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Crassostrea gigas

Crassostrea gigas is a species of oyster, commonly known as the Pacific oyster or Miyagi oyster.
It is a bivalve mollusk that is widely cultivated for food production around the world.
This oyster species is native to the Pacific coast of Asia, but has been introduced to many other regions due to its commercial importance.
Crassostrea gigas is known for its large size, robust shell, and distinctive flavor, making it a popular choice for seafood consumption.
Reserach on this species can provide valuable insights into aquaculture, ecology, and the biology of bivalve molusks.

Most cited protocols related to «Crassostrea gigas»

1
Experimental Infection of Oysters with OsHV-1
Cited 13 times
Three batches of moribund Crassostrea gigas oysters were collected on the field along the French coasts during abnormal mortality outbreaks in 2008 (Table 1). The first batch was composed of oysters collected at Gouville (Normandy - Cotentin), the second of oysters collected in the estuary of the Etel river (Brittany - Morbihan), and the last one corresponded to oysters collected on the site of Aulne located in the Bay of Brest (Brittany - Finistère). These animals were checked for OsHV-1 detection and served for the preparation of tissue homogenates. A control tissue homogenate was prepared from the batch of healthy appearing oysters used for experimental assays and showing no mortality in 2008 (see below; Table 1).
Experimental infection trials were performed on healthy appearing C. gigas spat (one year old) purchased in November 2008 from a shellfish farm located on the French Mediterranean coast. No mortality event has been reported at this shellfish farm location during 2008. Oyster spat sized around 40 mm in length, with a mean weight of 5 grams. Oysters were placed in the Ifremer's facilities (Laboratoire de Génétique et Pathologie, La Tremblade, France) in a single tank of 200 L containing filtered (1 μm) seawater and slowly acclimated to 22°C increasing the temperature of 1°C per day. During this period, oysters were fed daily by addition of 2 liters of microalgae Skeletonema costatum (1.5 103 cells/mL). Oysters did not present any mortality or other symptom of disease at this time. At the end of the acclimatization period and just before the beginning of the experiment, a set of 20 individuals was assessed by real time quantitative PCR in order to evaluate the initial OsHV-1 DNA detection.
No ethical approval has been requested for the present study because experimental research has been conducted on Pacific oysters (invertebrates). Oysters don't possess a central nervous system.
Schikorski D., Renault T., Saulnier D., Faury N., Moreau P, & Pépin J.F. (2011). Experimental infection of Pacific oyster Crassostrea gigas spat by ostreid herpesvirus 1: demonstration of oyster spat susceptibility. Veterinary Research, 42(1), 27.
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Publication 2011
Acclimatization Animals Biological Assay Cells Central Nervous System Crassostrea gigas Disease Outbreaks Estuaries Infection Invertebrates Microalgae Oysters Real-Time Polymerase Chain Reaction Rivers Shellfish Tissues
2
Producing Pathogen-Free Crassostrea gigas Oysters
Cited 7 times
In 2015, fifty different biparental Crassostrea gigas oyster families were produced from wild seed broodstocks sampled in farming and non-farming areas in two geographic regions (French Mediterranean and Atlantic coasts, Supplementary Table 1). In the Atlantic area, 73 oysters were collected at Logonna Daoulas (farming area) and 70 oysters at Dellec (non-farming area). In the Mediterranean area, 125 oysters were collected in the Thau lagoon (farming area) and 65 at the Vidourle river mouth (non-farming area). In addition, 84 oysters issued from a mass selection programme to enhance their resistance to mortality syndrome were used28 (link). All the collected oysters were transferred to the Ifremer facility at Argenton (Brittany, France) between 6 and 8 January 2015 and treated for 6 days with chloramphenicol (8 mg/l).
