Chromosomal rearrangement in pectinidae revealed by rRNA loci and implications for bivalve evolution

Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment

The blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical-chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex.

Chromosome Diversity and Evolution in Helicoide a (Gastropoda: Stylommatophora): A Synthesis from Original and Literature Data

Simple Summary

The superfamily Helicoidea is a large and diverse group of Eupulmonata. The superfamily has been the subject of several molecular and phylogenetic studies which greatly improved our knowledge on the evolutionary relationships and historical biogeography of many families. In contrast, the available karyological information on Helicoidea still results in an obscure general picture, lacking a homogeneous methodological approach and a consistent taxonomic record. Nevertheless, the available karyological information highlights the occurrence of a significant chromosomal diversity in the superfamily in terms of chromosome number (varying from 2n = 40 to 2n = 62), chromosome morphology and the distribution of different karyological features among different taxonomic groups. Here we performed a molecular and a comparative cytogenetic analysis on of 15 Helicoidea species of three different families. Furthermore, to provide an updated assessment of the chromosomal diversity of the superfamily we reviewed all the available chromosome data. Finally, superimposing all the chromosome data gathered from different sources on the available phylogenetic relationships of the studied taxa, we discuss the overall observed chromosome diversity in Helicoidea and advance a hypothesis on its chromosomal evolution.

Abstract

We performed a molecular and a comparative cytogenetic analysis on different Helicoidea species and a review of all the available chromosome data on the superfamily to provide an updated assessment of its karyological diversity. Standard karyotyping, banding techniques, and Fluorescence in situ hybridization of Nucleolus Organizer Region loci (NOR-FISH) were performed on fifteen species of three families: two Geomitridae, four Hygromiidae and nine Helicidae. The karyotypes of the studied species varied from 2n = 44 to 2n = 60, highlighting a high karyological diversity. NORs were on a single chromosome pair in Cernuella virgata and on multiple pairs in four Helicidae, representing ancestral and derived conditions, respectively. Heterochromatic C-bands were found on pericentromeric regions of few chromosomes, being Q- and 4′,6-diamidino-2-phenylindole (DAPI) negative. NOR-associated heterochromatin was C-banding and chromomycin A₃ (CMA₃) positive. Considering the available karyological evidence on Helicoidea and superimposing the chromosome data gathered from different sources on available phylogenetic inferences, we describe a karyotype of 2n = 60 with all biarmed elements as the ancestral state in the superfamily. From this condition, an accumulation of chromosome translocations led to karyotypes with a lower chromosome number (2n = 50–44). This process occurred independently in different lineages, while an augment of the chromosome number was detectable in Polygyridae. Chromosome inversions were also relevant chromosome rearrangements in Helicoidea, leading to the formation of telocentric elements in karyotypes with a relatively low chromosome count.

Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species

Background

The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer’s 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control.

Results

Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons.

Conclusions

Tested building-loci pipelines for selection of SNP panels seem to have low influence on population genetics inference across the diverse case-study scenarios here studied. However, preliminary trials with different bioinformatic pipelines are suggested to evaluate their influence on population parameters according with the specific goals of each study.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07465-w.

The evo-devo of molluscs: Insights from a genomic perspective

Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo-devo studies; however, understanding of the evo-devo of molluscs has been largely hampered by incomplete fossil records and limited molecular data. Recent advancement of genomics and other technologies has greatly fueled the molluscan "evo-devo" field, and decoding of several molluscan genomes provides unprecedented insights into molluscan biology and evolution. Here, we review the recent progress of molluscan genome sequencing as well as novel insights gained from their genomes, by emphasizing how molluscan genomics enhances our understanding of the evo-devo of molluscs.

A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis)

To consolidate the genetic, physical, and cytogenetic maps of scallop (Patinopecten yessoensis), we constructed a molecular cytogenetic map by localizing 84 fosmid clones that contain different SNP markers from 19 linkage groups (LGs) using fluorescence in situ hybridization (FISH). Among these 84 SNP-anchored clones, 56 clones produced specific and stable signals on one pair of chromosomes. Dual-color FISH assigned 19 LGs to their corresponding chromosomes with 38 SNP-anchored clones as probes. Among these 19 LGs, 17 LGs were assigned to their corresponding one pair of chromosomes, while two clones containing SNPs from LG10 and LG19 were located on two different pairs of chromosomes separately. The orientation of 7 LGs was corrected according to the chromosome location of SNPs within the same LG. In addition, a probe panel of SNP-anchored clones was developed to identify each chromosome of P. yessoensis. The molecular cytogenetic map will facilitate molecular breeding in scallop and enable comparative studies on chromosome evolution of bivalve mollusk.

