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Article ; Online: Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge

Arredondo-Espinoza, Roberto / Ibarra, Ana M. / Roberts, Steven / Sicard-González, Maria Teresa / Escobedo-Fregoso, Cristina

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics. 2023 May 26, p.101089-

2023 , Page(s) 101089–

Abstract: Since the introduction of the Pacific oyster Crassostrea gigas in Baja California Sur, Mexico, its culture has faced environmental challenges, specifically increasing temperatures that result in high mortalities. The inter-tidal zone seawater temperature ...

Abstract	Since the introduction of the Pacific oyster Crassostrea gigas in Baja California Sur, Mexico, its culture has faced environmental challenges, specifically increasing temperatures that result in high mortalities. The inter-tidal zone seawater temperature during a year at the Baja California Peninsula broadly ranges from 7 °C to 39 °C. Therefore, to understand how oysters respond to heat stress during daily temperature oscillations, heat-resistant (RR, father, and mother resistant) and heat-susceptible (SS, both parents susceptible) phenotypes families from a C. gigas breeding program were exposed to a thermal challenge. Based on a laboratory-simulated daily oscillatory thermal challenge (26 to 34 °C) for 30 days, RR phenotype presented differences compared to SS phenotype since the beginning (day 0) of the thermal challenge. Gene expression analyses revealed 1822 differentially expressed up-regulated transcripts in RR, related to functions of metabolic processes, biological regulation, and response to stimulus and signaling. At the end of the experiment (day 30), 2660 differentially expressed up-regulated transcripts were identified in RR. Functional analysis of the genes expressed indicates responses of regulation of biological processes and response to a stimulus. Additionally, 340 genes were differentially expressed among RR vs. SS from the beginning to the end of the thermal challenge, where 170 genes were up-regulated, and 170 were down-regulated. These transcriptomic profiles represent the first report to identify gene expression markers associated with RR phenotypes for the Pacific oyster to the future broodstock selection.
Keywords	Crassostrea gigas ; biochemistry ; breeding stock ; gene expression ; genomics ; heat ; heat stress ; phenotype ; proteomics ; seawater ; temperature ; transcriptome ; transcriptomics ; Mexico ; Transcriptomic ; Oscillatory-heat-challenge ; Heat-resistant-phenotype ; Heat-susceptible-phenotype ; Gene markers
Language	English
Dates of publication	2023-0526
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	2212119-5
ISSN	1878-0407 ; 1744-117X
ISSN (online)	1878-0407
ISSN	1744-117X
DOI	10.1016/j.cbd.2023.101089
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge.

Arredondo-Espinoza, Roberto / Ibarra, Ana M / Roberts, Steven B / Sicard-González, Maria Teresa / Escobedo-Fregoso, Cristina

Comparative biochemistry and physiology. Part D, Genomics & proteomics

2023 Volume 47, Page(s) 101089

Abstract	Since the introduction of the Pacific oyster Crassostrea gigas in Baja California Sur, Mexico, its culture has faced environmental challenges, specifically increasing temperatures that result in high mortalities. The inter-tidal zone seawater temperature during a year at the Baja California Peninsula broadly ranges from 7 °C to 39 °C. Therefore, to understand how oysters respond to heat stress during daily temperature oscillations, heat-resistant (RR, father, and mother resistant) and heat-susceptible (SS, both parents susceptible) phenotypes families from a C. gigas breeding program were exposed to a thermal challenge. Based on a laboratory-simulated daily oscillatory thermal challenge (26 to 34 °C) for 30 days, RR phenotype presented differences compared to SS phenotype since the beginning (day 0) of the thermal challenge. Gene expression analyses revealed 1822 differentially expressed up-regulated transcripts in RR, related to functions of metabolic processes, biological regulation, and response to stimulus and signaling. At the end of the experiment (day 30), 2660 differentially expressed up-regulated transcripts were identified in RR. Functional analysis of the genes expressed indicates responses of regulation of biological processes and response to a stimulus. Additionally, 340 genes were differentially expressed among RR vs. SS from the beginning to the end of the thermal challenge, where 170 genes were up-regulated, and 170 were down-regulated. These transcriptomic profiles represent the first report to identify gene expression markers associated with RR phenotypes for the Pacific oyster to the future broodstock selection.
MeSH term(s)	Animals ; Transcriptome ; Crassostrea/metabolism ; Mexico ; Gene Expression Profiling ; Heat-Shock Response/genetics
Language	English
Publishing date	2023-05-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2212119-5
ISSN	1878-0407 ; 1744-117X
ISSN (online)	1878-0407
ISSN	1744-117X
DOI	10.1016/j.cbd.2023.101089
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Article: Development of SNP markers for identification of thermo-resistant families of the Pacific oyster Crassostrea gigas based on RNA-seq