For gametogenesis induction, animals were held for 8 weeks in 500 l flow-through tanks with seawater enriched with a phytoplankton mixture at a constant temperature of 17 °C13 (link),22 (link). Seawater was UV-treated and filtered through 10-μm mesh. The daily mixed diet consisted of Tisochrysis lutea (CCAP 927/14; 40 μm3, 12 pg cell−1) and Chaetoceros muelleri (CCAP 1010/3; 80 μm3, 25 pg cell−1). Once the oysters were reproductively mature, gametes from 91 individuals (46 males, 45 females) were obtained by stripping. Gametes from one male and one female from the same origin were mixed in a 5-l cylinder at a ratio of 50 spermatozoids per oocyte (day 0). The fertilized oocytes completed their embryonic development in 5-l tubes filled with 1-μm-filtered, UV-treated seawater at 21 °C for 48 h. The D-larvae (day 2) were then collected and reared in flow-through rearing systems at 25 °C45 (link). At the end of the pelagic phase (day 15), all the larvae were collected on a 100-μm sieve and allowed to settle on cultch. Post-larvae were maintained in downwelling systems, where they were continuously supplied with enriched seawater until the experiments began. In the larval and post-larval stages, the oysters were fed the same diet as the broodstock at a concentration between 1500–2000 μm3 μl−145 (link).
Of the 50 families of oyster seed produced, 3 families from each location were kept, along with 3 other families from the mass selected broodstock, for ‘natural’ experimental infections. These 15 oyster families were maintained under highly controlled biosecured conditions to be sure that no oyster pathogens would interfere with further experiments. The ‘pathogen-free’ status of the animals was confirmed by (i) the absence of OsHV-1 DNA detection by qPCR and (ii) a low Vibrio presence (~10 cfu−1 tissue) determined by isolation on selective culture medium (thiosulfate-citrate-bile salts-sucrose agar, TCBS)12 (link). Oysters were observed to remain free of any abnormal mortality throughout the larvae until the beginning of the ‘natural’ experimental infections.
de Lorgeril J., Lucasson A., Petton B., Toulza E., Montagnani C., Clerissi C., Vidal-Dupiol J., Chaparro C., Galinier R., Escoubas J.M., Haffner P., Dégremont L., Charrière G.M., Lafont M., Delort A., Vergnes A., Chiarello M., Faury N., Rubio T., Leroy M.A., Pérignon A., Régler D., Morga B., Alunno-Bruscia M., Boudry P., Le Roux F., Destoumieux-Garzόn D., Gueguen Y, & Mitta G. (2018). Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters. Nature Communications, 9, 4215.
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Publication 2018
Agar Animals ARID1A protein, human AT 17 Cells Chloramphenicol Citrates Crassostrea gigas Culture Media Diet Embryonic Development Females Gametes Gametogenesis Genitalia, Female Infection isolation katacalcin Larva Males Oocytes Oral Cavity Ovum Oysters Pathogenicity Phytoplankton Rivers Salts, Bile Sucrose Syndrome Thiosulfates Tissues Vibrio
3
Automated Annotation of Bed Bug Genome
Cited 7 times
The bed bug is 1 of 30 i5K pilot genome assemblies that were subjected to automatic gene annotation using a Maker 2.0 (http://www.yandell-lab.org/software/maker.html) annotation pipeline tuned specifically for arthropods. The pipeline is designed to be systematic, providing a single consistent procedure for the species in the pilot study, scalable to handle 100s of genome assemblies, evidence guided using both protein and RNA-seq evidence to guide gene models and targeted to utilize extant information on arthropod gene sets. The core of the pipeline was a Maker 2 instance, modified slightly to enable efficient running on our computational resources. The genome assembly was first subjected to de novo repeat prediction and CEGMA analysis (http://korflab.ucdavis.edu/datasets/cegma/) to generate gene models for initial training of the ab initio gene predictors (Supplementary Data 33). Three rounds of training of the Augustus (http://bioinf.uni-greifswald.de/augustus/) and SNAP (http://korflab.ucdavis.edu/software.html) gene predictors within Maker were used to bootstrap to a high-quality training set. Input protein data included 1 million peptides from a non-redundant (nr) reduction (90% identity) of Uniprot Ecdysozoa (1.25 million peptides) supplemented with proteomes from 18 additional species (Strigamia maritima, Tetranychus urticae, Caenorhabditis elegans, Loa loa, Trichoplax adhaerens, Amphimedon queenslandica, Strongylocentrotus purpuratus, Nematostella vectensis, Branchiostoma floridae, Ciona intestinalis, Ciona savignyi, Homo sapiens, Mus musculus, Capitella teleta, Helobdella robusta, Crassostrea gigas, Lottia gigantea and Schistosoma mansoni) leading to a final nr peptide evidence set of 1.03 million peptides. RNA-seq from C. lectularius adult males and females was used judiciously to identify exon–intron boundaries but with a heuristic script to identify and split erroneously joined gene models. We used CEGMA models for QC purposes: for C. lectularius, of 1,977 CEGMA single-copy orthologue gene models, 1,928 were found in the assembly, and 1,892 in the final predicted gene set. Finally, the pipeline uses a nine-way homology prediction with human, Drosophila and C. elegans, and InterPro Scan5 to allocate gene names. The automated gene set is available from the BCM-HGSC website (https://www.hgsc.bcm.edu/arthropods/bed-bug-genome-project) and at the National Agricultural Library (https://i5k.nal.usda.gov).
