First observations of intersex development in paddlefish Polyodon spathula

This study reports the first cases of intersex (abnormal development of both male and female reproductive tissues in a gonad) paddlefish Polyodon spathula, an Acipenseriform species of large rivers in the central U.S. and in aquaculture worldwide. Despite a large, multi-decadal data set in Oklahoma, Montana, and North Dakota, intersex development was not observed until 2019, when two individuals were harvested from the Grand Lake/Neosho River stock in Oklahoma. This suggests that intersex development in mid-water, zooplanktivorous paddlefish is rarer than in bottom-dwelling sturgeons for which intersex development is regularly observed. Although contaminants are implicated in causing intersex development in other Acipenseriformes, more investigation is needed.     

Evolution of MHC class I genes in two ancient fish, paddlefish (Polyodon spathula) and Chinese sturgeon (Acipenser sinensis)

Here we present the first isolation of major histocompatibility complex (MHC) class I genes from two ancient fish, paddlefish (Polyodon spathula) and Chinese sturgeon (Acipenser sinensis). Seventeen sequences obtained showed high polymorphism and positive natural selection with d_N/d_S > 1. Evolutionary relationships revealed that sequences from paddlefish and Chinese sturgeon distinguished from other vertebrate class I and had an intermingling of alleles, which indicates that Acipenseriformes have a common ancestral gene of class I and a trans-species polymorphism across Acipenseriformes. We also found clear evidence of recombination among class I genes of paddlefish and Chinese sturgeon.     

Making teeth to order: conserved genes reveal an ancient molecular pattern in paddlefish (Actinopterygii)

Ray-finned fishes (Actinopterygii) are the dominant vertebrate group today (+30 000 species, predominantly teleosts), with great morphological diversity, including their dentitions. How dental morphological variation evolved is best addressed by considering a range of taxa across actinopterygian phylogeny; here we examine the dentition of Polyodon spathula (American paddlefish), assigned to the basal group Acipenseriformes. Although teeth are present and functional in young individuals of Polyodon, they are completely absent in adults. Our current understanding of developmental genes operating in the dentition is primarily restricted to teleosts; we show that shh and bmp4, as highly conserved epithelial and mesenchymal genes for gnathostome tooth development, are similarly expressed at Polyodon tooth loci, thus extending this conserved developmental pattern within the Actinopterygii. These genes map spatio-temporal tooth initiation in Polyodon larvae and provide new data in both oral and pharyngeal tooth sites. Variation in cellular intensity of shh maps timing of tooth morphogenesis, revealing a second odontogenic wave as alternate sites within tooth rows, a dental pattern also present in more derived actinopterygians. Developmental timing for each tooth field in Polyodon follows a gradient, from rostral to caudal and ventral to dorsal, repeated during subsequent loss of teeth. The transitory Polyodon dentition is modified by cessation of tooth addition and loss. As such, Polyodon represents a basal actinopterygian model for the evolution of developmental novelty: initial conservation, followed by tooth loss, accommodating the adult trophic modification to filter-feeding.     

几种鲟鱼基因组大小、倍体的特性及鲟形目细胞进化的探讨

采用Ｆｅｕｌｇｅｎ－显微分光光度计方法,以鸡红细胞为标准ＤＮＡ（３．２２ｐｇ／２Ｃ）测定了长江白鲟、达氏鲟、中华鲟、史氏鲟和北美匙吻鲟的体细胞基因组大小（ＤＮＡ含量）。结果表明,上述五种鲟鱼ＤＮＡ含量分别为４．１１、８．２６、９．０７、６．０７和３．９６ｐｇ。长江白鲟和北美匙吻鲟均属于四倍体鱼类,分布在长江水系的中华鲟和达氏鲟两种鲟属鱼类为八倍体类型。史氏鲟初步判断为八倍体,据分析可能存在四倍体的     

Comparative protein profiles: Potential molecular markers from spermatozoa of Acipenseriformes (Chondrostei,Pisces)

