Hongtao Nie

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species, Ruditapes philippinarum. For the consensus linkage map, a total of 9658 markers spanning 1926.98 cM were mapped to 18 sex-averaged linkage groups, with an average marker distance of 0.42 cM. Based on the high-density linkage map, ten QTLs for growth-related traits and shell color were detected. The coverage and density of the current map are sufficient for us to effectively detect QTL for segregating traits, and two QTL positions were all coincident with the closest markers. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of R. philippinarum and other bivalve molluscan species.

Development and characterization of 38 microsatellite makers for Manila clam (Ruditapes philippinarum)

Thirty-eight polymorphic microsatellite makers were developed and characterized from expressed sequence tag sequence of the Manila clam, Ruditapes philippinarum. The number of alleles at each locus ranged from 2 to 13 with an average of six alleles per locus. The observed and expected heterozygosity varied from 0.036 to 0.719 and from 0.105 to 0.868, respectively. These microsatellite loci will be useful for further investigation of population structure and conversation genetics of this species.

High throughput sequencing of RNA transcriptomes in Ruditapes philippinarum identifies genes involved in osmotic stress response

Ruditapes philippinarum, is an economically important marine bivalve species. The ability to cope with low salinity stress is quite important for the survival of aquatic species under natural conditions. In this study, the transcriptional response of the Manila clam to low salinity stress was characterized using RNA sequencing. The transcriptomes of a low salinity-treatment group (FRp1, FRp2), which survived under low salinity stress, and control group (SRp1, SRp2), which was not subjected to low salinity stress, were sequenced with the Illumina HiSeq platform. A total of 196,578 unigenes were generated. GO and KEGG analyses revealed that signal transduction, immune response, cellular component organization or biogenesis, and energy production processes were the most highly enriched pathways among the genes that were differentially expressed under low salinity stress. All these pathways could be assigned to the following biological functions in the low salinity tolerant Manila clam: signal response to low salinity stress, antioxidant response, intracellular free amino acid transport and metabolism, energy production and conversion, cell signaling pathways, and regulation of ionic content and cell volume. In summary, this is the first study using high-throughput sequencing to identify gene targets that could explain osmotic regulation mechanisms under salinity stress in R. philippinarum.

Characterization of fourteen single nucleotide polymorphism markers in the Manila clam (Ruditapes philippinarum)

Abstract Fourteen single nucleotide polymorphisms (SNPs) were developed and characterized from expressed sequence tag sequence of the Manila clam, Ruditapes philippinarum. All loci had two alleles and the minor allele frequency ranged from 0.146 to 0.467. The observed and expected heterozygosities ranged from 0.259 to 0.792 and from 0.252 to 0.503. These are the first SNPs developed for assessing genetic variation and population structure in the Manila clam and will provide a useful complement to currently available genetic markers.

Isolation and characterization of fourteen polymorphic microsatellite loci in the Manila clam (Ruditapes philippinarum)

Ruditapes philippinarum is a commercially important mollusk species, but has been suffering from severe population decline due to over-exploitation and habitat destruction in China. In this study, fourteen polymorphic microsatellite loci were isolated and characterized in R. philippinarum. The number of alleles per polymorphic microsatellite locus ranged from 2 to 6, and the observed and expected heterozygosities varied from 0.036 to 0.688 and from 0.280 to 0.733, respectively. These microsatellite loci will be useful for further studies on the population structure and genetic variation of this species.

Genetic Variation and Differentiation in Wild and Selected Manila Clam Inferred from Microsatellite Loci

ABSTRACT Manila clam is widely distributed and cultured along the coasts of China. To assess genetic variation in selected strains cultured in China, four selected strains or populations, zebra (Z), white (W), orange (O), and white zebra (WZ), along with one wild population from Lvshun were analyzed with 10 microsatellite loci. The observed heterozygosity ranged from 0.335–0.538 across populations. The highest expected heterozygosity value was detected in the Z strain (0.716), whereas the lowest value was found in the WZ strain (0.578). FST revealed significant differentiation between all pairs of populations. The differentiation between the W strain and the O strain is the lowest (FST = 0.086). whereas the differentiation between Z and WZ strains was the highest (FST = 0.337). There was no significant reduction in heterozygosity in all four selected strains; however, the number of alleles per locus was considerably lower in the selected strains than in the wild population. These results provide valuable genetic information for the preservation, management, and further selective breeding of the Manila clam.

Publisher Correction: Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

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RNA-Seq analysis of differentially expressed genes in the grand jackknife clam Solen grandis under aerial exposure.

Aerial exposure tolerance has been long considered as an important trait for the life survival under acute environmental stress. In this study, we utilized RNA-seq-based transcriptomic profiling to characterize the molecular responses of grand jackknife clam in response to aerial exposure. This assembly yielded 190,856 unigenes with an average length of 1147 bp, a minimum length of 201 bp, and a maximum length of 51,869 bp, with an N50 length of 1875 bp. After differential expression analysis, a total of 1344 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, immune alteration, and apoptosis. GO and KEGG analyses revealed that signal transduction, immune response, cellular component organization or biogenesis, and energy production processes were the most highly enriched pathways among the genes that were differentially expressed under aerial exposure stress. All these pathways could be assigned to the following biological functions in the aerial exposure tolerant Solen grandis: signaling, transporter activity, macromolecular complex, cellular component organization or biogenesis, and molecular transducer activity. This study highlighted candidate genes linked to stress response during aerial exposure and provide a useful resource for further work on gills tissue or for selection of aerial exposure tolerant phenotypes.

Polymorphic Microsatellite Markers for Solen grandis and Their Cross-Species Amplification in Three Other Species

ABSTRACT The grand jackknife clam Solen grandis is a commercially important mollusk species, but has been suffering from severe population decline due to over-exploitation and habitat destruction in China. To promote a conservation program for this species, it is necessary to evaluate its genetic diversity and population genetics. In this study, 10 novel polymorphic microsatellite makers were developed and characterized from the S. grandis through high throughput sequencing. The number of alleles at each locus ranged from 10 to 34 with an average of 20.8 alleles per locus. The observed and expected heterozygosities varied from 0.433 to 1.000 and from 0.696 to 0.976, with an average of 0.793 and 0.884, respectively. The polymorphism information content (PIC) value ranged from 0.633 (Sg43838) to 0.958 (Sg3754), with an average of 0.858. The cross-species amplification transferability of 10 loci to three closely related species ranged from 4.17 to 62.5%. These microsatellite loci will be useful for further investigation of population structure and conversation genetics of this species.