Applications of AFLP technology in genetic and phylogenetic analysis of penaeid shrimp

Phylogenetic relations and mitogenome-wide similarity metrics reveal monophyly of Penaeus sensu lato

Splitting of the genus Penaeus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of Penaeus sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera. For the first time, the present study targeted the testing of all the six genera of Penaeus sensu lato for phylogenetic relations utilizing complete mitochondrial genome sequence. In addition, the study reports for the first time about the complete mitochondrial DNA genome sequence of Fenneropenaeus indicus, an important candidate species in aquaculture and fisheries, and utilized it for phylogenomics. The maximum likelihood and Bayesian approaches were deployed to generate and comprehend the phylogenetic relationship among the shrimp in the suborder, Dendrobranchiata. The phylogenetic relations established with limited taxon sampling considered in the study pointed to the monophyly of Penaeus sensu lato and suggested collapsing of the new genera to a single genus. Further, trends in mitogenome-wide estimates of average amino acid identity in the order Decapoda and the genus Penaeus sensu lato supported restoration of the old genus, Penaeus, rather promoting the creation of new genera.

The development of species-specific AFLP-derived SCAR and SSCP markers to identify mantis shrimp species

Mantis shrimp has become commercially valuable in many countries, while the commercially aquaculture still unsuccessful. The stable supply of the species-specific markers for precise identification can play a key role of foods authentication as well as restoring/enhancing mantis shrimp stocks in future. The aim of this research was to identify species-specific markers for Squillid and Harpiosquillid mantis shrimp taxa using Amplified fragment length polymorphism-Single strand conformation polymorphism (AFLP-SSCP) approaches. Selective amplification would be substituted as a total of 40 primer combinations was performed using either three-base (i.e., EcoRI+3 and MseI+3 in 20 primer combinations) or two-base (i.e., EcoRI+2 and MseI+2 in 20 primer combinations) selective primers. These had been size-fractionated via 6% denaturing polyacrylamide gel electrophoresis, ten AFLP fragments exhibiting species or genus-specific characteristics were cloned, sequenced, and GenBank interrogated. A primer pair was designed and their specificity was tested versus the genomic DNA of various species. Results show that the primer E₊₂-13/M₊₂-13Hr₁₅₈ generated PCR products for just H. harpax, while E₊₃-14/M₊₃-2HhHr₁₅₁ and E₊₂-13/M₊₂-13Hh₁₅₀ generated PCR products for both H. harpax and H. raphidea and not others (i.e., M. nepa, O. oratoria, and E. woodmasoni). SSCP was then applied in order to differentiate between H. harpax and H. raphidea. These SSCP results indicate that species can be differentiated based on polymorphic fragment nucleotides. Indeed, primers E₊₂-13/M₊₂-13Hr₁₅₈, E₊₃-14/M₊₃-2HhHr_151, and E₊₂-13/M₊₂-13Hh₁₅₀ were all successfully confirmed as present in processed mantis shrimp samples (i.e., saline-preserved and heat-dried). These results provide new species-specific markers for mantis shrimp identification.

The State of "Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization

Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.

Genetic diversity among red swamp crayfish (Procambarus clarkii) populations in the middle and lower reaches of the Yangtze River based on AFLP markers

The red swamp crayfish has become one of the most important freshwater aquaculture species in China. At present, although it is widely distributed in the middle and lower reaches of the Yangze River basin, little is known about its population genetics and geographic distribution in China. We estimated the genetic diversity among 6 crayfish populations from 4 lakes (Hongze Lake, Poyang Lake, Dongting Lake, and Yue Lake) using AFLPs. A total of 129 loci were generated with 5 EcoRI-MseI primer combinations and scored as binary data in 139 individuals. These data were analyzed by cluster methods with the NTSYSpc software package. The 6 populations were separated into 3 major clusters by principal coordinate analysis and cluster analysis. Among the 6 populations, the highest gene diversity was found within the Nanjing population. Analysis of molecular variance demonstrated that most variation occurred within populations (91.20%). The estimated average GST value across all loci was 0.4186, suggesting (very) low gene flow among the different localities. We conclude that there is high genetic differentiation among crayfish in the middle and lower reaches of the Yangze River. This information will help in the selection of high-quality individuals for artificial reproduction.