Benoit J.B., Adelman Z.N., Reinhardt K., Dolan A., Poelchau M., Jennings E.C., Szuter E.M., Hagan R.W., Gujar H., Shukla J.N., Zhu F., Mohan M., Nelson D.R., Rosendale A.J., Derst C., Resnik V., Wernig S., Menegazzi P., Wegener C., Peschel N., Hendershot J.M., Blenau W., Predel R., Johnston P.R., Ioannidis P., Waterhouse R.M., Nauen R., Schorn C., Ott M.C., Maiwald F., Johnston J.S., Gondhalekar A.D., Scharf M.E., Peterson B.F., Raje K.R., Hottel B.A., Armisén D., Crumière A.J., Refki P.N., Santos M.E., Sghaier E., Viala S., Khila A., Ahn S.J., Childers C., Lee C.Y., Lin H., Hughes D.S., Duncan E.J., Murali S.C., Qu J., Dugan S., Lee S.L., Chao H., Dinh H., Han Y., Doddapaneni H., Worley K.C., Muzny D.M., Wheeler D., Panfilio K.A., Vargas Jentzsch I.M., Vargo E.L., Booth W., Friedrich M., Weirauch M.T., Anderson M.A., Jones J.W., Mittapalli O., Zhao C., Zhou J.J., Evans J.D., Attardo G.M., Robertson H.M., Zdobnov E.M., Ribeiro J.M., Gibbs R.A., Werren J.H., Palli S.R., Schal C, & Richards S. (2016). Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nature Communications, 7, 10165.
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Publication 2016
Adult Arthropods Bedbugs Branchiostoma floridae Caenorhabditis elegans Ciona intestinalis Ciona savignyi Crassostrea gigas DNA Library Drosophila Exons Females Gene Annotation Genes Genome Homo sapiens Introns Loa loa Males Mice, House Peptides Proteins Proteome RNA-Seq Schistosoma mansoni Strongylocentrotus purpuratus Trichoplax
4
Identification of Putative Opsin Genes
Cited 7 times
To obtain the sequences of putative opsin genes from the transcriptome of H. dujardini, BLAST v2.2.27+ (Altschul et al. 1997 (link)) and HMMER v3.1b1 (http://hmmer.org/, last accessed September 10, 2014; Eddy 1998 (link)) were used in custom Perl scripts on nine assemblies in total as described by Hering et al. (2012) (link) with the following modifications: For the tBLASTn/BLASTP searches, 16 opsin sequences from all major opsin groups were used as bait sequences with an E value of 1e-5 as a threshold (for accession numbers of all query sequences, see supplementary table S2, Supplementary Material online). For the HMMER search, the same value was used, and the search was performed by applying previously built HMMER profiles (Hering et al. 2012 (link)). In total, 1,634 nonredundant contigs were obtained as putative opsin genes and used as candidates in further analyses. For reciprocal BLAST searches against the nr database of GenBank, 530 nonredundant contigs from a BLASTP search with the E value 1e-10 and a HMMER search with the E value 1e-20 were used and every best hit was stored (101 hits after the removal of redundant sequences). Furthermore, we mined the publicly available genomes of the annelids Capitella teleta and Helobdella robusta, and the mollusks Lottia gigantea (http://genome.jgi.doe.gov/, last accessed September 10, 2014) and Crassostrea gigas (http://gigadb.org/, last accessed September 10, 2014) to enrich our metazoan opsin data set by using BLAST searches. In addition, we screened the genomes of the aphid Acyrthosiphon pisum (http://www.aphidbase.com/, last accessed September 10, 2014) and the water flea Daphnia pulex (http://genome.jgi.doe.gov/, last accessed September 10, 2014) to identify putative orthologs of the new opsin-5 gene (vertebrate opsin-5/neuropsin-like gene) from H. dujardini. All identified putative opsin genes from these genomes were checked for the presence of lysine at the retinal-binding site corresponding to the K296 position of bovine rhodopsin (Palczewski et al. 2000 (link)). Due to the uncertain placement of one of the opsins of the ctenophore Mnemiopsis leidyi (MleiOpsin3; see Schnitzler et al. 2012 (link)) and an unusual insertion downstream of the predicted retinal-binding site corresponding to the K296 position of bovine rhodopsin, it is unclear whether or not MleiOpsin3 is a functional opsin gene. We therefore decided to exclude MleiOpsin3 before our analyses (supplementary fig. S8, Supplementary Material online).