Genomic in situ hybridization in interspecific hybrids of scallops (Bivalvia, Pectinidae) and localization of the satellite DNA Cf303, and the vertebrate telomeric sequences (TTAGGG)n on chromosomes of scallop Chlamys farreri (Jones & Preston, 1904)

Mitotic chromosome preparations of the interspecific hybrids Chlamys farreri (Jones & Preston, 1904) × Patinopecten yessoensis (Jay, 1857), C. farreri × Argopecten irradians (Lamarck, 1819) and C. farreri × Mimachlamys nobilis (Reeve, 1852) were used to compare two different scallop genomes in a single slide. Although genomic in situ hybridization (GISH) using genomic DNA from each scallop species as probe painted mitotic chromosomes of the interspecific hybrids, the painting results were not uniform; instead it showed species-specific distribution patterns of fluorescent signals among the chromosomes. The most prominent GISH-bands were mainly located at centromeric or telomeric regions of scallop chromosomes. In order to illustrate the sequence constitution of the GISH-bands, the satellite Cf303 sequences of C. farreri and the vertebrate telomeric (TTAGGG)_n sequences were used to map mitotic chromosomes of C. farreri by fluorescence in situ hybridization (FISH). The results indicated that the GISH-banding pattern presented by the chromosomes of C. farreri is mainly due to the distribution of the satellite Cf303 DNA, therefore suggesting that the GISH-banding patterns found in the other three scallops could also be the result of the chromosomal distribution of other species-specific satellite DNAs.

Structural differences and differential expression among rhabdomeric opsins reveal functional change after gene duplication in the bay scallop, Argopecten irradians (Pectinidae)

Background

Opsins are the only class of proteins used for light perception in image-forming eyes. Gene duplication and subsequent functional divergence of opsins have played an important role in expanding photoreceptive capabilities of organisms by altering what wavelengths of light are absorbed by photoreceptors (spectral tuning). However, new opsin copies may also acquire novel function or subdivide ancestral functions through changes to temporal, spatial or the level of gene expression. Here, we test how opsin gene copies diversify in function and evolutionary fate by characterizing four rhabdomeric (G_q-protein coupled) opsins in the scallop, Argopecten irradians, identified from tissue-specific transcriptomes.

Results

Under a phylogenetic analysis, we recovered a pattern consistent with two rounds of duplication that generated the genetic diversity of scallop G_q-opsins. We found strong support for differential expression of paralogous G_q-opsins across ocular and extra-ocular photosensitive tissues, suggesting that scallop G_q-opsins are used in different biological contexts due to molecular alternations outside and within the protein-coding regions. Finally, we used available protein models to predict which amino acid residues interact with the light-absorbing chromophore. Variation in these residues suggests that the four G_q-opsin paralogs absorb different wavelengths of light.

Conclusions

Our results uncover novel genetic and functional diversity in the light-sensing structures of the scallop, demonstrating the complicated nature of G_q-opsin diversification after gene duplication. Our results highlight a change in the nearly ubiquitous shadow response in molluscs to a narrowed functional specificity for visual processes in the eyed scallop. Our findings provide a starting point to study how gene duplication may coincide with eye evolution, and more specifically, different ways neofunctionalization of G_q-opsins may occur.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0823-9) contains supplementary material, which is available to authorized users.

Chromosomal mapping of tandem repeats in the Yesso Scallop, Patinopecten yessoensis (Jay, 1857), utilizing fluorescence in situ hybridization

Construction of cytogenetic maps can provide important information for chromosome identification, chromosome evolution and genomic research. However, it hasn't been conducted in many scallop species yet. In the present study, we attempted to map 12 fosmid clones containing tandem repeats by fluorescence in situ hybridization (FISH) in the Yesso scallop Patinopecten yessoensis (Jay, 1857). The results showed 6 fosmid clones were successfully mapped and distributed in 6 different pairs of chromosomes. Three clones were respectively assigned to a pair of metacentric chromosomes, a pair of submetacentric chromosomes and a pair of telocentric chromosomes and the remaining 3 clones showed their loci on three different pairs of subtelocentric chromosomes by co-hybridization. In summary, totally 8 pairs of chromosomes of the Yesso scallop were identified by 6 fosmid clones and two rDNA probes. Furthermore, 6 tandem repeats of 5 clones were sequenced and could be developed as chromosome specific markers for the Yesso scallop. The successful localization of fosmid clones will undoubtedly facilitate the integration of linkage groups with cytogenetic map and genomic research for the Yesso scallop.

Immune and stress responses in oysters with insights on adaptation

Oysters are representative bivalve molluscs that are widely distributed in world oceans. As successful colonizers of estuaries and intertidal zones, oysters are remarkably resilient against harsh environmental conditions including wide fluctuations in temperature and salinity as well as prolonged air exposure. Oysters have no adaptive immunity but can thrive in microbe-rich estuaries as filter-feeders. These unique adaptations make oysters interesting models to study the evolution of host-defense systems. Recent advances in genomic studies including sequencing of the oyster genome have provided insights into oyster's immune and stress responses underlying their amazing resilience. Studies show that the oyster genomes are highly polymorphic and complex, which may be key to their resilience. The oyster genome has a large gene repertoire that is enriched for immune and stress response genes. Thousands of genes are involved in oyster's immune and stress responses, through complex interactions, with many gene families expanded showing high sequence, structural and functional diversity. The high diversity of immune receptors and effectors may provide oysters with enhanced specificity in immune recognition and response to cope with diverse pathogens in the absence of adaptive immunity. Some members of expanded immune gene families have diverged to function at different temperatures and salinities or assumed new roles in abiotic stress response. Most canonical innate immunity pathways are conserved in oysters and supported by a large number of diverse and often novel genes. The great diversity in immune and stress response genes exhibited by expanded gene families as well as high sequence and structural polymorphisms may be central to oyster's adaptation to highly stressful and widely changing environments.