Resolution of the Acanthopagrus black seabream complex based on mitochondrial and amplified fragment-length polymorphism analyses

In this study, DNA analyses were employed to verify the identity of six morphologically similar species that occur in the coastal waters of Taiwan: the black seabream complex (Acanthopagrus latus, Acanthopagrus schlegelii, Acanthopagrus sivicolus, Acanthopagrus taiwanensis, Acanthopagrus chinshira and Acanthopagrus pacificus). Amplified fragment-length polymorphism (AFLP) analyses clearly distinguished the same six species that are morphologically diagnosable based on subtle differences in scale counts and anal-fin colouration. In contrast, mitochondrial DNA analyses based on cytochrome b gene sequences did not distinguish individuals of A. schlegelii and A. sivicolus, reflecting either historical introgression or recent speciation and incomplete sorting of their mitochondrial lineages. Phylogenetic relationships among these six north-west Pacific Ocean species of Acanthopagrus analysed using AFLP data were consistent with scale rows above the lateral line (TRac), sperm ultrastructure and geographical distribution. The study provides molecular tools for future research relevant to improved management of these resources, and an increased understanding of the evolutionary history of this radiation.

Two spinefoot colour morphs: mottled spinefoot Siganus fuscescens and white-spotted spinefoot Siganus canaliculatus are synonyms

Mottled spinefoot Siganus fuscescens and white-spotted spinefoot Siganus canaliculatus are two similar species that differ subtly in colouration and morphology. Three major mtDNA clades were identified for these species, but individuals were clustered by amplified fragment length polymorphism (AFLP) according to geography rather than morphology, suggesting that the colour morphs are interbreeding.

Species identification of the Northern shrimp (Pandalus borealis) by polymerase chain reaction-restriction fragment length polymorphism and proteomic analysis

Genomic and proteomic techniques for species identification of meat and seafood products are being widely used. In this study, a genomic approach was used to differentiate Pandalus borealis (the Northern shrimp), which belongs to the superfamily Pandaloidea, from 30 crustaceans consisting of 19 commercially relevant prawns/shrimps species that belong to the superfamily Penaeoidea, which include the families Penaeidae and Solenoceridae, and 11 other crustacean species, including prawns, shrimps, lobsters, and crabs. For this purpose, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was designed based on the amplification of the 16S rRNA/tRNA(Val)/12S rRNA mitochondrial regions using the primers 16S-CruF and 16S-CruR. The 966-bp PCR products were produced and cleaved with the restriction enzymes AluI, TaqI, and HinfI, which provided species-specific restriction patterns. In addition, a proteomic approach, based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization-ion trap (ESI-IT) mass spectrometry, was used to identify and characterize new P. borealis-specific peptides that could be useful as potential markers of this species in protein-based detection methods. To our knowledge, this is the first time a molecular method has been successfully applied to identify a wide range of prawn and shrimp species, including P. borealis, for either whole individuals or processed products. However, validation of the methods proposed here is required by applying them to a larger sample of individuals from different populations and geographic origins in order to avoid mainly false-negative results.

Accurate inference of subtle population structure (and other genetic discontinuities) using principal coordinates

Background

Accurate inference of genetic discontinuities between populations is an essential component of intraspecific biodiversity and evolution studies, as well as associative genetics. The most widely-used methods to infer population structure are model-based, Bayesian MCMC procedures that minimize Hardy-Weinberg and linkage disequilibrium within subpopulations. These methods are useful, but suffer from large computational requirements and a dependence on modeling assumptions that may not be met in real data sets. Here we describe the development of a new approach, PCO-MC, which couples principal coordinate analysis to a clustering procedure for the inference of population structure from multilocus genotype data.