Juárez, Oscar E / Escobedo-Fregoso, Cristina / Arredondo-Espinoza, Roberto / Ibarra, Ana M

Aquaculture. 2021 June 30, v. 539

2021

Abstract: The Pacific oyster Crassostrea gigas is the most cultivated oyster species around the world. However, massive mortalities linked to high temperatures have been reported in different countries, becoming one of the most significant challenges for oyster ... ...

Abstract	The Pacific oyster Crassostrea gigas is the most cultivated oyster species around the world. However, massive mortalities linked to high temperatures have been reported in different countries, becoming one of the most significant challenges for oyster culture. High mortality episodes have been reported also in Mexico due to temperature stress, mainly in Sonora and Baja California Sur. In this region, areas with shallow waters can reach 34 °C, causing severe physiological stress, mostly in juvenile oysters. Recently and as a strategy to address this problem in Mexico, a selective breeding program has been implemented, aiming to develop families with high survival at high temperatures through marker-aided selection. The objective of the present study was the identification of SNP markers from the transcriptome of families phenotypically different: thermo-resistant (‘R’) versus thermo-susceptible (‘S’) and analyzing whether these variants were present in transcripts potentially involved in thermal resistance. Several SNP variants were detected between ‘R’ and ‘S’ families, affecting multiple transcripts and molecular pathways. Four SNP markers provided accurate differentiation between ‘R’ and ‘S’ oysters. Additionally, 66 SNPs were suitable for pedigree reconstruction and sibling clustering. The discriminant SNPs were associated with changes in gene transcripts that were related to biological processes such as the activation of HSP90, zinc uptake, collagen biosynthesis, ion transport, and the immune response. The use of SNPs markers associated with thermo-resistant families can help to improve the yields in oyster production at high temperatures, especially in Mexico.
Keywords	Crassostrea gigas ; biosynthesis ; collagen ; genes ; heat tolerance ; immune response ; juveniles ; marker-assisted selection ; mortality ; oyster culture ; oysters ; pedigree ; sequence analysis ; temperature ; transcriptome ; zinc ; Mexico
Language	English
Dates of publication	2021-0630
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	185380-6
ISSN	0044-8486 ; 0044-8516
ISSN	0044-8486 ; 0044-8516
DOI	10.1016/j.aquaculture.2021.736618
Database	NAL-Catalogue (AGRICOLA)

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Article: Triploid-induced complete sterility in the scallop Nodipecten subnodosus might be triggered by an early and sustained DNA damage response

Galindo-Torres, Pavel / Abreu-Goodger, Cei / Llera-Herrera, Raul / Escobedo-Fregoso, Cristina / García-Gasca, Alejandra / Ibarra, Ana M.

Aquaculture. 2022 Oct. 15, v. 559

2022

Abstract: Triploid Nodipecten subnodosus scallops, unlike other mollusks, are completely sterile. In this study we focused on understanding the underlying molecular changes of triploid sterility using a transcriptomic approach. Total RNA from the gonad of diploid ... ...