Hering L, & Mayer G. (2014). Analysis of the Opsin Repertoire in the Tardigrade Hypsibius dujardini Provides Insights into the Evolution of Opsin Genes in Panarthropoda. Genome Biology and Evolution, 6(9), 2380-2391.
Publication 2014
Annelida Aphids Binding Sites Cattle Crassostrea gigas Ctenophora Daphnia FCER2 protein, human Genes Genome Lysine Mnemiopsis Mollusca Opsins Pisum Retina Rhodopsin Rod Opsins Transcriptome Vertebrates Water Flea
5
Comprehensive Genome Annotation Pipeline
Cited 5 times
A custom RepeatModeler33 library was built and used to mask repetitive elements in the genome assembly with RepeatMasker34 (Supplementary Material SM 3). Ab initio gene prediction was performed with Augustus35 and SNAP.36 (link) Homology-based prediction was performed with GeneWise based on the alignment of the complete annotated protein coding transcriptomes of five species (Crassostrea gigas, Octopus bimaculoides, Lottia gigantea, Lingula anatina and Drosophila melanogaster) to the Dreissena genome with TBLASTN (e value ≤ 1e-5) to produce accurate spliced alignments. De novo transcriptome assemblies from the four developmental RNA-seq libraries were produced with Binpacker37 using five different kmer values (k23, k25, k27, k29 and k32) which were subsequently merged with Velvet38 (link) and de-duplicated with Dedupe.39 Open reading frames were predicted with Transdecoder40 (link) and these putative protein coding transcripts were mapped back to the genome assembly with GMAP.41 (link) For reference-based transcriptome assembly, the trimmed RNA-seq libraries were mapped against the genome assembly with STAR aligner42 (link) and then assembled with StringTie.43 (link) These assemblies were merged with the StringTie merge function and open reading frames predicted with Transdecoder. The de novo transcriptome assembly, the reference-based transcriptome assembly, the two ab initio gene prediction outputs and the homology-based gene prediction were used as input for EvidenceModeler.44 (link) The resulting set of transcripts were filtered to include those that have homology to either the Pfam, uniref90 (link) or CDD databases or for which there is evidence of expression in one of the 22 developmental RNA-seq databases. Gene models that overlapped with repetitive sequences as assessed by RepeatMasker for at least 50% of their length were also excluded. Final transcriptome ‘completeness’ was assessed with BUSCO.45 (link)
Calcino A.D., de Oliveira A.L., Simakov O., Schwaha T., Zieger E., Wollesen T, & Wanninger A. (2019). The quagga mussel genome and the evolution of freshwater tolerance. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 26(5), 411-422.