Divergent evolutionary behavior of H3 histone gene and rDNA clusters in venerid clams

BACKGROUND

Histone H3 gene clusters have been described as highly conserved chromosomal markers in invertebrates. Surprisingly, in bivalves remarkable interspecific differences were found among the eight mussels and between the two clams in which histone H3 gene clusters have already been located. Although the family Veneridae comprises 10 % of the species of marine bivalves, their chromosomes are poorly studied. The clams belonging to this family present 2n = 38 chromosomes and similar karyotypes showing chromosome pairs gradually decreasing in length. In order to assess the evolutionary behavior of histone and rRNA multigene families in bivalves, we mapped histone H3 and ribosomal RNA probes to chromosomes of ten species of venerid clams.

RESULTS

In contrast with the reported conservation of histone H3 gene clusters and their intercalary location in invertebrates, these loci varied in number and were mostly subterminal in venerid clams. On the other hand, while a single 45S rDNA cluster, highly variable in location, was found in these organisms, 5S rDNA clusters showed interspecific differences in both number and location. The distribution patterns of these sequences were species-specific and mapped to different chromosomal positions in all clams but Ruditapes decussatus, in which one of the minor rDNA clusters and the major rDNA cluster co-located.

CONCLUSION

The diversity in the distribution patterns of histone H3 gene, 5S rDNA and 28S rDNA clusters found in venerid clams, together with their different evolutionary behaviors in other invertebrate taxa, strongly suggest that the control of the spreading of these multigene families in a group of organisms relies upon a combination of evolutionary forces that operate differently depending not only on the specific multigene family but also on the particular taxa. Our data also showed that H3 histone gene and rDNA clusters are useful landmarks to integrate nex-generation sequencing (NGS) and evolutionary genomic data in non-model species.

Genomic in situ hybridization identifies parental chromosomes in hybrid scallop (Bivalvia, Pectinoida, Pectinidae) between female Chlamysfarreri and male Argopectenirradiansirradians

Interspecific crossing was artificially carried out between Chlamysfarreri (Jones & Preston, 1904) ♀ and Argopectenirradiansirradians (Lamarck, 1819) ♂, two of the dominant cultivated scallop species in China. Genomic in situ hybridization (GISH) was used to examine the chromosome constitution and variation in hybrids at early embryonic stage. The number of chromosomes in 66.38% of the metaphases was 2n = 35 and the karyotype was 2n = 3 m + 5 sm + 16 st + 11 t. After GISH, two parental genomes were clearly distinguished in hybrids, most of which comprised 19 chromosomes derived from their female parent (Chlamysfarreri) and 16 chromosomes from their male parent (Argopectenirradiansirradians). Some chromosome elimination and fragmentation was also observed in the hybrids.

An integrated genetic and cytogenetic map for Zhikong scallop, Chlamys farreri, based on microsatellite markers

The reliability of genome analysis and proficiency of genetic manipulation requires knowledge of the correspondence between the genetic and cytogenetic maps. In the present study, we integrated cytogenetic and microsatellite-based linkage maps for Zhikong scallop, Chlamys farreri. Thirty-eight marker-anchored BAC clones standing for the 19 linkage groups were used to be FISH probes. Of 38 BAC clones, 30 were successfully located on single chromosome by FISH and used to integrate the genetic and cytogenetic map. Among the 19 linkage groups, 12 linkage groups were physically anchored by 2 markers, 6 linkage groups were anchored by 1 marker, and one linkage group was not anchored any makers by FISH. In addition, using two-color FISH, six linkage groups were distinguished by different chromosomal location; linkage groups LG6 and LG16 were placed on chromosome 10, LG8 and LG18 on chromosome 14. As a result, 18 of 19 linkage groups were localized to 17 pairs of chromosomes of C. farreri. We first integrated genetic and cytogenetic map for C. farreri. These 30 chromosome specific BAC clones in the cytogenetic map could be used to identify chromosomes of C. farreri. The integrated map will greatly facilitate molecular genetic studies that will be helpful for breeding applications in C. farreri and the upcoming genome projects of this species.

Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima

Pearl oysters are not only farmed for their gemstone quality pearls worldwide, but they are also becoming important model organisms for investigating genetic mechanisms of biomineralisation. Despite their economic and scientific significance, limited genomic resources are available for this important group of bivalves, hampering investigations into identifying genes that regulate important pearl quality traits and unique biological characteristics (i.e. biomineralisation). The silver-lipped pearl oyster, Pinctada maxima, is one species where there is interest in understanding genes that regulate commercially important pearl traits, but presently, there is a dearth of genomic information. The objective of this study was to develop and validate a large number of type I genome-wide single nucleotide polymorphisms (SNPs) for P. maxima suitable for high-throughput genotyping. In addition, sequence annotations and Gene Ontology terms were assigned to a large mantle tissue 454 expressed sequence tag assembly (96,794 contigs) and information on known bivalve biomineralisation genes was incorporated into SNP discovery. The SNP discovery effort resulted in the de novo identification of 172,625 SNPs, of which 9,108 were identified as high value [minor allele frequency (MAF)≥ 0.15, read depth  ≥ 8]. Validation of 2,782 of these SNPs using Illumina iSelect Infinium genotyping technology returned some of the highest assay conversion (86.6 %) and validation (59.9 %; mean MAF 0.28) rates observed in aquaculture species to date. Genomic resources presented here will be pivotal to future research investigating the biological mechanisms behind biomineralisation and will form a strong foundation for genetic selective breeding programs in the P. maxima pearling industry.