Abstract	Triploid Nodipecten subnodosus scallops, unlike other mollusks, are completely sterile. In this study we focused on understanding the underlying molecular changes of triploid sterility using a transcriptomic approach. Total RNA from the gonad of diploid scallops in inactive and initial gametogenic stages and triploid scallops of the same cohort and ages were sequenced employing Illumina RNA-Seq. From 68,244 assembled and annotated transcripts, 1120 had terms associated with meiosis checkpoint or arrest, DNA damage response, or recombination. Differential gene expression analyses were conducted by contrasting initial vs. inactive stages of gametogenesis in each ploidy. In diploids, genes participating in homologous recombination during meiosis (msh5 and kdm8), spindle organization (nup62), centrosome formation (cenp-T), and sex differentiation (Ns-dmta2 and pum3), were up-regulated during initial gametogenesis. In triploids, a different set of genes were up-regulated during initial gametogenesis, and included genes involved in the DNA damage response and double strand break repair (rad51-C, xpc, myoVI), in the transition of metaphase/anaphase of mitosis (slp1 and nuf2), as well as genes that trigger both the intrinsic and extrinsic (caspase-3, icad, bmcc1) and extrinsic apoptosis pathways only (tnfr1, dab2ip). The results suggest significant DNA damage in triploids initial gametogenesis, possibly as a consequence of failing to repair double-strand breaks during DNA replication. This coincides with previous observations in which few triploid scallops showed gametic stages more advanced than oogonia or spermatogonia, and when present they were few.
Keywords	DNA damage ; DNA repair ; DNA replication ; Nodipecten subnodosus ; anaphase ; apoptosis ; aquaculture ; caspase-3 ; centrosomes ; diploidy ; gametogenesis ; gene expression regulation ; homologous recombination ; meiosis ; metaphase ; mitosis ; oogonia ; scallops ; sequence analysis ; sexual development ; spermatogonia ; transcriptomics ; triploidy
Language	English
Dates of publication	2022-1015
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	185380-6
ISSN	0044-8486 ; 0044-8516
ISSN	0044-8486 ; 0044-8516
DOI	10.1016/j.aquaculture.2022.738422
Database	NAL-Catalogue (AGRICOLA)

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Article: Effects of the Tetraploid Condition on Gamete Size and on Testis Versus Ovary Allocation in the True Functional Hermaphroditic Scallop Argopecten ventricosus (Sowerby II, 1842)

Ibarra, Ana M / José L. Ramírez / Rosalío Maldonado

Journal of shellfish research. 2017 Dec., v. 36, no. 3

2017

Abstract: The Catarina scallop Argopecten ventricosus is a true functional hermaphrodite, in which male and female gamete cells develop synchronously in one gonad organ spatially divided into a testis and an ovary. Tetraploid Catarina scallops were produced and ... ...

Abstract	The Catarina scallop Argopecten ventricosus is a true functional hermaphrodite, in which male and female gamete cells develop synchronously in one gonad organ spatially divided into a testis and an ovary. Tetraploid Catarina scallops were produced and macroscopic observations showed a significant reduction in the total area allocated to the testis of this functional hermaphrodite when compared with diploids. Further micro and ultrastructure analyses indicated that gamete cells are larger in tetraploids than diploids and that the clear separation between sexual gonadal areas usually observed in diploids was partially lost in tetraploids, with some male acini projecting into the ovary area adjacent to the testis area. The reduced testis area was present in two generations of tetraploids mated between them, indicating its inheritance. A genetic mechanism of sex determination similar to that observed in the nematode Caenorhabditis elegans is proposed to explain the reduced testis area in tetraploid scallops and the rare occurrence of “only males” or “only females” in this and other true hermaphroditic scallops.
Keywords	animal ovaries ; Argopecten ventricosus ; Caenorhabditis elegans ; diploidy ; females ; hermaphroditism ; males ; scallops ; sex determination ; testes ; tetraploidy ; ultrastructure
Language	English
Dates of publication	2017-12
Size	p. 641-648.
Publishing place	National Shellfisheries Association
Document type	Article
ZDB-ID	22976-3
ISSN	0730-8000 ; 0077-5711
ISSN	0730-8000 ; 0077-5711
DOI	10.2983/035.036.0313
Database	NAL-Catalogue (AGRICOLA)

