Microsatellite evidence for high frequency of multiple paternity in the marine gastropod Rapana venosa

Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844)

BACKGROUND

The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of the population genetic structure of this species is limited by the low number of molecular markers currently described.

METHODS AND RESULTS

In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16 (average = 7.89). The results showed that, the polymorphism information content (PIC) of these simple sequence repeat (SSR) loci varied from 0.254 to 0.888. The observed heterozygosity (H_O) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (H_E) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05).

CONCLUSIONS

These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate and other closely related species.

Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago

Background

In the marine realm, dispersal ability is among the major factors shaping the distribution of species. In the Northeast Atlantic Ocean, the Azores Archipelago is home to a multitude of marine invertebrates which, despite their dispersal limitations, maintain gene flow among distant populations, with complex evolutionary and biogeographic implications. The mechanisms and factors underlying the population dynamics and genetic structure of non-planktotrophic gastropods within the Azores Archipelago and related mainland populations are still poorly understood. The rissoid Cingula trifasciata is herewith studied to clarify its population structure in the Northeast Atlantic Ocean and factors shaping it, with a special focus in intra-archipelagic dynamics.

Results

Coupling microsatellite genotyping by amplicon sequencing (SSR-GBAS) and mitochondrial datasets, our results suggest the differentiation between insular and continental populations of Cingula trifasciata, supporting previously raised classification issues and detecting potential cryptic diversity. The finding of connectivity between widely separated populations was startling. In unique ways, dispersal ability, habitat type, and small-scale oceanographic currents appear to be the key drivers of C. trifasciata’s population structure in the remote Azores Archipelago. Dispersal as non-planktotrophic larvae is unlikely, but its small-size adults easily engage in rafting. Although the typical habitat of C. trifasciata, with low hydrodynamics, reduces the likelihood of rafting, individuals inhabiting algal mats are more prone to dispersal. Sea-surface circulation might create dispersal pathways for rafts, even between widely separated populations/islands.

Conclusions

Our results show that gene flow of a marine non-planktotrophic gastropod within a remote archipelago can reveal unanticipated patterns, such that the understanding of life in such areas is far from well-understood. We expect this work to be the starting of the application of SSR-GBAS in other non-model marine invertebrates, providing insights on their population dynamics at distinct geographical scales and on hidden diversity. How transversal is the role played by the complex interaction between functional traits, ecological features, and sea-surface circulation in the population structure of marine invertebrates can be further addressed by expanding this approach to more taxa.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01862-1.

Ovarian transcriptome profiles associated with sexual maturation in Pacific abalone (Haliotis discus hannai)

BACKGROUND

There is now abundant information on genes involved in molluscan oogenesis and their associations with ovarian development. However, few studies have investigated the ovarian transcriptome of Pacific abalone (Haliotis discus hannai).

OBJECTIVE

The objective of this study was to identify genes related to ovarian development and maturation in Pacific abalone utilizing RNA-sequencing (RNA-seq) and to verify the genes most relevant to different stages of maturation.

METHODS

RNA samples from the ovarian tissues of sexually immature and mature abalone were used to construct cDNA libraries, which were paired-end sequenced on an Illumina HiSeq 2500 platform. Reads from individual samples (unigenes) were aligned to reference transcriptome databases for identification of differentially expressed genes (DEGs) between immature and mature ovarian libraries. Reverse transcription-quantitative polymerase chain reaction was used to verify the RNA-seq data.

RESULTS

A total of 8779 unigenes were obtained from the ovaries of immature and mature abalone, with a total length of 3323,279 bp and an average length of 379 bp per gene. Gene ontology analysis assigned 5860 unigenes to biological processes, 855 to cellular components, and 1352 to molecular functions. Overall, 470 DEGs were identified, including 213 and 257 genes down-regulated and up-regulated in mature abalone, respectively. Among these, 13 relevant transcripts, including VTG1 and FZD7, were significantly highly expressed in the ovaries of mature abalone (p < 0.05, fold change > 2).

CONCLUSION

This H. discus hannai ovary transcriptome provides molecular targets to better understand ovarian development, oogenesis, and sexual maturation, and to enhance Pacific abalone production.