Methodology/Principal Findings

PCO-MC uses data from all principal coordinate axes simultaneously to calculate a multidimensional “density landscape”, from which the number of subpopulations, and the membership within subpopulations, is determined using a valley-seeking algorithm. Using extensive simulations, we show that this approach outperforms a Bayesian MCMC procedure when many loci (e.g. 100) are sampled, but that the Bayesian procedure is marginally superior with few loci (e.g. 10). When presented with sufficient data, PCO-MC accurately delineated subpopulations with population F_st values as low as 0.03 (G'_st>0.2), whereas the limit of resolution of the Bayesian approach was F_st = 0.05 (G'_st>0.35).

Conclusions/Significance

We draw a distinction between population structure inference for describing biodiversity as opposed to Type I error control in associative genetics. We suggest that discrete assignments, like those produced by PCO-MC, are appropriate for circumscribing units of biodiversity whereas expression of population structure as a continuous variable is more useful for case-control correction in structured association studies.

Development of 11 polymorphic microsatellite loci in the small abalone (Haliotis diversicolor Reeve)

Eleven polymorphic microsatellite loci for Haliotis diversicolor were isolated and characterized from (CT)(n) - and (AC)(n) -enriched library. They were tested in 24 individuals from a natural population. All of them were polymorphic, with the number of alleles varying between three and 10. The observed heterozygosities and expected heterozygosities ranged from 0.083 to 0.913 and from 0.159 to 0.856, respectively. The 11 isolated microsatellite loci, except SA-JMU6 and SA-JMU12, followed Hardy-Weinberg expectations. Seven sets of primers also amplify in closely related species, H. ovina and H. asinine. These 11 polymorphic microsatellites will be useful for analysing the population structure and genetic diversity in H. diversicolor.

Microsatellite-centromere mapping in large yellow croaker (Pseudosciaena crocea) using gynogenetic diploid families

The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. Inheritance of 22 heterozygous microsatellite loci was examined in normal crossed diploid families and meio-gynogenetic families in P. crocea. Two gynogenetic families were produced via inhibition of the second polar body in eggs fertilized with UV-irradiated sperm. The ratio of gynogenesis was proven to be 100% and 96.9% in the two families, respectively. Of the 22 examined loci, 4 showed a segregation distortion in both control and gynogenetic families. Microsatellite-centromere (M-C) map distances were examined using 18 loci with normal Mendelian segregation. Estimated recombination rates ranged between 0 and 1.0 under the assumption of complete interference. High recombinant frequencies between heterozygous markers and the centromere were found in large yellow croaker, as in other teleosts. The average recombination frequency was 0.586. Ten loci showed high M-C recombination with frequency greater than 0.67. M-C distances provide useful information for gene mapping in large yellow croaker.

Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis

Genetic diversity and population differentiation of the blue swimming crab (Portunus pelagicus) in Thailand, originating from Ranong and Krabi located in the Andaman Sea (west) and Chanthaburi, Prachuap Khiri Khan, and Suratthani located in the Gulf of Thailand (east), were examined by AFLP analysis. High genetic diversity of P. pelagicus in Thai waters was found (N=72). The four primer combinations generated 227 AFLP fragments, and the percentage of polymorphic bands in each geographic sample was 66.19-94.38%. The mean genetic distance between pairs of samples was 0.1151-0.2440. Geographic heterogeneity analyses using the exact test and FST-based statistics between all pairwise comparisons were statistically significant (P<0.01), indicating a fine-scale level of intraspecific population differentiation of Thai P. pelagicus. The estimated number of migrants per generation (Nem) was 0.26-0.76, suggesting restricted gene flow levels of P. pelagicus in Thai waters.