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Publication 2019
Crassostrea gigas DNA Library Dreissena Drosophila melanogaster Genes Genome Genome Components Octopus Open Reading Frames Proteins Repetitive Region RNA-Seq Transcriptome

Most recents protocols related to «Crassostrea gigas»

1
Gene prediction and annotation for C. bisecta
Ab initio, homology-based and gene expression evidence were combined to predict protein-coding genes in the genome of C. bisecta. Augustus v3.1 was first employed on repeat-masked genome for ab initio gene prediction [106 (link)]. For the homology-based annotation, gene sets from 10 molluscan species (Archivesica marissinica, Biomphalaria glabrata, Crassostrea gigas, Gigantidas platifrons, Lottia gigantea, Lutraria rhynchaena, Modiolus philippinarum, Octopus bimaculoides, Pinctada fucata, and P. canaliculate) were used. These homologous protein sequences were first aligned onto the genome of C. bisecta using Blast v2.2.26 with an e-value cut-off of 1 × 10−5 [107 (link)], and then we linked the alignment hits to candidate gene loci by GenBlastA [108 (link)]. Secondly, genomic sequences of candidate gene regions together with their 2-kb flanking sequences were extracted and used GeneWise v2.2.0 to determine gene models [109 (link)]. Moreover, Stringtie v 1.3.4 was employed to generated gene annotation files on RNA-Seq alignments generated by HISAT v2.1.0 of different tissues (adductor muscle, mantle, foot, and gill) [110 (link), 111 (link)]. Then these files were merged together to predict candidate coding regions open reading frames (ORFs) using Transdecoder v5.5.0 and were aligned to genomes to obtain a gene annotation file with transcript evidence. Finally, these three evidences were integrated using EVM v1.1.1 to obtain a final version of protein-coding genes [112 (link)], and their function were annotated by searching against the following public databases: Swiss-Prot v201709, KEGG v87.0, InterPro v55.0, and TrEMBL v201709. The other 7 species used in gene family analysis were functionally annotated in the same way.
Guo Y., Meng L., Wang M., Zhong Z., Li D., Zhang Y., Li H., Zhang H., Seim I., Li Y., Jiang A., Ji Q., Su X., Chen J., Fan G., Li C, & Liu S. (2023). Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves. BMC Biology, 21, 51.
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Publication 2023
Amino Acid Sequence Australorbis glabratus Crassostrea gigas FCER2 protein, human Foot Gene Annotation Gene Expression Gene Products, Protein Genes Genes, vif Genome Gills Homologous Sequences Muscle Tissue Octopus Open Reading Frames Pinctada Protein C Proteins RNA-Seq Tissues
2
Lophotrochozoan Phylogenomic Analysis
Twenty-four well-assembled lophotrochozoan genomes were selected for phylogenetic analysis, include one annelid (Helobdella robusta) as outgroup, 21 bivalves (Archivesica marissinica, Argopecten concentricus, Argopecten irradians, Conchocele bisecta, Crassostrea gigas, Crassostrea virginica, Cyclina sinensis, Gigantidas platifrons, Lutraria rhynchaena, Mactra quadrangularis, Mercenaria mercenaria, Mizuhopecten yessoensis, Modiolus philippinarum, Mytilus coruscus, Pecten maximus, Pinctada fucata, Pinctada imbricata, Ruditapes philippinarum, Saccostrea glomerata, Scapharca broughtonii, Sinonovacula constricta), 5 gastropods (Aplysia californica, Chrysomallon squamiferum, Lottia gigantea, Haliotis rufescens, Pomacea canaliculata), and 2 cephalopods (Octopus bimaculoides and Octopus vulgaris) [22 (link), 26 (link), 52 (link), 113 (link)–132 ]. SonicParanoid v1.3.0 was used to define gene family clusters among different species [133 (link)]. The amino acid sequences of one-to-one single-copy orthologous genes were used to reconstruct their phylogenetic topology. The protein sequences were aligned using MAFFT v7.407 under default settings [134 (link)], and then were concatenated for phylogenetic analysis using a maximum-likelihood method implemented in IQ-TREE v 2.0.6 with the “-m MFP” parameter was applied to each protein partition [135 (link)]. To estimate divergence times, the rooted maximum-likelihood tree, along with a concatenated fourfold degenerate site sequence extracted from single-copy CDS (coding sequence), was used as the input of MCMCtree software implemented in PAML v4.8 [136 (link)]. For calibration, nine nodes were constrained by either fossil records obtained from website of TimeTree.