Sturgeon and paddlefish (Acipenseriformes), the source of roe consumed as caviar, are a unique and commercially valuable group of ancient fishes. In this study, comparative proteomics was used to analyze protein profiles of spermatozoa from five sturgeon species and one paddlefish: Siberian sturgeon (Acipenser baerii), sterlet (A. ruthenus), Russian sturgeon (A. gueldenstaedtii), starry sturgeon (A. stellatus), beluga (Huso huso), and Mississippi paddlefish (Polyodon spathula). Protein profiles of spermatozoa were determined by isoelectric focusing and two-dimensional electrophoresis (2-DE) high-resolution gels. The peptides, previously selected by 2-DE analysis as potentially species-specific, were obtained by “in-gel” tryptic digestion, followed by matrix-associated laser desorption/ionization time-of-flight/mass spectrometry (MALDI-TOF/MS). Among the 23 protein spots selected, 14 were identified as isoforms of enolase B present in all species, but with different isoelectric points or molecular mass. Exceptions were A. ruthenus and H. huso, species with a close phylogenetic relationship. Glycerol-3-phosphate dehydrogenase was detected exclusively in P. spathula. Phosphoglycerate kinase was detected only in A. ruthenus and H. huso, and 3 additional proteins (fructose bisphosphate aldolase A-2, glycogen phosphorylase type IV and glyceraldehyde-3-phosphate dehydrogenase) were found exclusively in A. gueldenstaedtii and H. huso. This study points to the application of proteomics for differential characterization and comparative studies of acipenseriform species at the molecular level.     

Unusual intraindividual variation of the nuclear 18S rRNA gene is widespread within the Acipenseridae

Significant intraindividual variation in the sequence of the 18S rRNA gene is unusual in animal genomes. In a previous study, multiple 18S rRNA gene sequences were observed within individuals of eight species of sturgeon from North America but not in the North American paddlefish, Polyodon spathula, in two species of Polypterus (Polypterus delhezi and Polypterus senegalus), in other primitive fishes (Erpetoichthys calabaricus, Lepisosteus osseus, Amia calva) or in a lungfish (Protopterus sp.). These observations led to the hypothesis that this unusual genetic characteristic arose within the Acipenseriformes after the presumed divergence of the sturgeon and paddlefish families. In the present study, a survey of nearly all Eurasian acipenseriform species was conducted to examine 18S rDNA variation. Intraindividual variation was not found in the polyodontid species, the Chinese paddlefish, Psephurus gladius, but variation was detected in all Eurasian acipenserid species. The comparison of sequences from two major segments of the 18S rRNA gene and identification of sites where insertion/deletion events have occurred are placed in the context of evolutionary relationships within the Acipenseriformes and the evolution of rDNA variation in this group.     

Modelling bioenergetic and population-level impacts of invasive bigheaded carps (Hypophthalmichthys spp.) on native paddlefish (Polyodon spathula) in backwaters of the lower Mississippi River

1. While invasions of large rivers by exotic fish species are well documented, assessing actual or potential impacts on native species is a challenge. Rapid assessments may be possible through the application of a combination of bioenergetic and population dynamic models.
2. Paddlefish (Polyodon spathula) is a native species in the central USA with a history of population decline due to waterway development and overharvesting for roe. It is not known whether paddlefish are impacted by resource competition from invasive bigheaded carp populations, including silver (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), which have expanded dramatically in the Mississippi River.
3. We used bioenergetic models to project the potential impact of invasive silver and bighead carp on zooplankton density and paddlefish somatic growth in backwater habitat. Bioenergetic outputs were translated to impacts on fecundity, becoming inputs for 50-year metapopulation simulations of backwater habitat connected to the main-stem Mississippi River by episodic flood events.
4. Competition with carp reduced growth and increased the risk of population decline for paddlefish. Impacts increased disproportionately with increased carp abundance and were further exacerbated in scenarios with increased diet overlap or decreased zooplankton abundance.
5. We also analysed paddlefish condition data collected at sites near the lower Mississippi River with varying histories of carp invasion. These data give credence to the bioenergetic model output; paddlefish had reduced body condition at sites with long-established, high-density carp populations.
6. We conclude that invasive bigheaded carps have great potential to reduce paddlefish growth, fecundity, and abundance. The pairing of bioenergetics and population models is likely to be broadly useful in assessing the risks posed by other invasive species.

