will contribute to a better understanding of the selective pressures and rates of molecular evolution in marine eusocial animals.

Automatic Quality Assessment of Transperineal Ultrasound Images of the Male Pelvic Region, Using Deep Learning

Ultrasound guidance is not in widespread use in prostate cancer radiotherapy workflows. This can be partially attributed to the need for image interpretation by a trained operator during ultrasound image acquisition. In this work, a one-class regressor, based on DenseNet and Gaussian processes, was implemented to automatically assess the quality of transperineal ultrasound images of the male pelvic region. The implemented deep learning approach was tested on 300 transperineal ultrasound images and it achieved a scoring accuracy of 94%, a specificity of 95% and a sensitivity of 92% with respect to the majority vote of 3 experts, which was comparable with the results of these experts. This is the first step toward a fully automatic workflow, which could potentially remove the need for ultrasound image interpretation and make real-time volumetric organ tracking in the radiotherapy environment using ultrasound more appealing.

Life history traits and reproductive performance of the caridean shrimp Lysmata boggessi, a heavily traded invertebrate in the marine aquarium industry

The most intense commercial harvest of marine aquarium species in North America occurs in the coastal waters surrounding Florida, yet very often little information exists on the life histories, population dynamics, or reproductive characteristics of these organisms. The peppermint shrimp Lysmata boggessi is one such species and is heavily targeted along the west coast of Florida. It is known primarily among aquarists for its ability to control pest anemones and in the scientific community for its unique sexual system, protandric simultaneous hermaphroditism. However, no study has addressed fishery interactions or long-term population dynamics for L. boggessi. We used monthly fisheries-dependent sampling, with a trained observer present, for a full year to assess seasonality in sex phase ratio (males to males + hermaphrodites), size at sex change, fecundity, embryo volume and reproductive output of an exploited L. boggessi population. L. boggessi exhibited distinct seasonality in size distribution, sex phase ratio, size at sex phase change and reproductive activity. The peak reproductive season was in spring, when the population was dominated by small but fecund hermaphrodites. Reproduction decreased during fall and winter and sex phase ratios favored male phase shrimp that exhibited delayed sex change. This population and individual level information is the first of its kind for L. boggessi and fills a much needed data gap for the informed management of this fishery.

The complete mitochondrial genome and description of a new cryptic species of Benedenia Diesing, 1858 (Monogenea: Capsalidae), a major pathogen infecting the yellowtail kingfish Seriola lalandi Valenciennes in the South-East Pacific

Background

The monogenean Benedenia seriolae parasitizes fishes belonging to the genus Seriola, represents a species complex, and causes substantial impact on fish welfare in aquaculture systems worldwide. This study reports, for the first time, the complete mitochondrial genome of B. humboldti n. sp., a new cryptic species from the South-East Pacific (SEP).

Methods

The mitogenome of B. humboldti n. sp. was assembled from short Illumina 150 bp pair-end reads. The phylogenetic position of B. humboldti n. sp. among other closely related congeneric and confamiliar capsalids was examined using mitochondrial protein-coding genes (PCGs). Morphology of B. humboldti n. sp. was examined based on fixed and stained specimens.

Results

The AT-rich mitochondrial genome of B. humboldti is 13,455 bp in length and comprises 12 PCGs (atp8 was absent as in other monogenean genomes), 2 ribosomal RNA genes, and 22 transfer RNA genes. All protein-coding, ribosomal RNA, and transfer RNA genes are encoded on the H-strand. The gene order observed in the mitochondrial genome of B. humboldti n. sp. was identical to that of B. seriolae from Japan but different from that of B. seriolae from Australia. The genetic distance between B. humboldti n. sp. and B. seriolae from Japan was high. Minor but reliable differences in the shape of the penis were observed between Benedenia humboldti n. sp. and congeneric species.

Conclusions

Phylogenetic analyses based on PCGs in association with differences in the shape of the penis permitted us to conclude that the material from the South-East Pacific represents a new species of Benedenia infecting S. lalandi off the coast of Chile. The discovery of this parasite represents the first step to improving our understanding of infestation dynamics and to develop control strategies for this pathogen infecting the farmed yellowtail kingfish, Seriola lalandi, in the South-East Pacific.