Guo Y., Meng L., Wang M., Zhong Z., Li D., Zhang Y., Li H., Zhang H., Seim I., Li Y., Jiang A., Ji Q., Su X., Chen J., Fan G., Li C, & Liu S. (2023). Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves. BMC Biology, 21, 51.
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Publication 2023
Amino Acid Sequence Aplysia Bivalves Cephalopoda Crassostrea gigas Crassostrea virginica Gastropods Genes Genome Mercenaria Mizuhopecten yessoensis Mytilus Octopus Open Reading Frames Pecten maximus Pinctada Proteins Scapharca Trees
3
Comparative Genomics of Symbiotic Bivalves
For expansion and contraction analysis, in addition to genome of C. bisecta, we selected 7 representatives with good BUSCO performance out of the 15 collected bivalve genomes. The selected genomes include that of the only two published endosymbiotic bivalves (A. marissinica, G. platifrons) [22 (link), 26 (link)], and 5 asymbiotic bivalves (Crassostrea gigas, L. rhynchaena, M. yessoensis, Modiolus philippinarum, P. fucata) which were separated in different bivalve clades and not known to host chemosynthetic bacteria. Before analysis, HMMSCAN (HMMER v3.1) was applied to identify Pfam domains in protein-coding gene sequences among the selected bivalve. The Pfam domains of the respective species were counted to construct a data frame, while multiple copies of a same domain in the same gene were counted as one.
Gene family analyses in the symbiotic bivalves were conducted using one-tailed Fisher’s exact tests for either expansion or contraction. In detail, for gene expansion/contraction at the protein domain level, we first calculated the counts of each Pfam domain in each genome of the 8 analyzed species, and the Pfam domain counts in each of the symbiotic bivalves (A. marissinica, C. bisecta, G. platifrons) was compared against the background average domain counts of the five asymbiotic bivalve genomes (Crassostrea gigas, L. rhynchaena, M. yessoensis, Modiolus philippinarum, P. fucata), which method was employed by Sun et al. for comparative genomic analysis [26 (link)]. Furthermore, we conducted the same analysis with the gene counts of each KEGG ortholog on each of the three symbiotic bivalves. After that, Pfam domain or KEGG ortholog with a P value less than 0.05 is considered statistically expanded or contracted in the three symbiotic bivalves. Finally, the evolutionary patterns of A. marissinica, C. bisecta, and G. platifrons were compared according to the expansion/contraction results by Fisher’s exact tests.
For phylogenetic analysis of each gene family, we employed Muscle v3.8.31 for multiple sequence alignment [137 (link)], and the phylogenetic trees were constructed with FastTreeMP v2.1.10 [138 (link)]. Specially, for reported expansion events of subfamilies of hemoglobin, which were not included in the KEGG database, we performed additional alignment with the sequences mentioned in Ip et al. [22 (link)] using Diamond, and phylogenetic analysis was conducted as the same.
Guo Y., Meng L., Wang M., Zhong Z., Li D., Zhang Y., Li H., Zhang H., Seim I., Li Y., Jiang A., Ji Q., Su X., Chen J., Fan G., Li C, & Liu S. (2023). Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves. BMC Biology, 21, 51.
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Publication 2023
Bacteria Biological Evolution Bivalves Comparative Genomic Hybridization Crassostrea gigas Diamond Endosymbiosis Gene Products, Protein Genes Genome Hemoglobin Muscle Tissue Protein Domain Reading Frames Sequence Alignment Symbiosis
4
Evolutionary Dynamics of ADAR/ADAD Genes
Protein sequences of Nematostella vectensis (GenBank: XP_001642062.2, XP_001629615.2), Drosophila melanogaster (GenBank: NP_569940.2), Caenorhabditis elegans (GenBank: NP_492153.2, NP_498594.1), Crassostrea gigas (GenBank: EKC20855.1, EKC32699.1, XP_011441313.2), Strongylocentrotus purpuratus (GenBank: XP_011680614.1, XP_781832.1, XP_030847369.1), Ciona intestinalis (GenBank: XP_002128212.1), Danio rerio (GenBank: NP_571671.2, NP_571685.2, XP_021334693.1, XP_686426.5, NP_001277142.1, XP_687183.1) and Homo sapiens (GenBank: XP_024305442.1, NP_056648.1, NP_061172.1, NP_640336.1, NP_631913.3) collected from NCBI were used as queries to search for ADAR/ADAD genes in the public reference genome and the de novo transcriptome assemblies (assembled by Trinity92 (link)) of the 22 species by TBLASTN93 (link) with parameters -F F -e 1e-5, followed by the determination of protein sequences in the target species with GeneWise.94 (link) The predicted proteins were then aligned to the NCBI nr database to confirm whether they were ADARs/ADADs. Domain organizations of the manually confirmed ADAR/ADAD proteins were predicted using the CD-Search tool in NCBI (CDD)95 (link) and Pfam96 (link) with default settings.