     

Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes

The Acipenseriformes, as one of the earliest extant vertebrates, plays an important role in the evolution of fishes and even the whole vertebrates. Here we collected and analyzed all complete mitochondrial genomes of Acipenseriformes species. Phylogenetic analyses demonstrated that the polytomous branch included Acipenseridae and Polyodontidae formed five clades. The Polyodontidae clade and the Scaphirhynchus clade both were monophyletic group, whereas the Acipenser species and the Huso species both were polyphyletic group. The Bayesian divergence times showed that the origin time for Acipenseriformes was at 318.0 Mya, which was similar to the some previous results of 312.1 Mya, 346.9 Mya and 389.7 Mya. The result was in good consistent with the paleontological data available and the split time of the Pacific and Atlantic Oceans from the Jurassic to the Cretaceous (Laurasia splits in North America and Eurasia). The dN/dS ratios showed the evolutionary rates gradually slow down in five major Acipenseriformes clades from the Clade A (the Pacific sturgeons species) to Clade C (the genus Scaphirhynchus), which was related to the process of geographical formation.     

Genome assembly and annotation at the chromosomal level of first Pleuronectidae: Verasper variegatus provides a basis for phylogenetic study of Pleuronectiformes

High quality genome is of great significance for the mining of biological information resources of species. Up to now, the genomic information of several important economic flatfishes has been well explained. All these fishes are eyes on left side-type, and no high-quality genome of eyes on right side-type species has been reported. In this study, we applied a combined strategy involving stLFR and Hi-C technologies to generate sequencing data for constructing the chromosomal genome of Verasper variegates, which belongs to Pleuronectidae with characteristic of eyes on right side. The size of genome of V. variegatus is 556 Mb. More than 97.2% of BUSCO genes were detected, and N50 lengths of the contigs and scaffolds reached 79.8 Kb and 23.8 Mb, respectively, demonstrating the outstanding completeness and sequence continuity of the genome. A total of 22,199 protein-coding genes were predicted in the assembled genome, and more than 95% of those genes could be functionally annotated. Meanwhile, the genomic collinearity, gene family and phylogenetic analyses of similar species in Pleuronectiformes were also investigated and portrayed for metamorphosis and benthic adaptation. Sex related genes mapping has also been achieved at the chromosome level. This study is the first chromosomal level genome of a Pleuronectidae fish (V. variegatus). The chromosomal genome assembly constructed in this work will not only be valuable for conservation and aquaculture studies of the V. variegatus but will also be of general interest in the phylogenetic and taxonomic studies of Pleuronectiformes.     

Characteristics of sperm acrosin-like activity of paddlefish (Polyodon spathula Walbaum)

Spermatozoa of paddlefish and sturgeon fishes (Acipenseriformes), unlike teleost fish, have an acrosome. The objectives of this study were to characterize acrosin-like activity of cryopreserved sperm of paddlefish (Polyodon spathula) and to test and compare stability of paddlefish acrosin-like activity with that of lake sturgeon and bull spermatozoa. Mean acrosin-like activity of cryopreserved paddlefish sperm was 0.372 +/- 0.067 microU/10(6) spermatozoa. This activity was 79% higher in the whole semen than in spermatozoa. Highest activity was recorded at pH 8.0 and 8.5. Triton X-100, zinc ions and 4'-acetamidophenyl 4-guanidinobenzoate (AGB) inhibited the activity. Amidase activity was also inhibited by N-alpha-p-tosyl-L-lysine chloromethyl ketone (TLCK) and N-tosyl-L-phenylalanine chloromethyl ketone (TPCK). TLCK at concentrations of 0.1 and 1.0 mM gave a significant decrease in activity of 19 and 61%, respectively. However, TPCK significantly inhibited amidase activity (by 19%) only at concentration 1.0 mM. After acidification and 60 min incubation at 4 degrees C of sperm suspensions only 4% of the activity was retained. A similar phenomenon was observed in the case of lake sturgeon but not bull sperm. These results suggest that trypsin-like activity of Acipenserid fish resembles rather fish trypsin that mammalian one. In frozen-thawed paddlefish sperm a minute chymotrypsin-like activity was also indicated, when GPNA was used as substrate. This activity amounted to 0.0415 +/- 0.0138 microU/10(6) spermatozoa and was 18% of total amidase activity. This suggests that chymotrypsin-like activity may also be present in paddlefish spermatozoa.     