Analysis of the genetic relationships among Thai gibbon species using AFLP markers

Cytogenetic studies of three gibbon species using conventional banding patterns were investigated showing an identical number of 44 diploid chromosomes. They are assumed to have common evolutionary relationships. For in depth study, molecular markers were assessed using the Amplified Fragment Length Polymorphism (AFLP) method. With seven successful primer combinations, a total of 1669 scorable bands were generated. The resulting bands were used for dendrogram construction. From the dendrogram, the individuals of Hylobates lar are closely related to H. agilis more than H. pileatus with a bootstrap value of 78%. Averages of inter-specific genetic similarity values among all gibbon species studied are 67.15% (between H. lar and H. pileatus) to 71.03% (between H. lar and H. agilis). In summary three gibbon species show genetic stability within a species. The development of specific molecular markers of a species is beneficial for genetic differentiation of this group of primates.

Glycosyl linkage characteristics and classifications of exo-polysaccharides of some regionally different strains of Lentinula edodes by amplified fragment length polymorphism assay and cluster analysis

We report here the first combined amplified fragment length polymorphism (AFLP) analysis of genomic DNA fingerprinting data and cluster analysis of the exo-polysaccharide glycosyl linkage data of 10 regionally different strains of Lentinula edodes to compare their genetic and structural similarities and differences. In addition, the monosaccharide compositions, molecular weights, glycosyl structural linkages were investigated for the exo-polysaccharides extracted from these different phylogenetic groups of regionally different L. edodes. All exo-polysaccharides had similar molecular weight distribution between 1x10(4) and 3x10(6) Da and the monosaccharide composition analysis revealed the presence of heterogeneous materials containing glucose, mannose, xylose, galactose, fucose, rhamnose and arabinose in different ratios. Among these monosaccharides, the glucose contents are the highest for all but one strain, indicating that glucose probably is the building block of the backbones of these exo-polysaccharides. The AFLP assay data helped to classify the 10 L. edodes strains into three distinct genetic groups. Gas chromatographic and mass spectrometric (GC-MS) data revealed five different glycosyl linkage types for these exo-polysaccharides. Most of the exo-polysaccharide backbone structures contain (1-->4)-linked-D-glucopyranosyl and (1-->6)-linked-D-glucopyranosyl moieties. Arabinose 1-->4 linkages and mannose 1-->2 linkages also exist in all strains. The only differences among these linkages are their monosaccharide compositions leading to different degree of backbone and branch formations. Cluster analyses of the GC-MS data of the exo-polysaccharides of the 10 strains resulted in 10 dendrograms. However, four of the 10 dendrograms were identical and were obtained using the average, Ward and weighted linkage type method of Manhattan distance and using the Ward method of Euclidean distance. The results of cluster analyses were not very much different from that of the AFLP assay and allowed the comparison of genetic and structural similarities and differences.

Species identification of five penaeid shrimps using PCR-RFLP and SSCP analyses of 16S ribosomal DNA

DNA-based molecular markers for differentiation of five penaeid shrimps (Penaeus monodon, P. semisulcatus, Feneropenaeus merguiensis, Litopenaeus vannamei and Marsupenaeus japonicus) were developed based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and single-stranded conformation polymorphism (SSCP) of 16S ribosomal (r) DNA. Differentiation of P. monodon, P. semisulcatus and L. vannamei can be unambiguously carried out by PCRRFLP of 16S rDNA(560) whereas P. semisulcatus and M. japonicus shared a BABB mitotype. These shrimps were successfully discriminated by SSCP analysis of 16S rDNA(560). Nevertheless, the amplification success for L. vannamei and F. merguiensis was not consistent when tested against larger sample sizes. As a result, 16S rDNA(560) of an individual representing the most common mitotype of each species was cloned and sequenced. The new primer pair was designed and tested against the large sample sizes (312 bp product, N = 185). The amplification success was consistent across all species. PCR-RFLP of 16S rDNA(312) was as effective as that of 16S rDNA(560). Differentiation of all shrimp species were successfully carried out by SSCP analysis.