Chromosomal evolution of rDNA and H3 histone genes in representative Romaleidae grasshoppers from northeast Brazil

BACKGROUND

Grasshoppers from the Romaleidae family are well distributed in the Neotropical Region and represent a diversified and multicolored group in which the karyotype is conserved. Few studies have been conducted to understand the evolutionary dynamics of multigene families. Here, we report the chromosomal locations of the 18S and 5S rDNA and H3 histone multigene families in four grasshopper species from the Romaleidae family, revealed by fluorescent in situ hybridization (FISH).

RESULTS

The 5S rDNA gene was located in one or two chromosome pairs, depending on the species, and was found in a basal distribution pattern. Its chromosomal location was highly conserved among these species. The 18S rDNA was located in a single medium-sized chromosomal pair in all species analyzed. Its chromosomal location was near the centromere in the proximal or pericentromeric regions. The location of the H3 histone gene was highly conserved, with slight chromosomal location differences among some species. To our knowledge, this is the first report of a megameric chromosome carrying both the chromosomal markers 18S rDNA and the H3 histone genes, thereby expanding our understanding of such chromosomes.

CONCLUSIONS

The 5S and 18S rDNA genes and the H3 histone genes showed a conservative pattern in the species that we analyzed. A basal distribution pattern for 5S rDNA was observed with a location on the fourth chromosomal pair, and it was identified as the possible ancestral bearer. The 18S rDNA and H3 histone genes were restricted to a single pair of chromosomes, representing an ancestral pattern. Our results reinforce the known taxonomic relationships between Chromacris and Xestotrachelus, which are two close genera.

Genomic characterization of interspecific hybrids between the scallops Argopecten purpuratus and A. irradians irradians

The Peruvian scallop (Argopecten purpuratus) has been introduced to China and has successfully been hybridized with the bay scallop (A. irradians irradians). The F1 hybrids of these two scallops exhibited a large increase in production traits and some other interesting new characteristics. To understand the genetic basis of this heterosis, nuclear gene and partial mtDNA sequences, and genomic in situ hybridization (GISH) were employed to analyze the genomic organization of the hybrids. Amplification of the ribosomal DNA internal transcribed spacer (ITS) showed that the parental ITS sequences were present in all the hybrid individuals, illustrating that the hybrid offspring inherited nuclear DNA from both parents. Sequence analyses of the ITS region further confirmed that the hybrids harbored alleles from their parents; some recombinant variants were also detected, which revealed some alterations in the nuclear genetic material of the hybrids. The analysis of mitochondrial 16S rDNA showed that the hybrids possessed sequences that were identical to the 16S rDNA of the female parents, proving a matrilineal inheritance of mitochondrial genes in scallops. In addition, GISH clearly discriminated between the parental chromosomes and indicated a combination of haploid genomes of duplex parents in the hybrids. The genetic analyses in our study illustrated that the F1 hybrids inherited nuclear material from both parents and cytoplasmic genetic material maternally, and some variations occurred in the genome, which might contribute to a further understanding of crossbreeding and heterosis in scallop species.

Chromosomes of Lepidochitona caprearum (Scacchi, 1836) (Polyplacophora, Acanthochitonina, Tonicellidae) provide insights into Acanthochitonina karyological evolution

We describe the karyotype, location of nucleolus-organizing regions (NORs) and heterochromatin composition and distribution in Lepidochitona caprearum (Scacchi, 1836). The examined specimens had 2n=24 chromosomes; the elements of pairs 1-4 were metacentric, subtelocentric those of the fifth pair, telocentric the elements of other pairs. NOR-FISH, Ag-NOR- and CMA3 banding showed NORs localized on pericentromeric regions of a medium small sized, telocentric chromosome pair. After C-banding or digestions with restriction enzyme NOR associate heterochromatin only was cytologically evident, resulting CMA3 positive. The comparison with chromosome data of other chitons, other than to evidence a karyotypic similarity of Lepidochitona caprearum to species of suborder Acanthochitonina, allows us to infer that chromosome evolution in the suborder mainly occurred via reduction of the number of the chromosomes by centric fusions, which took place repeatedly and independently in the different lineages of Acanthochitonina.

A consensus microsatellite-based linkage map for the hermaphroditic bay scallop (Argopecten irradians) and its application in size-related QTL analysis

Bay scallop (Argopecten irradians) is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color) markers were mapped to 16 linkage groups (LGs), which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13:1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL), shell height (SH), shell width (SW) and total weight (TW) were measured for quantitative trait loci (QTL) analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively) were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH) was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS) in bay scallop.

Novel polymorphism of internal transcribed spacers (ITS) and their utilization in phylogenetic analysis of Neanthes glandicincta (Annelida: Polychaeta: Nereididae)

Sequences of internal transcribed spacers (ITS1 and ITS2) are increasingly being used to infer phylogenetic relationships at or below species levels. Here we report a novel case of ITS polymorphism within Neanthes glandicincta (Annelida: Polychaeta: Nereididae). Two types of ITS sequence (Type I and Type II) were cloned and sequenced, which showed significant differences both in nucleotide composition and length. Variations of these two types sequences also differed from each other with Type I was highly divergent while Type II was highly conserved. Phylogenetic trees inferred from ITS1 and ITS2 sequences showed striking discrepancy in N. glandicincta. Non-concerted evolution of multi-gene is suggested to be responsible for the high degree of polymorphism in ITS regions. Due to the two divergent types of ITS presented within a single N. glandicincta individual, the utilization of ITS regions for delineation of population or closely related species cannot be substantiated. The finding of different types of ITS in a single individual also stresses the need for analyzing a large number of clones whenever ITS sequences obtained by PCR amplification and cloning are being used in phylogenetic reconstruction.

