Characterization of transcriptome and identification of biomineralization genes in winged pearl oyster ( Pteria penguin ) mantle tissue

Li, Haimei; Liu, Bao-Suo; Huang, Guiju; Fan, Sigang; Zhang, Bo; Su, Jiaqi; Yu, Dahui

doi:10.1016/j.cbd.2016.12.002

Cited by 13 publications

(11 citation statements)

References 40 publications

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“…The database that had the most sequence similarities with P. maximus assembled transcripts was Ensembl C. gigas, which provided a putative function for 27 842 contigs (35%). While available data on larval transcriptomes remains scarce, the total number of contigs assembled and the annotation percentages were similar to those reported recently for other bivalve tissues (Li et al 2016;Li et al 2017;Mun et al 2017).…”

Section: Discussionsupporting

confidence: 80%

Understanding the mechanisms involved in the high sensitivity of Pecten maximus larvae to aeration

et al. 2018

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Among reared bivalves, some "novel species", such as the great scallop, Pecten maximus, have experienced more difficulty with routine reproduction due to their high sensitivity to biological, chemical, and physical stress during stages of early development. Working with high larval densities requires the use of aeration systems to provide optimal larval suspension and feed distribution. The high susceptibility of the great scallop to aeration in small-volume systems may impose an important limitation in hatchery-based practices. The present study aimed to investigate the processes impacted by aeration in P. maximus veliger larvae exposed to continuous aeration in small-volume tanks (10 L). Aeration appeared as major stressor that was responsible for early mortality among exposed animals (at 96 h after aeration started, haa) when exposure started 13 days after fertilization. Exposed larvae and controls were collected at 12, 24 and 72 haa, and a total of 18 cDNA libraries, each representing a pool of approximately 7,500 larvae, were sequenced, obtaining 358,817,016 raw reads. RNA-seq data were first used to build a de novo transcriptome assembly, and differential transcript abundance was assessed in exposed and control groups; thus, the molecular mechanisms involved in high sensitivity to aeration were deciphered. More than 2,000 transcripts were differentially expressed between exposed and control larvae across the entire time series (logFC > 1, FDR < 5%). Functional analysis revealed that transcriptional changes in larvae exposed to aeration mainly involved the genes that regulate digestive activity and energy metabolism, immune defense, inflammation, apoptosis, larval growth, and development. The results of this study demonstrate that, overall, aeration affects the feeding capacity and energy metabolism of larvae, with expected consequences on the animal's fitness, including its swimming efficiency. Aeration also triggered immune responses and apoptosis, which then increased through opportunistic infections. Notably, infections may be a consequence of a bacterial bloom triggered by the first mortality events that occurred in the culture. This study provides insights into the interactions between environmental variables and great scallop larvae physiology, and the results may contribute to the development of strategies for improving larval rearing practices and ensuring long-term sustainability of P. maximus aquaculture. Highlights ► Pecten maximus is highly susceptible to mild aeration, a desirable rearing practice yielding optimal larvae and feed distribution. ► Water turbulence reduced lipid and carbohydrate metabolism in scallop larvae, thus resulting in delayed growth and development. ► As a symptom of stress condition, larvae died, exhausted due to continuous swimming and inability to feed. ► These findings may contribute to develop strategies for improving rearing practices and for long-term sustainability of scallop aquaculture.

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Section: Discussionsupporting

confidence: 80%

Understanding the mechanisms involved in the high sensitivity of Pecten maximus larvae to aeration

et al. 2018

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“…Here, we used a common transcriptomic approach (RNA-seq) to obtain an overview of differences in gene expression and alternative splicing between high and low cultured pearl quality. Recently, RNA-seq has been successfully used to explore genes related to pearl oyster growth and response to environmental stressors ( P. fucata ) [35, 36] and biomineralization ( P. martensii and P. penguin ) [37–39]. The use of RNA-seq in P. margaritifera for biomineralization related studies has been held back by the relatively limited coverage of previous transcriptome references (Roche 454; [40]) or their reduced tissue representation [41].…”