Multiple and Extra-Pair Mating in a Pair-Living Hermaphrodite, the Intertidal Limpet Siphonaria gigas

Pair-living is a common social system found across animal taxa, and the relationship between pair-living and reproduction varies greatly among species. Siphonaria gigas, hermaphroditic pulmonate gastropods, often live in pairs in the rocky intertidal zone of the tropical Eastern Pacific. Combining genetic parentage analysis using four polymorphic microsatellite loci with behavioral observations from a 10-week field study, we provide the first description of the mating system of a Siphonaria species incorporating genetic data. S. gigas mated both within-pair and extra-pair and three out of four paired S. gigas individuals produced egg masses with extra-pair paternity. Multiple paternity was detected, but at a relatively low frequency (19% of egg masses) compared to other marine gastropods. Behavioral data indicate one potential advantage of pair-living: paired S. gigas produced almost twice as many egg masses as their solitary counterparts over four reproductive cycles. These observations, together with constraints on the movement of S. gigas, suggest that pairing may ensure mate access and increase reproductive success.

Microsatellite instability testing in colorectal cancer using the QiaXcel advanced platform

Background

Microsatellite instability (MSI) is a major predictive and diagnostic marker in several cancers including colorectal carcinomas. Diagnostic testing for microsatellites is generally performed using capillary sequencers, which requires expensive high-end equipment including expensive chemistry using fluorescent dyes labelling the PCR products of interest. In this study we have modified such a diagnostic protocol and established the microsatellite testing on the QiaXcel Advanced platform.

Methods

MSI testing was based on a previously established protocol describing a multiplex PCR followed by fluorescent detection of PCR products in a capillary sequencing device. Ten microsatellites were included in the new protocol: BAT25, BAT26, BAT40, D2s123, D10s197, D13s153, D17s250, D18s58, D5s346, and MycI. In this protocol the PCR was demultiplexed and established on the QiaXcel Advanced system (Qiagen, Hilden, Germany).

Results

Making use of a series of FFPE control samples with known MSI status including those with and without MSI a protocol for MSI testing was successfully established on the QiaXcel Advanced platform.

Conclusions

MSI testing for human colorectal cancers using the QiaXcel Advanced system could serve as an economic acceptable tool for rapid diagnostics in laboratories that do not have access to a capillary sequencing unit.

A rapid and cost-effective approach for the development of polymorphic microsatellites in non-model species using paired-end RAD sequencing

As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective "RAD-seq-Assembly-Microsatellite" approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design. A total of 121,750 RAD contigs were generated with a mean length of 522 bp, and 19,782 contigs contained microsatellite motifs. A total of 156,150 primer pairs were successfully designed based on 16,497 contigs containing priming sites. Experimental validation of 52 randomly selected microsatellite loci demonstrated that 45 (86.54%) loci were successfully amplified and polymorphic in two geographically isolated populations of T. fasciatus. Compared with traditional approaches based on DNA cloning and other approaches based on next-generation sequencing, our newly developed approach could yield thousands of microsatellite loci with much higher successful amplification rate and lower costs, especially for non-model species with shallow background of genomic information. The "RAD-seq-Assembly-Microsatellite" approach holds great promise for microsatellite development in future ecological and evolutionary studies of non-model species.

Paternity Outcomes in the Freshwater Gastropod, Chilina dombeiana in the Biobío River, Chile

Studying the mating system of obligate aquatic organisms that inhabit river ecosystems is important for understanding its evolution as well as the role of biological and environmental factors in modulating population dynamics and species distributional patterns. Here, we studied the reproductive strategy of the Chilean endemic freshwater snail, Chilina dombeiana, in the Biobío River, one of the largest rivers in Chile. This species has a low potential for dispersal given the absence of a free-swimming larval stage (benthic larval development) and given that adults have a low capacity for mobility. We hypothesized that: 1. Females would mate with different males (polyandry) resulting in intrabrood multiple paternity, 2. Individuals from closer sites would be more related than individuals from distant sites, and 3. Male parental contributions would be unevenly distributed within broods. Individuals from three different sites were sampled along the river: upper, mid, and river mouth. In the laboratory, hatching juveniles from a total of 15 broods were collected for paternity analyses. We used microsatellite markers and the programs GERUD and COLONY to determine whether multiple paternity exists and to estimate the contribution of different males to the brood. We found that multiple paternity was very common at all of the sites analyzed with as many as 8 males fertilizing a single female and a mean of 4.2 fathers per brood estimated by COLONY. Sire contribution was skewed to particular males in several broods. In addition, overall relatedness among broods for the three sites ranged from 0.17 to 0.45 with evidence of many half-siblings. Relatedness differed among the three sites. Particularly in upstream sites or in anthropogenically disturbed populations, the high levels of multiple paternity observed in C. dombeiana may be an efficient strategy to avoid inbreeding and prevent the loss of genetic diversity within populations.

Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling

During the life cycle of shellfish, larval development, especially metamorphosis, has a vital influence on the dynamics, distribution, and recruitment of natural populations, as well as seed breeding. Rapana venosa, a carnivorous gastropod, is an important commercial shellfish in China, and is an ecological invader in the United States, Argentina, and France. However, information about the mechanism of its early development is still limited, because research in this area has long suffered from a lack of genomic resources. In this study, 15 digital gene expression (DGE) libraries from five developmental stages of R. venosa were constructed and sequenced on the IIIumina Hi-Sequation 2500 platform. Bioinformaticsanalysis identified numerous differentially and specifically expressed genes, which revealed that genes associated with growth, nervous system, digestive system, immune system, and apoptosis participate in important developmental processes. The functional analysis of differentially expressed genes was further implemented by gene ontology, and Kyoto encyclopedia of genes and genomes enrichment. DGE profiling provided a general picture of the transcriptomic activities during the early development of R. venosa, which may provide interesting hints for further study. Our data represent the first comparative transcriptomic information available for the early development of R. venosa, which is a prerequisite for a better understanding of the physiological traits controlling development.

Influences of population density on polyandry and patterns of sperm usage in the marine gastropod Rapana venosa

Polyandry is a common mating strategy in animals, with potential for sexual selection to continue post-copulation through sperm competition and/or cryptic female choice. Few studies have investigated the influences of population density on polyandry and sperm usage, and paternity distribution in successive broods of marine invertebrates. The marine gastropod Rapana venosa is ideal for investigating how population density influences the frequency of polyandry and elucidating patterns of sperm usage. Two different population density (12 ind/m³ and 36 ind/m³) treatments with two replications were set to observe reproductive behaviors. Five microsatellite markers were used to identify the frequency of multiple paternity and determine paternal contributions to progeny arrays in 120 egg masses. All of the mean mating frequency, mean number of sires and mean egg-laying frequency were higher at high population density treatment relative to low population density treatment, indicating population density is an important factor affecting polyandry. The last sperm donors achieved high proportions of paternity in 74.77% of egg masses, which supported the “last male sperm precedence” hypothesis. In addition, high variance in reproductive success among R. venosa males were detected, which might have an important influence on effective population size.

The seminal receptacle and implications for reproductive processes in the invasive gastropod Crepidula fornicata

The calyptraeid gastropod Crepidula fornicata is the object of considerable research attention, due to its invasive status in the North-Eastern Atlantic, its introduction to habitats throughout the Northern hemisphere, and its scientific interest as a model organism for the study of developmental and reproductive processes in the Metazoa. Since the knowledge concerning the structural foundations for its reproductive processes is surprisingly weak, we investigated the seminal receptacle, a key structure in the reproductive biology of other metazoans, using histology, scanning electron and transmission electron microscopy. The seminal receptacle consists of 9-11 lobes, each subdivided into small, narrow lobules. The inner epithelium of the lobules appears to be highly dynamic, characterised by the perforation and attachment of received spermatozoa, the progressive degeneration of this epithelium, and the concomitant detachment of the spermatozoa. The allocation of spermatozoa to many different lobules, in different phases, may explain the extended reproductive season of C. fornicata, and thereby contribute to its colonizing and invasive success. The same compartmentalisation, as well as the complete covering of the inner epithelium of the lobules by spermatozoa and the large amount of spermatozoan debris in the lumina, suggest that the C. fornicata seminal receptacle may be a site of sperm competition in this polyandrous species.