Development and linkage analysis of 104 new microsatellite markers for bay scallop (Argopecten irradians)

For genetic analysis and linkage mapping of bay scallop (Argopecten irradians), a set of 120 novel simple sequence repeat markers were developed from microsatellite-enriched libraries and expressed sequence tags. An inter-subspecies hybrid bay scallop family (CC5) of 46 progeny was analyzed as the reference population to confirm polymorphism and test the segregation patterns of these loci. A total of 104 microsatellite markers were polymorphic in the reference family, among which 36 in female, 28 in male, and 40 in both parents, respectively. Linkage analysis allowed mapping these markers to 15 linkage groups, which is close to the haploid chromosome number of bay scallop (n = 16). Analysis of the 40 markers segregating in both parents showed a higher recombination rate in the female parent, with the average of female-to-male recombination ratio of 1.09:1 between linked pairs of markers. When null alleles were considered, there were 17 loci showing segregation distortion at the 5% significance level using the chi-square test. The microsatellite markers developed in this study provide a useful resource for future linkage mapping and quantitative loci analysis in A. irradians.

Two different and functional nuclear rDNA genes in the abalone Haliotis tuberculata: tissue differential expression

Analysis of the 18S rDNA sequences of Haliotis tuberculata tuberculata and H. t. coccinea subtaxa identified two different types of 18S rDNA genes and ITS1 regions. These two different genes were also detected in H. marmorata, H. rugosa and H. diversicolor that are separated from H. tuberculata by 5-65 mya. The mean divergence value between type I and type II sequences ranged from 7.25% for 18S to 80% for ITS1. ITS1 type II is homologous with the ITS1 consensus sequences published for many abalone species, whereas ITS1 type I presented only minor homology with a unique database entry for H. iris ITS1. A phylogenetic analysis makes a clear separation between type I and type II ITS1 sequences and supports grouping H. t. tuberculata, H. t. coccinea and H. marmorata together. The two subtaxa do not show any significant differences between the homologous 18S rDNA sequences. A general structure of the ITS1 transcript was proposed, with four major helices for the two types. The two genes were expressed and, for the first time, a putative differential expression of ITS1 type I was detected in the gills, digestive gland and gonads whereas ITS1 type II was expressed in all tissues.

Chromosomal organization of the 18S and 5S rRNAs and histone H3 genes in Scarabaeinae coleopterans: insights into the evolutionary dynamics of multigene families and heterochromatin

BACKGROUND

Scarabaeinae beetles show a high level of macro-chromosomal variability, although the karyotypic organization of heterochromatin and multigene families (rDNAs and histone genes) is poorly understood in this group. To better understand the chromosomal organization and evolution in this group, we analyzed the karyotypes, heterochromatin distribution and chromosomal locations of the rRNAs and histone H3 genes in beetles belonging to eight tribes from the Scarabaeinae subfamily (Coleoptera, Scarabaeidae).

RESULTS

The number of 18S rRNA gene (a member of the 45S rDNA unit) sites varied from one to 16 and were located on the autosomes, sex chromosomes or both, although two clusters were most common. Comparison of the 45S rDNA cluster number and the diploid numbers revealed a low correlation value. However, a comparison between the number of 45S rDNA sites per genome and the quantity of heterochromatin revealed (i) species presenting heterochromatin restricted to the centromeric/pericentromeric region that contained few rDNA sites and (ii) species with a high quantity of heterochromatin and a higher number of rDNA sites. In contrast to the high variability for heterochromatin and 45S rDNA cluster, the presence of two clusters (one bivalent cluster) co-located on autosomal chromosomes with the 5S rRNA and histone H3 genes was highly conserved.

CONCLUSIONS

Our results indicate that the variability of the 45S rDNA chromosomal clusters is not associated with macro-chromosomal rearrangements but are instead related to the spread of heterochromatin. The data obtained also indicate that both heterochromatin and the 45S rDNA loci could be constrained by similar evolutionary forces regulating spreading in the distinct Scarabaeinae subfamily lineages. For the 5S rRNA and the histone H3 genes, a similar chromosomal organization could be attributed to their association/co-localization in the Scarabaeinae karyotypes. These data provide evidence that different evolutionary forces act at the heterochromatin and the 45S rDNA loci compared to the 5S rRNA and histone H3 genes during the evolution of the Scarabainae karyotypes.

Chromosomal organization of the 18S and 5S rRNAs and histone H3 genes in Scarabaeinae coleopterans: insights into the evolutionary dynamics of multigene families and heterochromatin

Background

Scarabaeinae beetles show a high level of macro-chromosomal variability, although the karyotypic organization of heterochromatin and multigene families (rDNAs and histone genes) is poorly understood in this group. To better understand the chromosomal organization and evolution in this group, we analyzed the karyotypes, heterochromatin distribution and chromosomal locations of the rRNAs and histone H3 genes in beetles belonging to eight tribes from the Scarabaeinae subfamily (Coleoptera, Scarabaeidae).