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Article: A natural antisense transcript of the fem-1 gene was found expressed in female gonads during the characterization, expression profile, and cellular localization of the fem-1 gene in Pacific white shrimp Penaeus vannamei

Galindo-Torres, Pavel / Ventura-López, Claudia / Llera-Herrera, Raúl / Ibarra, Ana M

Gene. 2019 July 20, v. 706

2019

Abstract: The fem-1 gene in Caenorhabditis elegans is involved in sex differentiation; it is specifically required for all aspects of male development. In this study, the full-length cDNA of the fem-1 (Pvfem-1) gene was isolated from the Pacific whiteleg shrimp ... ...

Abstract	The fem-1 gene in Caenorhabditis elegans is involved in sex differentiation; it is specifically required for all aspects of male development. In this study, the full-length cDNA of the fem-1 (Pvfem-1) gene was isolated from the Pacific whiteleg shrimp Penaeus vannamei. The Pvfem-1 transcript is 3778 nt long and encodes a putative protein (PvFEM-1) of 638 amino acids that presented eight ankyrin repeats. The translated protein showed a significant (P < 0.05) structural similitude by superposition with C. elegans FEM-1 protein. Pvfem-1 expression was evaluated by qPCR and in situ hybridization (ISH) during embryogenesis, larval development, and gonads of both genders in subadult and adult life stages. Pvfem-1 was found expressed in brain, intestine, hepatopancreas, and in the gonads of both genders in subadults and adults when quantified by RT-qPCR. A significant finding was the discovery of a natural antisense transcript (NAT) of Pvfem-1 by ISH. It was present in the oocyte nucleus of subadult female shrimp gonads but was not seen within oocytes from adult females, although it was detected in follicular cells, suggesting a possible post-transcriptional regulation of Pvfem-1 in female gonad. Conversely, in males, no NAT was observed, and Pvfem-1 was found expressed in spermatogonia of both, subadult and adult shrimps indicating a function in male sexual differentiation and gametes generation. This study represents the first step for future functional analysis that is expected to contribute to clarifying the role of Pvfem-1 in sex differentiation and determination.
Keywords	Caenorhabditis elegans ; Litopenaeus vannamei ; adults ; amino acids ; brain ; complementary DNA ; embryogenesis ; females ; genes ; gonads ; hepatopancreas ; in situ hybridization ; intestines ; larval development ; males ; messenger RNA ; oocytes ; quantitative polymerase chain reaction ; reverse transcriptase polymerase chain reaction ; sexual development ; shrimp ; spermatogonia
Language	English
Dates of publication	2019-0720
Size	p. 19-31.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2019.04.066
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A natural antisense transcript of the fem-1 gene was found expressed in female gonads during the characterization, expression profile, and cellular localization of the fem-1 gene in Pacific white shrimp Penaeus vannamei.

Galindo-Torres, Pavel / Ventura-López, Claudia / Llera-Herrera, Raúl / Ibarra, Ana M