Phylogenetic analysis of ADARs and ADADs identified above, were performed with the adenosine-deaminase (AD) domains (around 324 amino acids in length; see Table S2 for the sequences) using RAxML97 (link) with the Maximum Likelihood (ML) method (parameter: -m PROTGAMMAIJTT) and using Mrbayes98 (link) with Bayesian Inference (BI) method (parameters: prset aamodelpr = fixed(Wag); lset rates = invgamma; mcmcp ngen = 1000000 nchains = 4 samplefreq = 100 burnin = 200), respectively. The AD peptide sequences used for phylogenetic analysis were aligned using PRANK.99 (link) Reliability of the ML tree was estimated based on 1,000 bootstrap replications. The structures of phylogenetic trees generated by the two methods were generally consistent with each other (Figure S2). The information of ADAR genes annotated in each species, including the coding nucleotide sequences, protein sequences, domain annotations are presented in Table S2.
Zhang P., Zhu Y., Guo Q., Li J., Zhan X., Yu H., Xie N., Tan H., Lundholm N., Garcia-Cuetos L., Martin M.D., Subirats M.A., Su Y.H., Ruiz-Trillo I., Martindale M.Q., Yu J.K., Gilbert M.T., Zhang G, & Li Q. (2023). On the origin and evolution of RNA editing in metazoans. Cell Reports, 42(2), 112112.
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Publication 2023
Amino Acids Amino Acid Sequence Caenorhabditis elegans Ciona intestinalis Crassostrea gigas Deaminase, Adenosine DNA Replication Drosophila melanogaster Genes Genome Homo sapiens Open Reading Frames Peptides Protein Domain Proteins Protein Sequence Determination Strongylocentrotus purpuratus Transcriptome Trees Zebrafish
5
Metazoan RNA Editing Site Identification Protocol
To rule out that false positives resulted from genetic variation during RNA-editing site identification, matching DNA and RNA sequences generated from the same individual/specimen are the ideal data for use in RNA editing studies.41 (link),107 (link) Thus, for the metazoan species with sufficient body mass, both genomic DNA and total RNA were extracted from the same individual, after grinding of the tissue/whole organism in liquid nitrogen. Two to three individuals were collected as biological replicates. These species included the comb jelly Mnemiopsis leidyi (three whole adults), the sponge Amphimedon queenslandica (three biopsies from three adults), the sea anemone Nematostella vectensis (three whole adults), the sea hare Aplysia californica (three whole juveniles), the oyster Crassostrea gigas (three whole adults after removing shells), the sea urchin Strongylocentrotus purpuratus (three pairs of gonad and non-gonad tissues dissected from one female and two male adults; non-gonad tissues comprised the digestive, water vascular, and nervous systems), the acorn worm Ptychodera flava (three whole adults), the lancelet Branchiostoma belcheri (three whole adults), the sea squirt Ciona savignyi (two whole adults) and the zebrafish Danio rerio (three whole adults).
For metazoan species from which a single individual is not sufficient to allow the simultaneous extraction of sufficient DNA and RNA for sequencing library construction, 10-15 individuals with similar genetic background were pooled together, then both genomic DNA and total RNA were extracted from the same pool of organisms after the whole pool was ground in liquid nitrogen. These included the hydra Hydra vulgaris (10 adults per pool, two pools to serve as biological replicates), the fruit fly Drosophila melanogaster (15 male adults per pool, two pools), and Drosophila simulans (15 male adults per pool, two pools).