Results

The number of 18S rRNA gene (a member of the 45S rDNA unit) sites varied from one to 16 and were located on the autosomes, sex chromosomes or both, although two clusters were most common. Comparison of the 45S rDNA cluster number and the diploid numbers revealed a low correlation value. However, a comparison between the number of 45S rDNA sites per genome and the quantity of heterochromatin revealed (i) species presenting heterochromatin restricted to the centromeric/pericentromeric region that contained few rDNA sites and (ii) species with a high quantity of heterochromatin and a higher number of rDNA sites. In contrast to the high variability for heterochromatin and 45S rDNA cluster, the presence of two clusters (one bivalent cluster) co-located on autosomal chromosomes with the 5S rRNA and histone H3 genes was highly conserved.

Conclusions

Our results indicate that the variability of the 45S rDNA chromosomal clusters is not associated with macro-chromosomal rearrangements but are instead related to the spread of heterochromatin. The data obtained also indicate that both heterochromatin and the 45S rDNA loci could be constrained by similar evolutionary forces regulating spreading in the distinct Scarabaeinae subfamily lineages. For the 5S rRNA and the histone H3 genes, a similar chromosomal organization could be attributed to their association/co-localization in the Scarabaeinae karyotypes. These data provide evidence that different evolutionary forces act at the heterochromatin and the 45S rDNA loci compared to the 5S rRNA and histone H3 genes during the evolution of the Scarabainae karyotypes.

Comparative Cytogenetics Analysis of Chlamys farreri, Patinopecten yessoensis, and Argopecten irradians with Ct-1 DNA by Fluorescence In Situ Hybridization

The chromosomes of Chlamys farreri, Patinopecten yessoensis, and Argopecten irradians were studied by FISH using C. farreri C₀t-1 DNA probes. The results showed that C₀t-1 DNA signals spread on all chromosomes in the three scallops, whereas signal density and intensity were different strikingly. Clustering brighter signals presented in the centromeric and telomeric regions of most C. farreri chromosomes, and in the centromeric or pericentromeric regions of several P. yessoensis chromosomes. Comparative analysis of the mapping indicated a relatively higher homology in the repetitive DNA sequences of the genome between C. farreri and P. yessoensis than that between C. farreri and A. irradians. In addition, FISH showed that the distribution of C₀t-1 DNA clustering signals in C. farreri displayed completely similar signal bands between homologous chromosomes. Based on the C₀t-1 DNA fluorescent bands, a more exact karyotype of C. farreri has been obtained. In this study, the comparative analysis based on C₀t-1 DNA provides a new insight into the chromosomal reconstructions during the evolution process, and it is helpful for understanding an important source of genomic diversity, species relationships, and genome evolution.

Cytogenetic characterization and mapping of rDNAs, core histone genes and telomeric sequences in Venerupis aurea and Tapes rhomboides (Bivalvia: Veneridae)

We describe the chromosomal location of GC-rich regions, 28S and 5S rDNA, core histone genes, and telomeric sequences in the veneroid bivalve species Venerupis aurea and Tapes (Venerupis) rhomboides, using fluorochrome staining with propidium iodide, DAPI and chromomycin A3 (CMA) and fluorescent in situ hybridization (FISH). DAPI dull/CMA bright bands were coincident with the chromosomal location of 28S rDNA in both species. The major rDNA was interstitially clustered at a single locus on the short arms of the metacentric chromosome pair 5 in V. aurea, whereas in T. rhomboides it was subtelomerically clustered on the long arms of the subtelocentric chromosome pair 17. 5S rDNA also was a single subtelomeric cluster on the long arms of subtelocentric pair 17 in V. aurea and on the short arms of the metacentric pair 9 in T. rhomboides. Furthermore, V. aurea showed four telomeric histone gene clusters on three metacentric pairs, at both ends of chromosome 2 and on the long arms of chromosomes 3 and 8, whereas histone genes in T. rhomboides clustered interstitially on the long arms of the metacentric pair 5 and proximally on the long arms of the subtelocentric pair 12. Double and triple FISH experiments demonstrated that rDNA and H3 histone genes localized on different chromosome pairs in the two clam species. Telomeric signals were found at both ends of every single chromosome in both species. Chromosomal location of these three gene families in two species of Veneridae provides a clue to karyotype evolution in this commercially important bivalve family.

Chromosomal mapping of rRNA genes, core histone genes and telomeric sequences in Brachidontes puniceus and Brachidontes rodriguezi (Bivalvia, Mytilidae)

Background

Chromosome rearrangements are an important part of the speciation process in many taxa. The study of chromosome evolution in bivalves is hampered by the absence of clear chromosomal banding patterns and the similarity in both chromosome size and morphology. For this reason, obtaining good chromosome markers is essential for reliable karyotypic comparisons. To begin this task, the chromosomes of the mussels Brachidontes puniceus and B. rodriguezi were studied by means of fluorochrome staining and fluorescent in situ hybridization (FISH).

Results

Brachidontes puniceus and B. rodriguezi both have 2n = 32 chromosomes but differing karyotype composition. Vertebrate-type telomeric sequences appear at both ends of every single chromosome. B. puniceus presents a single terminal major rRNA gene cluster on a chromosome pair while B. rodriguezi shows two. Both mussels present two 5S rDNA and two core histone gene clusters intercalary located on the long arms of two chromosome pairs. Double and triple-FISH experiments demonstrated that one of the 5S rDNA and one of the major rDNA clusters appear on the same chromosome pair in B. rodriguezi but not in B. puniceus. On the other hand, the second 5S rDNA cluster is located in one of the chromosome pairs also bearing one of the core histone gene clusters in the two mussel species.

