Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity

Yan, Xiwu; Nie, Hongtao; Huo, Zhongming; Ding, Jianfeng; Li, Zhenzhen; Yan, Lulu; Jiang, Liwen; Mu, Zhengqiang; Wang, Huamin; Meng, Xiangyu; Chen, Peng; Zhou, Min; Rbbani, Golam; Liu, Guangjian; Li, Dongdong

doi:10.1016/j.isci.2019.08.049

Cited by 92 publications

(66 citation statements)

References 47 publications

(48 reference statements)

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“…Immune effectors are usually induced by PRRs recognition and produced by epithelial cells from various organs, including AMPs, lysozymes, cytokines, antioxidant enzymes, and acute phase proteins [19]. In this study, two kind of AMPs (DEF, CATH) were annotated in DEGs in response to PAMPs.…”

Section: Discussionmentioning

confidence: 99%

“…In the present study, the PO gene was found significantly down-regulated (− 4.32 fold change) in the LPS group, indicating the efficiency of ROS removing was decreased and the immune system was affected in R. philippinarum after LPS challenge. Heat shock proteins (HSPs) are evolutionarily ancient and highly conserved intracellular molecular chaperones [19]. The primary role of HSP is to function as molecular chaperones to modulate stress response [12].…”

Section: Discussionmentioning

confidence: 99%

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New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C)

Jiang

Nie

et al. 2020

BMC Genomics

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Background: Manila clam (Ruditapes philippinarum) is a worldwide commercially important marine bivalve species. In recent years, however, microbial diseases caused high economic losses and have received increasing attention. To understand the molecular basis of the immune response to pathogen-associated molecular patterns (PAMPs) in R. philippinarum, transcriptome libraries of clam hepatopancreas were constructed at 24 h post-injection with Lipopolysaccharide (LPS), peptidoglycan (PGN), and polyinosinic-polycytidylic acid (poly(I:C)) and phosphatebuffered saline (PBS) control by using RNA sequencing technology (RNA-seq). Results: A total of 832, 839, and 188 differentially expressed genes (DEGs) were found in LPS, PGN, and poly(I:C) challenge group compared with PBS control, respectively. Several immune-related genes and pathways were activated in response to the different PAMPs, suggesting these genes and pathways might specifically participate in the immune response to pathogens. Besides, the analyses provided useful complementary data to compare different PAMPs challenges in vivo. Functional enrichment analysis of DEGs demonstrated that PAMPs responsive signal pathways were related to apoptosis, signal transduction, immune system, and signaling molecules and interaction. Several shared or specific DEGs response to different PAMPs were revealed in R. philippinarum, including pattern recognition receptors (PRRs), antimicrobial peptides (AMPs), interferon-induced proteins (IFI), and some other immune-related genes were found in the present work. Conclusions: This is the first study employing high throughput transcriptomic sequencing to provide valuable genomic resources and investigate Manila clam response to different PAMPs through in vivo challenges with LPS, PGN, and poly(I:C). The results obtained here provide new insights to understanding the immune characteristics of R. philippinarum response to different PAMPs. This information is critical to elucidate the molecular basis of R. philippinarum response to different pathogens invasion, which potentially can be used to develop effective control strategies for different pathogens.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C)

Jiang

Nie

et al. 2020

BMC Genomics

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“…using EvalFrags.pl from 2bRAD_utilities). For instance, in Manila clam was predicted that the percentage of the genome constituted by repetitive elements and combined transposable elements could exceed 70% [31]. This genomic information should be considered to make the best technical decisions.…”

Section: Discussionmentioning

confidence: 99%

“…The two marine bivalve species from the Order Veneroida show high polymorphism and low population structure [25,26]; the brown trout belongs to the order Salmoniformes, which suffered a speci c genome duplication event [27], and shows one of the highest population structuring among vertebrates [28]; isolated populations from different ecosystems were analysed in the silver cat sh, a freshwater species from the order Siluriformes living in uvial and costal lagoon environments [29]; nally, the small-spotted catshark (order Carcharhiniformes) is a benthic species which populations here used show low genetic differentiation [30]. To date, two of the species used in this study have a reference genome available: Manila clam (genome size: 1.123 Gb; 19 chromosomes [31]) and brown trout (2.370 Gb; 40 chromosomes [32]). Wang and Guo [33] hypothesized that bivalves with 19 chromosomes could have a tetraploid origin, due to its ability to tolerate chromosomal aneuploidies.…”

Section: Introductionmentioning

confidence: 99%

Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

Casanova

Maroso

Blanco

et al. 2020

Preprint

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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 Building-loci pipelines seem not to have a substantial influence on population genetics inference. Anyway, we recommend being careful with certain building-loci pipeline parameters and SNP filtering steps, especially when a de novo approach is used. Preliminary trials with subsets of data should be performed for comparison of genetic diversity and differentiation, but always considering the specific goals of the study.

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“…The Manila clam, Ruditapes philippinarum, is an economically and scientifically important marine bivalve species, which has a wide geographic distribution from Europe to Asia [23]. Manila clam is one of the major aquaculture species in the world and the production of R. philippinarum reached over 4.0 million tons, equivalent to 3.7 million USD, in 2015 [24]. In recent years, however, this species faces greater risk of exposure to hypoxia as eutrophication worsens throughout its coastal habitats.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals differential immune related genes expression in Ruditapes philippinarum under hypoxia stress: potential HIF and NF-κB crosstalk in immune responses in clam

et al. 2020

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Background: Hypoxia is an important environmental stressor in aquatic ecosystems, with increasingly impacts on global biodiversity. Benthic communities are the most sensitive parts of the coastal ecosystem to eutrophication and resulting hypoxia. As a filter-feeding organism living in the seafloor sediment, Ruditapes philippinarum represents an excellent "sentinel" species to assess the quality of marine environment. In order to gain insight into the molecular response and acclimatization mechanisms to hypoxia stress in marine invertebrates, we examined hypoxia-induced changes in immune-related gene expression and gene pathways involved in hypoxia regulation of R. philippinarum. Results: We investigated the response of the Manila clam R. philippinarum to hypoxia under experimental conditions and focused on the analysis of the differential expression patterns of specific genes associated with hypoxia response by RNA-seq and time course qPCR analysis. A total of 75 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, chaperones/heat shock proteins, immune alteration, and cell proliferation/apoptosis. Fourteen hypoxia responsive genes were validated significantly up/down regulated at different time 0, 2, 5, and 8 d in gills of R. philippinarum in hypoxia challenged group. Functional enrichment analysis revealed the HIF signaling pathway and NF-κB signaling pathway play pivotal roles in hypoxia tolerance and resistance in R. philippinarum. Conclusion: The HIF signaling pathway and NF-κB signaling pathway play a critical role in hypoxia tolerance and resistance in Manila clam. The immune and defense related genes and pathways obtained here gain a fundamental understanding of the hypoxia stress in marine bivalves and provide important insights into the physiological acclimation, immune response and defense activity under hypoxia challenge. The reduced metabolism is a consequence of counterbalancing investments in immune defense against other physiological processes.

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Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity

Cited by 92 publications

References 47 publications

New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C)

New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C)

Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

Transcriptome analysis reveals differential immune related genes expression in Ruditapes philippinarum under hypoxia stress: potential HIF and NF-κB crosstalk in immune responses in clam

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