Section: Discussionmentioning

confidence: 99%

Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera

et al. 2019

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BackgroundCultured pearls are unique gems produced by living organisms, mainly molluscs of the Pinctada genus, through the biomineralization properties of pearl sac tissue. Improvement of P. margaritifera pearl quality is one of the biggest challenges that Polynesian research has faced to date. To achieve this goal, a better understanding of the complex mechanisms related to nacre and pearl formation is essential and can now be approached through the use of massive parallel sequencing technologies. The aim of this study was to use RNA-seq to compare whole transcriptome expression of pearl sacs that had producing pearls with high and low quality. For this purpose, a comprehensive reference transcriptome of P. margaritifera was built based on multi-tissue sampling (mantle, gonad, whole animal), including different living stages (juvenile, adults) and phenotypes (colour morphotypes, sex).ResultsStrikingly, few genes were found to be up-regulated for high quality pearls (n = 16) compared to the up-regulated genes in low quality pearls (n = 246). Biomineralization genes up-regulated in low quality pearls were specific to prismatic and prism-nacre layers. Alternative splicing was further identified in several key biomineralization genes based on a recent P. margaritifera draft genome.ConclusionThis study lifts the veil on the multi-level regulation of biomineralization genes associated with pearl quality determination.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5443-5) contains supplementary material, which is available to authorized users.

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“…Outside deuterostomes, a number of transcriptome and proteome-based studies, predominately in molluscs, have linked EPDRs with a variety of functions. ‘S ometsuke’ , an EPDR described in the abalone (a gastropod mollusc), has a role in shell biomineralisation and pigmentation [ 15 , 16 ], and EPDRs have also been found in mantle transcriptomes and shell proteomes in other mollusc species [ 17 – 19 ]. In addition, EPDRs have been implicated in gastropod larval development [ 20 ], are upregulated in response to toxins and metal pollution in bivalves [ 21 – 24 ], and are differentially regulated during pathogen challenge trials in bivalves [ 25 – 27 ] and in response to environmental stressors in both bivalves and gastropods [ 28 – 30 ].…”

Section: Introductionmentioning

confidence: 99%

The evolution of ependymin-related proteins

et al. 2018

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BackgroundEpendymins were originally defined as fish-specific secreted glycoproteins involved in central nervous system plasticity and memory formation. Subsequent research revealed that these proteins represent a fish-specific lineage of a larger ependymin-related protein family (EPDRs). EPDRs have now been identified in a number of bilaterian animals and have been implicated in diverse non-neural functions. The recent discoveries of putative EPDRs in unicellular holozoans and an expanded EPDR family with potential roles in conspecific communication in crown-of-thorns starfish suggest that the distribution and diversity of EPDRs is significantly broader than currently understood.ResultsWe undertook a systematic survey to determine the distribution and evolution of EPDRs in eukaryotes. In addition to Bilateria, EPDR genes were identified in Cnidaria, Placozoa, Porifera, Choanoflagellatea, Filasterea, Apusozoa, Amoebozoa, Charophyta and Percolozoa, and tentatively in Cercozoa and the orphan group Malawimonadidae. EPDRs appear to be absent from prokaryotes and many eukaryote groups including ecdysozoans, fungi, stramenopiles, alveolates, haptistans and cryptistans. The EPDR family can be divided into two major clades and has undergone lineage-specific expansions in a number of metazoan lineages, including in poriferans, molluscs and cephalochordates. Variation in a core set of conserved residues in EPDRs reveals the presence of three distinct protein types; however, 3D modelling predicts overall protein structures to be similar.ConclusionsOur results reveal an early eukaryotic origin of the EPDR gene family and a dynamic pattern of gene duplication and gene loss in animals. This research provides a phylogenetic framework for the analysis of the functional evolution of this gene family.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1306-y) contains supplementary material, which is available to authorized users.

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Characterization of transcriptome and identification of biomineralization genes in winged pearl oyster ( Pteria penguin ) mantle tissue

Cited by 13 publications

References 40 publications

Understanding the mechanisms involved in the high sensitivity of Pecten maximus larvae to aeration

Understanding the mechanisms involved in the high sensitivity of Pecten maximus larvae to aeration

Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera

The evolution of ependymin-related proteins

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