Biology and conservation of sturgeon and paddlefish

The Acipenseriformes (sturgeon and paddlefish)live in the Northern Hemisphere; half of thesespecies live in Europe, mostly in thePonto-Caspian region, one third in NorthAmerica, and the rest in East Asia and Siberia.They reproduce in freshwater and most of themmigrate to the sea, either living in brackishwater (Caspian, Azov, Black and Baltic Seas) orin full seawater on the oceanic continentalshelf. Most species feed on benthic organisms.Puberty usually occurs late in life (5–30 yearsof age) and adult males and females do notspawn on an annual basis. Adults continue togrow and some species such as the beluga (Huso huso) have reached 100 years of age andmore than 1,000 kg weight. Stocks of sturgeonsare dramatically decreasing, particularly inEurasia; the world sturgeon catch was nearly28,000 t in 1982 and less than 2,000 t by 1999.This decline resulted from overfishing andenvironmental degradation such as: accumulationof pollutants in sediments, damming of rivers,and restricting water flows, which becomeunfavorable to migration and reproduction.Several protective measures have beeninstituted; for example, fishing regulation,habitat restoration, juvenile stocking, and theCITES listing of all sturgeon productsincluding caviar. In addition, sturgeon farmingpresently yields more than 2,000 t per year(equivalent to wild sturgeon landings) andabout 15 t of caviar. Hopefully, thisartificial production will contribute to areduction of fishing pressure and lead to therehabilitation of wild stocks.     

Effects of body mass and water temperature on routine metabolism of American paddlefish Polyodon spathula

This study quantified the effects of temperature and fish mass on routine metabolism of the American paddlefish Polyodon spathula. Thermal sensitivity, as measured by Q₁₀ value, was low in P. spathula. Mean Q₁₀ was 1·78 while poikilotherms are generally expected to have Q₁₀ values in the 2·00–2·50 range. Mass‐specific metabolism did not decrease with increased fish size to the extent that this phenomenon is observed in teleosts, as evidenced by a mass exponent (β) value of 0·92 for P. spathula compared with 0·79 in a review of teleost species. Other Acipenseriformes have exhibited relatively high β values for mass‐specific respiration. Overall P. spathula metabolism appears to be more dependent on body mass and less dependent on temperature than for many other fishes. An equation utilizing temperature and fish mass to estimate gross respiration for P. spathula was derived and this equation was applied to respiratory data from other Acipenseriformes to assess inter‐species variation. Polyodon spathula respiration rates across water temperature and fish mass appear most similar to those of Atlantic sturgeon Acipenser naccarii and white sturgeon Acipenser transmontanus.     