For the unicellular species and tiny metazoan species, biomass was first increased by the propagation of a single colony with the same genetic background, then both genomic DNA and total RNA were extracted from the same culture of organisms. These included the ichthyosporean Sphaeroforma arctica (three cultures to serve as biological replicates), the filasterean Capsaspora owczarzaki (three cultures), the choanoflagellate Salpingoeca rosetta (three cultures) and Monosiga brevicollis (three cultures), and the metazoan Trichoplax adhaerens (three cultures).
Genomic DNA of all species was extracted with the phenol/chloroform/isopentanol (25:24:1) protocol. The integrity of the DNA samples was assayed by agarose gel electrophoresis (concentration: 1%; voltage: 150 V; Time: 40 min) before DNA-seq library construction. Total RNA of all species except the choanoflagellates was extracted using TRIzol Reagent according to manufacturer’s protocol (Invitrogen, CA, USA). Total RNA of the choanoflagellates S. rosetta and M. brevicollis was extracted using the RNAqueous Kit (Ambion, CA, USA). The quality of the RNA samples was assayed by the Agilent 2100 Bioanalyzer (Thermo Fisher Scientific, MA, USA) before RNA-seq library construction. In summary, a total of 53 DNA and 53 RNA samples were obtained in this study. After quality control before library construction, two out of the three RNA samples of M. brevicollis and one out of the three RNA samples of N. vectensis were discarded due to poor RNA integrity (RIN <6).
Zhang P., Zhu Y., Guo Q., Li J., Zhan X., Yu H., Xie N., Tan H., Lundholm N., Garcia-Cuetos L., Martin M.D., Subirats M.A., Su Y.H., Ruiz-Trillo I., Martindale M.Q., Yu J.K., Gilbert M.T., Zhang G, & Li Q. (2023). On the origin and evolution of RNA editing in metazoans. Cell Reports, 42(2), 112112.
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Publication 2023
Adult Aplysia Biopharmaceuticals Biopsy Blood Vessel Branchiostoma belcheri Chloroform Choanoflagellata Ciona savignyi Crassostrea gigas Ctenophora Digestive System DNA, A-Form DNA Library Drosophila Drosophila melanogaster Drosophila simulans Electrophoresis, Agar Gel Females Genetic Background Genetic Diversity Genome Gonads Hares Helminths Human Body Hydra isopentyl alcohol Klippel-Feil Syndrome Lancelets Males Mnemiopsis Nitrogen Oysters Phenol Porifera RNA-Seq RNA Sequence Sea Anemones Sea Urchin Strongylocentrotus purpuratus Systems, Nervous Tissues Trichoplax trizol Urochordata Zebrafish

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More about "Crassostrea gigas"

Crassostrea gigas, also known as the Pacific oyster or Miyagi oyster, is a bivalve mollusk species that is widely cultivated for food production around the world.
This robust and large-sized oyster is native to the Pacific coast of Asia but has been introduced to many other regions due to its commercial importance.
Research on C. gigas can provide valuable insights into various aspects of aquaculture, ecology, and the biology of bivalve mollusks.
Scientists may utilize techniques such as TOPO TA cloning, DNeasy Blood & Tissue Kit, and RNAlater RNA Stabilization Reagent to study the genetic and molecular characteristics of this species.
The HiSeq X Ten sequencing platform can be employed to generate high-quality genomic data for C. gigas, while transglutaminase, an enzyme found in oysters, may be studied for its potential applications in food processing and biotechnology.
Analytical methods involving acetonitrile, O-phenylenediamine (OPD), and the PET32a(+) vector can also be leveraged to investigate the biochemical properties and physiological functions of this economically important oyster species.
Furthermore, the influence of serotonin, a neurotransmitter, on the behavior and physiology of C. gigas can be explored using tools like the Cell Counting Kit-8 (CCK-8).
Understanding the complex interactions between this oyster species and its environment is crucial for improving aquaculture practices and conservation efforts.
By incorporating these diverse research techniques and perspectives, scientists can uncover novel insights about the Pacific oyster, Crassostrea gigas, and its role in both natural and cultivated ecosystems.
This knowledge can ultimately lead to advancements in sustainable seafood production and the preservation of marine biodiversity.