Gene

2019 Volume 706, Page(s) 19–31

Abstract	The fem-1 gene in Caenorhabditis elegans is involved in sex differentiation; it is specifically required for all aspects of male development. In this study, the full-length cDNA of the fem-1 (Pvfem-1) gene was isolated from the Pacific whiteleg shrimp Penaeus vannamei. The Pvfem-1 transcript is 3778 nt long and encodes a putative protein (PvFEM-1) of 638 amino acids that presented eight ankyrin repeats. The translated protein showed a significant (P < 0.05) structural similitude by superposition with C. elegans FEM-1 protein. Pvfem-1 expression was evaluated by qPCR and in situ hybridization (ISH) during embryogenesis, larval development, and gonads of both genders in subadult and adult life stages. Pvfem-1 was found expressed in brain, intestine, hepatopancreas, and in the gonads of both genders in subadults and adults when quantified by RT-qPCR. A significant finding was the discovery of a natural antisense transcript (NAT) of Pvfem-1 by ISH. It was present in the oocyte nucleus of subadult female shrimp gonads but was not seen within oocytes from adult females, although it was detected in follicular cells, suggesting a possible post-transcriptional regulation of Pvfem-1 in female gonad. Conversely, in males, no NAT was observed, and Pvfem-1 was found expressed in spermatogonia of both, subadult and adult shrimps indicating a function in male sexual differentiation and gametes generation. This study represents the first step for future functional analysis that is expected to contribute to clarifying the role of Pvfem-1 in sex differentiation and determination.
MeSH term(s)	Amino Acid Sequence ; Animals ; Antisense Elements (Genetics)/genetics ; Antisense Elements (Genetics)/physiology ; Caenorhabditis elegans Proteins/genetics ; Cell Cycle Proteins/genetics ; DNA, Complementary/metabolism ; Female ; Gene Expression Regulation/genetics ; Gonads/metabolism ; In Situ Hybridization ; Male ; Ovary/metabolism ; Penaeidae/genetics ; Phylogeny ; RNA, Messenger/genetics ; Sequence Alignment ; Sequence Analysis, DNA/methods ; Sex Determination Processes/genetics ; Sex Factors
Chemical Substances	Antisense Elements (Genetics) ; Caenorhabditis elegans Proteins ; Cell Cycle Proteins ; DNA, Complementary ; FEM-1 protein, C elegans ; RNA, Messenger
Language	English
Publishing date	2019-04-24
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2019.04.066
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Article ; Online: Chromosomal and molecular characterization of 5S rRNA genes in the North American abalones Haliotis rufescens Swainson (red abalone) and H. fulgens Philippi (blue abalone).

Hernández-Ibarra, Norma K / Morelos, Rosa M / Ramírez, José L / Cruz, Pedro / Leitch, Andrew R / Ibarra, Ana M

Gene

2019 Volume 695, Page(s) 65–74

Abstract: Abalone is an extremely valuable food source derived from cultured and wild animals, the later from populations under intense fishing exploitation and of high conservation value. As part of a long-term study to characterize genes from abalone that can be ...

Abstract	Abalone is an extremely valuable food source derived from cultured and wild animals, the later from populations under intense fishing exploitation and of high conservation value. As part of a long-term study to characterize genes from abalone that can be used as markers for hybrids certification, we characterised 5S ribosomal DNA (5S rDNA) in red abalone (Haliotis rufescens) and blue abalone (H. fulgens). The 5S rDNA arrays occur to a single pair of metacentric chromosomes at interstitial positions in both species. Two types of 5S genes were found, named types I and II, each associated with different non-transcribed spacer (NTS) sequences. The structure of the 5S rRNA genes and the NTS indicate incomplete homogenisation of the 5S rDNA arrays. The divergence of the 5S genes between species provide polymorphisms which can be used to distinguish red from blue abalone in forensic analysis of commercial production.
MeSH term(s)	Animals ; Chromosomes/genetics ; Evolution, Molecular ; Gastropoda/genetics ; Genes, rRNA ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 5S/genetics
Chemical Substances	RNA, Ribosomal, 5S
Language	English
Publishing date	2019-02-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2019.02.003
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Article: Performance of Diploid and Triploid Crassostrea gigas (Thunberg, 1793) Grown in Tropical Versus Temperate Natural Environmental Conditions

Ibarra, Ana M / Carmen Rodríguez-Jaramillo / José L. Ramírez / Marlenne Manzano-Sarabia / Roberto Ascencio-Michel

Journal of shellfish research. 2017 Apr., v. 36, no. 1

2017

Abstract: This work was undertaken to assess the effects that different environmental conditions of tropical and temperate aquaculture sites have on growth, survival, and reproduction of diploid and triploid Pacific oyster Crassostrea gigas. Diploid and triploid ... ...