Conclusion

Knowledge of the chromosomal distribution of these sequences in the two species of Brachidontes is a first step in the understanding of the role of chromosome changes on bivalve evolution.

Molecular and cellular evidence for biased mitotic gene conversion in hybrid scallop

Background

Concerted evolution has been believed to account for homogenization of genes within multigene families. However, the exact mechanisms involved in the homogenization have been under debate. Use of interspecific hybrid system allows detection of greater level of sequence variation, and therefore, provide advantage for tracing the sequence changes. In this work, we have used an interspecific hybrid system of scallop to study the sequence homogenization processes of rRNA genes.

Results

Through the use of a hybrid scallop system (Chlamys farreri ♀ × Argopecten irradians ♂), here we provide solid molecular and cellular evidence for homogenization of the rDNA sequences into maternal genotypes. The ITS regions of the rDNA of the two scallop species exhibit distinct sequences and thereby restriction fragment length polymorphism (RFLP) patterns, and such a difference was exploited to follow the parental ITS contributions in the F1 hybrid during early development using PCR-RFLP. The representation of the paternal ITS decreased gradually in the hybrid during the development of the hybrid, and almost diminished at the 14th day after fertilization while the representation of the maternal ITS gradually increased. Chromosomal-specific fluorescence in situ hybridization (FISH) analysis in the hybrid revealed the presence of maternal ITS sequences on the paternal ITS-bearing chromosomes, but not vice versa. Sequence analysis of the ITS region in the hybrid not only confirmed the maternally biased conversion, but also allowed the detection of six recombinant variants in the hybrid involving short recombination regions, suggesting that site-specific recombination may be involved in the maternally biased gene conversion.

Conclusion

Taken together, these molecular and cellular evidences support rapid concerted gene evolution via maternally biased gene conversion. As such a process would lead to the expression of only one parental genotype, and have the opportunities to generate recombinant intermediates; this work may also have implications in novel hybrid zone alleles and genetic imprinting, as well as in concerted gene evolution. In the course of evolution, many species may have evolved involving some levels of hybridization, intra- or interspecific, the sex-biased sequence homogenization could have led to a greater role of one sex than the other in some species.

FISH mapping and identification of Zhikong scallop (Chlamys farreri) chromosomes

Chromosome identification is the first step in genomic research of a species, but it remains a challenge in scallops. In the present study, fluorescence in situ hybridization (FISH) mapping of 19 fosmid clones was attempted and used for chromosome identification in Zhikong scallop (Chlamys farreri Jones et Preston, 1904). Data showed that 10 clones were successfully mapped, including 7 without and 3 with C ( 0 ) t-1 DNA. Among them, 2 represented multiple signals and made no contribution to chromosome identification. Karyotypic analysis and cohybridization indicated that the remaining 8 clones realized the identification of 8 chromosomes. All 10 clones were sequenced at both ends, which could be developed as sequence-tagged sites and used for the unification of the cytological and genetic linkage maps. This study shows that fosmid clones can benefit chromosome identification and will undoubtedly be useful for cytogenetic research in Zhikong scallop.

Cytogenetic characterization of the bay scallop, Argopecten irradians irradians, by multiple staining techniques and fluorescence in situ hybridization

The chromosomes of Argopecten irradians irradians were studied by various cytogenetic approaches. Conventional chromosome characterization built on C-banding, DAPI-staining, and silver staining was complemented by the physical mapping of ribosomal DNA and telomeric sequence (TTAGGG)n by FISH. Results showed that the constitutive heterochromatin revealed by C-banding was mainly distributed at telomeric and centromeric regions. However, interstitial C-bands were also observed. The pattern of DAPI banding was almost consistent with that of C-banding. Silver staining revealed that NORs were located on the short arms of chromosome 3 and 10, and this was further confirmed by FISH using 18S-28S rDNA. 5S rDNA was mapped as two distinguishable loci on the long arm of chromosome 11. 18S-28S and 5S rDNA were located on different chromosomes by sequential FISH. FISH also showed that the vertebrate telomeric sequence (TTAGGG)n was located on both ends of each chromosome and no interstitial signals were detected. Sequential 18S-28S rDNA and (TTAGGG)n FISH demonstrated that repeated units of the two multicopy families were closely associated on the same chromosome pair.

Repetitive DNA, molecular cytogenetics and genome organization in the King scallop (Pecten maximus)

We studied the structure, organization and relationship of repetitive DNA sequences in the genome of the scallop, Pecten maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and Southern hybridisation with all repeat families to genomic DNA digests showed characteristic ladders of hybridised bands. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution.