An approach for assessing paddlefish Polyodon spathula (Walbaum, 1792) populations using mark‐recapture information

Historically, management of fish populations has been achieved through the use of age‐derived estimates of growth and mortality. For long‐lived species such as the paddlefish, Polyodon spathula, the validation of calcified structures is necessary to correct for the presence of false annuli or the absence of growth rings. Regardless, numerous studies on paddlefish populations throughout their range have continued the use of un‐validated age estimates to evaluate dynamic rate functions. The use of mark‐recapture studies has been applied widely to evaluate growth of short‐lived fishes, but only recently to a few long‐lived freshwater fishes (i.e. white sturgeon, shovelnose sturgeon, and pallid sturgeon). This study provides the first simultaneous evaluation of both mark‐recapture and age‐estimate information in determining population characteristics for paddlefish. In doing so, this study has determined that the P. spathula population in the Black River below Clearwater Dam, Missouri is sustainable. Additionally, mark‐recapture information is sufficient to produce accurate and reliable assessments of paddlefish populations in lieu of validated aging structures; future management should be centered on accurate scientific methods, which is not the case when using un‐validated aging structures (e.g. scales, otoliths, fin rays, dentary bones) to determine population parameters. Mark‐recapture information can provide an accurate, alternative source of growth and mortality information for use in evaluating and managing paddlefish populations throughout their range.     

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users.     

A New Saurichthyiform (Actinopterygii) with a Crushing Feeding Mechanism from the Middle Triassic of Guizhou (China)

Background

Equipped with an effective predatory feeding mechanism enhanced by large and sharp teeth, pointed snout and elongate body, saurichthyiform fishes are considered common fish-eaters in the early Mesozoic aquatic ecosystems. Additionally, because of the similar body plan across species, saurichthyiforms are also regarded evolutionally conservative, with few morphological and ecological changes during their long history. However, their phylogenetic affinity remains unclear as to whether they are chondrostean, neopterygian or stem-actinopteran, and likewise the intrarelationships of the group have rarely been explored.

Methodology/Principal Findings

Here we report a new saurichthyiform from the Middle Triassic of Guizhou, China, based on the well-preserved specimens including a 3-D braincase. The new taxon, Yelangichthys macrocephalus gen. et sp. nov., is unique among saurichthyiforms in having a peculiar neurocranium with a broad orbital tectum, paired posterior myodomes, a deep, transverse fossa in the posterodorsal part of the orbit, and a feeding mechanism structured for durophagy. Phylogenetic analysis places Yelangichthys gen. nov. at the most basal position in the Saurichthyiformes as the sister to Saurichthyidae, and a new family Yelangichthyidae is erected to include only Y. macrocephalus gen. et sp. nov. The monophyly of the Chondrostei comprising [Saurichthyiformes + Acipenseriformes] Birgeriiformes is supported, but not the monophyly of Saurichthys, the type genus of Saurichthyidae. With its outstanding osteological details, Yelangichthys gen. nov. greatly increases the neurocranial variations in saurichthyiforms, and its novel feeding structure suggests the consumption of hard-preys instead of fishes.

Conclusions/Significance

Our findings highlight the detailed osteology of a saurichthyiform braincase and its feeding design. We suggest that saurichthyiforms are closely allied to the Acipenseriformes. Saurichthyiforms were very diverse in the cranial osteology and they might have undergone a rapid evolutionary radiation via, for the new material here, transforming the feeding mechanism and thus exploiting the food resources unsuitable for other saurichthyiforms.     

The Internal Organization of Mycobacterial Partition Assembly: Does the DNA Wrap a Protein Core?

Before cell division in many bacteria, the ParBs spread on a large segment of DNA encompassing the origin-proximal parS site(s) to form the partition assembly that participates in chromosome segregation. Little is known about the structural organization of chromosomal partition assembly. We report solution X-ray and neutron scattering data characterizing the size parameters and internal organization of a nucleoprotein assembly formed by the mycobacterial chromosomal ParB and a 120-meric DNA containing a parS-encompassing region from the mycobacterial genome. The cross-sectional radii of gyration and linear mass density describing the rod-like ParB-DNA assembly were determined from solution scattering. A “DNA outside, protein inside” mode of partition assembly organization consistent with the neutron scattering hydrogen/deuterium contrast variation data is discussed. In this organization, the high scattering DNA is positioned towards the outer region of the partition assembly. The new results presented here provide a basis for understanding how ParBs organize the parS-proximal chromosome, thus setting the stage for further interactions with the DNA condensins, the origin tethering factors and the ParA.     