Abstract	This work was undertaken to assess the effects that different environmental conditions of tropical and temperate aquaculture sites have on growth, survival, and reproduction of diploid and triploid Pacific oyster Crassostrea gigas. Diploid and triploid oysters were evaluated with the purpose of determining if the triploid condition results in any advantage on growth and survival that can be exploited for aquaculture of this species in tropical environments. The evaluations were performed by comparing three sites: two tropical sites in the Gulf of California and one temperate site in the Pacific Coast of the Baja California Peninsula, Mexico. When comparing tropical versus temperate sites, C. gigas growth and survival were less at the tropical sites regardless of ploidy. This can be attributed to environmental conditions, that is, high temperatures causing low productivity, in addition to an earlier-onset and sustained reproductive condition in the tropical sites when compared with the temperate site regardless of ploidy. Analyses of gonad maturation stages and number of oocytes among triploids indicated that a larger reproductive effort occurs at the tropical sites than at the temperate site. Regardless of the lower performance of both ploidy groups in the tropical environmental conditions, triploids grew significantly better than diploids in both tropical sites, and survival was the same for both ploidy groups. This contrasts with the marginal differences observed in growth between ploidies at the temperate site, where triploids showed lower survival than diploids. Possible causes for the lower triploid survival at this site are discussed.
Keywords	aquaculture ; coasts ; Crassostrea gigas ; diploidy ; environmental factors ; oocytes ; oysters ; reproduction ; temperature ; triploidy ; Gulf of California ; Mexico
Language	English
Dates of publication	2017-04
Size	p. 119-139.
Publishing place	National Shellfisheries Association
Document type	Article
ZDB-ID	22976-3
ISSN	0730-8000 ; 0077-5711
ISSN	0730-8000 ; 0077-5711
DOI	10.2983/035.036.0113
Database	NAL-Catalogue (AGRICOLA)

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Article: Genotype by environment interaction for adult body weights of shrimp Penaeus vannamei when grown at low and high densities.

Ibarra, Ana M / Famula, R

Genetics, selection, evolution : GSE

2008 Volume 40, Issue 5, Page(s) 541–551

Abstract: Shrimp is one of few marine species cultured worldwide for which several selective breeding programs are being conducted. One environmental factor that can affect the response to selection in breeding programs is the density at which the shrimp are ... ...

Abstract	Shrimp is one of few marine species cultured worldwide for which several selective breeding programs are being conducted. One environmental factor that can affect the response to selection in breeding programs is the density at which the shrimp are cultured (low-medium-high). Phenotypic plasticity in the growth response to different densities might be accompanied by a significant genotype by environment interaction, evidenced by a change in heritabilities between environments and by a genetic correlation less than one for a unique trait between environments. Our goal was to understand whether different growth densities affect estimates of those genetic parameters for adult body weight (BW) in the Pacific white shrimp (Penaeus vannamei). BW heritabilities were significantly different between environments, with the largest at high density. These differences resulted from both an increased additive genetic variance and a decreased environmental variance when grown at high density. The genetic correlation between BWs at the two environmental conditions was significantly less than one. Whereas these results might be suggestive for carrying out shrimp selective breeding for BW under high density conditions, further understanding of genetic correlations between growth and reproductive traits within a given environment is necessary, as there are indications of reduced reproductive fitness for shrimp grown at high densities.
MeSH term(s)	Animals ; Body Weight/genetics ; Crowding ; Environment ; Female ; Genotype ; Male ; Penaeidae/genetics ; Penaeidae/growth & development ; Penaeidae/physiology ; Population Density ; Quantitative Trait, Heritable
Language	English
Publishing date	2008-08-12
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1005838-2
ISSN	0999-193X
ISSN	0999-193X
DOI	10.1051/gse:2008020
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