Development and characterization of EST-SSR markers in the eastern oyster Crassostrea virginica

Simple sequence repeat (SSR) markers were developed from expressed sequence tags (ESTs) in the eastern oyster (Crassostrea virginica). ESTs of the eastern oyster were downloaded from GenBank and screened for SSRs with at least eight units of dinucleotide or five units of tri-, tetra-, penta-, and hexa-nucleotide repeats. The screening of 9101 ESTs identified 127 (1.4%) SSR-containing sequences. Primers were designed for 88 SSR-containing ESTs with good and sufficient flanking sequences. Polymerase chain reaction (PCR) amplification was successful for 71 primer pairs, including 19 (27%) pairs that amplified fragments longer than expected sizes, probably due to introns. Sixty-six pairs that produced fragments shorter than 800 bp were screened for polymorphism in five oysters from three populations via polyacrylamide gels, and 53 of them (80%) were polymorphic. Fifty-three polymorphic SSRs were labeled and genotyped in 30 oysters from three populations via an automated sequencer. Five of the SSRs amplified more than two fragments per oyster, suggesting locus duplication. The remaining 48 SSRs had 2 alleles per individual, including 11 with null alleles. In the 30 oysters analyzed, the SSRs had an average of 9.3 alleles per locus, ranging from 2 to 24. Forty-three loci segregated in a family with 100 progeny, with nine showing significant deviation from Mendelian ratios (three after Bonferroni correction). Seventy percent of the loci were successfully amplified in C. rhizophorae and 34% in C. gigas. This study demonstrates that ESTs are valuable resources for the development of SSR markers in the eastern oyster, and EST-derived SSRs are more transferable across species than genomic SSRs.

Karyology of the Antarctic scallop Adamussium colbecki, with some comments on the karyological evolution of pectinids

Karyotype, location of the nucleolar organiser region (NOR) and heterochromatin presence and composition were studied in the Antarctic scallop Adamussium colbecki Smith, 1902. The karyotype exhibits 2n = 38 chromosomes with 11 pairs of metacentrics, 5 of submetacentrics, one subtelocentric and two telocentrics. Ag-NOR, CMA(3), DA/MM and NOR-FISH evidenced paracentromeric NORs on the short arm of 2nd pair chromosomes. Digestion with three restriction endonucleases followed by sequential staining with Giemsa, CMA(3) and DAPI evidenced on all chromosomes centromeric heterochromatin positive for both DAPI and CMA(3). In situ hybridisation analysis showed the presence of an AT-rich satellite DNA in the centromeric heterochromatin of several chromosomes. A mosaicism was detected in the germinal cell lines of one specimen, as in six of the 20 plates examined the set had 37 chromosomes with a missing pair of telocentrics and an unpaired metacentric. Comparison of the chromosome sets of all the pectinids studied to date and comparison with a phyletic tree obtained from molecular mitochondrial genes studies yielded good agreement between karyotype morphology and taxonomic classification.

Chromosome rearrangements in Pectinidae (Bivalvia: Pteriomorphia) implied based on chromosomal localization of histone H3 gene in four scallops

Chromosomal structural rearrangement in four scallops, Chlamys farreri (n=19), Patinopecten yessoensis (n=19), Chlamys nobilis (n=16) and Argopecten irradians (n=16), was studied by fluorescence in situ hybridization using histone H3 gene probes. The results show that histone H3 gene sites differ strikingly with regard to number, location, and intensity among, or even within these species. For example, two histone H3 gene loci were detected on the metaphase chromosomes of P. yessoensis, while one locus was found in the others. In P. yessoensis, differing intensities of hybridization signals were detected between homologues 5 and 11, and within homologue 11. These data suggest that the histone H3 gene is a qualified chromosome marker for the preliminary understanding of the historical chromosomal reconstructing of the Pectinidae family. The variable distribution patterns of the histone H3 gene suggest that gene duplication/diminution as well as chromosome rearrangements by inversion and translocation may have played important roles in the genomic evolution of Pectinidae. We also compiled our present results with former published data regarding the chromosome mapping of rDNAs in species of the Pectinidae family. Such comparative chromosomal mapping should improve our understanding of historical chromosomal reconstructions of modern-day scallops.

Karyotype and Chromosomal Location of 18S–28S and 5S Ribosomal DNA in the Scallops Pecten maximus and Mimachlamys varia (Bivalvia: Pectinidae)

This work describes the karyotype and chromosomal location of the ribosomal DNA (rDNA) of Pecten maximus and Mimachlamys varia, two commercial scallop species from Europe. According to the chromosome centromeric index values found, the karyotype of P. maximus is composed of 1 metacentric, 2 metacentric-submetacentric, 1 telocentric-subtelocentric and 15 telocentric pairs, and that of M. varia of 4 metacentric, 2 subtelocentric-submetacentric, 9 subtelocentric, 3 subtelocentric-telocentric and 1 telocentric-subtelocentric pairs. In P. maximus, 18S-28S rDNA was located by FISH on a metacentric-submetacentric pair, and in M. varia on a subtelocentric-submetacentric pair using both silver staining and FISH. PCR amplification of the 5S rDNA unit yielded a single product of about 460 bp (P. maximus) and 450 bp (M. varia), that used as probe revealed a 5S rDNA site on a telocentric pair in P. maximus and a subtelocentric pair in M. varia. Two-color FISH or sequential silver staining of 5S rDNA-FISH-metaphases corroborated that the two gene families are located on different chromosomes in both species. A comparative analysis of the data allowed the inference of karyotypic relationships within scallops.

Estimation of preferential pairing rates in second-generation autotetraploid pacific oysters (Crassostrea gigas)

Although previously disregarded, polyploidy, and in particular autopolyploidy, is now believed to have played a prominent role in the evolution of plants and animals. We estimated the rate of preferential pairing in second-generation autotetraploid Pacific oysters from gametic frequencies. We found significant levels of preferential pairing in these recently generated autopolyploids, suggesting that genetic variation in standing populations may play a role in meiotic mechanisms of polyploids derived from these populations.