The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus

Panulirus argus is a keystone species and target of the most lucrative fishery in the Caribbean region. This study reports, for the first time, the complete mitochondrial genome of Panulirus argus (average coverage depth nucleotide-1 = 70×) assembled from short Illumina 150 bp PE reads. The AT-rich mitochondrial genome of Panulirus argus was 15 739 bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 801 bp long intergenic space was assumed to be the D-loop. Most of the PCGs were encoded on the H-strand. The gene order observed in the mitochondrial genome of Panulirus argus corresponds to the presumed Pancrustacean ground pattern. KA/KS ratios calculated for all mitochondrial PCGs showed values < 1, indicating that all these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n = 13], 154 arthropods) supported the monophyly of the Achelata and other infraorders within the Decapoda. Mitochondrial PCGs have enough phylogenetic informativeness to explore high-level genealogical relationships in the Pancrustacea. The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus will contribute to the better understanding of meta-population connectivity in this keystone overexploited species.

Lysmata arvoredensis nov. sp. a new species of shrimp from the south coast of Brazil with a key to species of Lysmata (Caridea: Lysmatidae) recorded in the southwestern Atlantic

Lysmata arvoredensis sp. nov. inhabits temperate waters in the south coast of Brazil and is named in tribute to the Marine Protected Area REBIO Arvoredo. This is the fourth species belonging to the genus Lysmata recorded for the region and the ninth for Brazil. L. arvoredensis sp. nov. can be distinguished from other species of Lysmata by the presence of a nearly completely fused accessory branch with a single free unguiform segment on the outer antennular flagellum; a rostrum with seven dorsal (2+5) and three ventral teeth; a stylocerite with a pointed tip bearing mesial setae; a second pereiopod with 22-24 carpal subsegments and 14-16 subsegments in the merus; a merus of the third pereiopod with five ventrolateral and 12 ventral spines on the propodus; and its color pattern, with red bands and patches in pleonites 2-3 that resemble a mask in dorsal view. Molecular characters demonstrate that L. arvoredensis sp. nov. is most closely related to other species of Lysmata belonging to the Neotropical and Cleaner clades. To support future ecological studies in the region, identification keys to the species of Lysmata recorded in the southwestern Atlantic Ocean are provided.

Embryonic Development in the Peppermint Shrimp, Lysmata boggessi (Caridea: Lysmatidae)

There are a limited number of model species for decapod experimental embryology. To improve our understanding of developmental pattern evolution in the Decapoda, here we describe the early embryonic development of the caridean shrimp Lysmata boggessi, from immediately after fertilization to the hatching of the zoea larva, using fluorescence microscopy and whole-mount nuclear staining with 4',6-diamidino-2-phenylindole. Lysmata boggessi follows the standard caridean pattern of early development, with early holoblastic cleavage that will later become superficial, to form a blastoderm. We found no evidence of stereotypical cleavage and the formation of blastomere interlocking bands, which suggests there is diversity in developmental patterns within the Caridea. Gastrulation starts 37 hours after fertilization, and the embryonized nauplius is formed 2 days later. Enlarged headlobes, early retinal differentiation, and delayed pereopod development are characteristics of the post-naupliar stages in this species. To facilitate comparative studies with other crustacean species, we propose a staging method based on our findings. Lysmata boggessi is a protandric simultaneous hermaphrodite that is relatively easy to breed in captivity and amenable to laboratory experimentation in studies of embryonic development.

A new species of <i>Lysmata</i> Risso, 1816 (Crustacea, Decapoda, Lysmatidae) from the Gulf of Mexico

A new species of peppermint shrimp, Lysmata baueri n. sp., is described based on a single specimen from the eastern Gulf of Mexico. The new species can be distinguished from other morphologically similar species of Lysmata Risso, 1816 by the number of teeth, length and shape of the rostrum, the length of the antennular peduncle relative to the scaphocerite, the number of meral and ischial articles in the second pereiopods, and the number of spines on the flexor margin of the dactyli from the third to fifth pereiopods. Morphological characters demonstrate that L. baueri n. sp., is most closely related to the eastern Pacific L. californica (Stimpson, 1866), L. nayaritensis Wicksten, 2000 and L. porteri (Rathbun, 1907).

Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide

The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across  550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.

A new species of Carcinonemertes, Carcinonemertes conanobrieni sp. nov. (Nemertea: Carcinonemertidae), an egg predator of the Caribbean spiny lobster, Panulirus argus

A new species of nemertean worm belonging to the genus Carcinonemertes is described from egg masses of the Caribbean spiny lobster Panulirus argus from the Florida Keys, Florida, USA. This is the first species of Carcinonemertes reported to infect P. argus or any other lobster species in the greater Caribbean and western Atlantic Ocean. Carcinonemertes conanobrieni sp. nov. varies in body color from a translucent white to a pale orange, with males ranging in total body length from 2.35 to 12.71 mm and females ranging from 0.292 to 16.73 mm. Among the traits that separate this new species from previously described species in the genus Carcinonemertes are a relatively wide stylet basis, minimal sexual size dimorphism, and a unique mucus sheath decorated with external hooks. Also, juvenile worms were found to encyst themselves next to lobster embryos and female worms lay both long strings of eggs wound throughout the lobster's setae as well as spherical cases that are attached to lobster embryos. The stylet length and stylet basis remain unchanged throughout ontogeny for both male and female worms. Maximum likelihood and Bayesian inference phylogenetic analyses separated this newly described species from all other species of Carcinonemertes with available COI sequences. Carcinonemertes spp. are voracious egg predators and have been tied to the collapse of various crustacean fisheries. The formal description of this new species represents the first step to understand putative impacts of this worm on the population health of one of the most lucrative yet already depressed crustacean fisheries.

Dose painting by means of Monte Carlo treatment planning at the voxel level

PURPOSE

To develop a new optimization algorithm to carry out true dose painting by numbers (DPBN) planning based on full Monte Carlo (MC) calculation.

METHODS

Four configurations with different clustering of the voxel values from PET data were proposed. An optimization method at the voxel level under Lineal Programming (LP) formulation was used for an inverse planning and implemented in CARMEN, an in-house Monte Carlo treatment planning system.

RESULTS

Beamlet solutions fulfilled the objectives and did not show significant differences between the different configurations. More differences were observed between the segment solutions. The plan for the dose prescription map without clustering was the better solution.

CONCLUSIONS

LP optimization at voxel level without dose-volume restrictions can carry out true DPBN planning with the MC accuracy.

Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor

Management of the few regulated ornamental fisheries relies on inadequate information about the life history of the target species. Herein, we investigated the reproductive biology of the most heavily traded marine invertebrate in the western Atlantic; the blue-legged hermit crab Clibanarius tricolor. We report on density, individual-level, and population-level reproductive parameters in 14 populations spanning the Florida Keys. In C. tricolor, abundance, population-level, and individual-level reproductive parameters exhibited substantial small-scale spatial variation in the Florida Keys. For instance, the proportion of brooding females varied between 10-94% across localities. In females, average (±SD) fecundity varied between 184 (±54) and 614 (±301) embryos crab-1 across populations. Fecundity usually increases with female body size in hermit crabs. However, we found no effect of female body size on fecundity in three of the populations. Altogether, our observations suggest that C. tricolor may fit a source-sink metapopulation dynamic in the Florida Keys with low reproductive intensity and absence of a parental body size-fecundity relationship resulting in net reproductive loses at some localities. We argue in favor of additional studies describing population dynamics and other aspects of the natural history of C. tricolor (e.g., development type, larval duration) to reveal 'source' populations, capable of exporting larvae to nearby populations. Our observations imply that future studies aimed at assessing standing stocks or describing other aspects of the life history of this hermit crab need to focus on multiple localities simultaneously. This and future studies on the reproductive biology of this species will form the baseline for models aimed at assessing the stock condition and sustainability of this heavily harvested crustacean.