Imaginal discs--a new source of chromosomes for genome mapping of the yellow fever mosquito Aedes aegypti

Background

The mosquito Aedes aegypti is the primary global vector for dengue and yellow fever viruses. Sequencing of the Ae. aegypti genome has stimulated research in vector biology and insect genomics. However, the current genome assembly is highly fragmented with only ∼31% of the genome being assigned to chromosomes. A lack of a reliable source of chromosomes for physical mapping has been a major impediment to improving the genome assembly of Ae. aegypti.

Methodology/Principal Findings

In this study we demonstrate the utility of mitotic chromosomes from imaginal discs of 4^th instar larva for cytogenetic studies of Ae. aegypti. High numbers of mitotic divisions on each slide preparation, large sizes, and reproducible banding patterns of the individual chromosomes simplify cytogenetic procedures. Based on the banding structure of the chromosomes, we have developed idiograms for each of the three Ae. aegypti chromosomes and placed 10 BAC clones and a 18S rDNA probe to precise chromosomal positions.

Conclusion

The study identified imaginal discs of 4^th instar larva as a superior source of mitotic chromosomes for Ae. aegypti. The proposed approach allows precise mapping of DNA probes to the chromosomal positions and can be utilized for obtaining a high-quality genome assembly of the yellow fever mosquito.     

Fort Peck paddlefish population survival and abundance in the Missouri River

Excessive fishing pressure can induce population declines or complete collapse of fisheries. Unless commercial and recreational fisheries for K-selected fishes, or those with slow growth and late maturation, are carefully managed, declines in abundance or fishery collapse is probable. Paddlefish Polyodon spathula,are a K-selected species that experienced historical declines in abundance as a result of habitat degradation and overfishing. Mark-recapture studies are well-suited for long-lived fishes by providing information on population density and vital rates. For sustainable commercial or recreational fisheries targeting species such as the paddlefish, managers require accurate estimates of population vital rates including survival, abundance, and exploitation. We used a Montana Fish, Wildlife & Parks (MFWP) mark-recapture dataset and modified Jolly-Seber (POPAN) models to estimate survival, recapture, probability of entry, and abundance of 8,518 tagged paddlefish over a 25-year period. With many supporting estimates including stable survival (0.92 for females, mean of 0.82 for males), low exploitation rates (means of 2.6% for females and 2.9% for males), and stable abundance estimates (25-year mean of 12,309 individuals for both sexes), the Fort Peck paddlefish population appears to be stable and well-managed over the past 25 years. Presently, this is the only study focused on paddlefish in North America that has estimated survival and abundance for both male and female paddlefish using contemporary analyses. This research provided a unique opportunity to highlight that the effort exerted by management agencies to collect long-term field data is extremely useful to our understanding of fish populations and management.     

The paddlefish rostrum functions as an electrosensory antenna in plankton feeding

A novel electrosensory function is presented for the large, plankton-feeding, freshwater paddlefish, Polyodon spathula, along with a hypothesis which accounts for the distinctive, elongated rostrum of this unusual fish. Behavioural experiments conducted in the ''dark'' (under infrared illumination), to eliminate vision, show that paddlefish efficiently capture planktonic prey to distances up to 80–90 mm. They make feeding strikes at dipole electrodes in response to weak low-frequency electrical currents. Fish also avoid metal obstacles placed in the water, again in the dark. Electrophysiological experiments confirm that the Lorenzinian ampullae of paddlefish are sensitive to weak, low-frequency electrical signals, and demonstrate unequivocally that they respond to the very small electrical signals generated by their natural zooplankton prey (Daphnia sp.). We propose that the rostrum constitutes the biological equivalent of an electrical antenna, enabling the fish to accurately detect and capture its planktonic food in turbid river environments where vision is severely limited. The electrical sensitivity of paddlefish to metallic substrates may interfere with their migrations through locks and dams.