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Amaral DT, Bombonato JR, da Silva Andrade SC, Moraes EM, Franco FF. The genome of a thorny species: comparative genomic analysis among South and North American Cactaceae. Planta 2021; 254:44. [PMID: 34357508 DOI: 10.1007/s00425-021-03690-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
The first South American cactus nuclear genome assembly associated with comparative genomic analyses provides insights into nuclear and plastid genomic features, such as size, transposable elements, and metabolic processes related to cactus development. Here, we assembled the partial genome, plastome, and transcriptome of Cereus fernambucensis (Cereeae, Cactaceae), a representative species of the South American core Cactoideae. We accessed other genomes and transcriptomes available for cactus species to compare the heterozygosity level, genome size, transposable elements, orthologous genes, and plastome structure. These estimates were obtained from the literature or using the same pipeline adopted for C. fermabucensis. In addition to the C. fernambucensis plastome, we also performed de novo plastome assembly of Pachycereus pringlei, Stenocereus thurberi, and Pereskia humboldtii based on the sequences available in public databases. We estimated a genome size of ~ 1.58 Gb for C. fernambucensis, the largest genome among the compared species. The genome heterozygosity was 0.88% in C. fernambucensis but ranged from 0.36 (Carnegiea gigantea) to 17.4% (Lophocereus schottii) in the other taxa. The genome lengths of the studied cacti are constituted by a high amount of transposable elements, ranging from ~ 57 to ~ 67%. Putative satellite DNAs are present in all species, excepting C. gigantea. The plastome of C. fernambucensis was ~ 104 kb, showing events of translocation, inversion, and gene loss. We observed a low number of shared unique orthologs, which may suggest gene duplication events and the simultaneous expression of paralogous genes. We recovered 37 genes that have undergone positive selection along the Cereus branch that are associated with different metabolic processes, such as improving photosynthesis during drought stress and nutrient absorption, which may be related to the adaptation to xeric areas of the Neotropics.
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Affiliation(s)
- Danilo Trabuco Amaral
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
- Graduate Program in Comparative Biology, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Juliana Rodrigues Bombonato
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
- Graduate Program in Comparative Biology, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Sónia Cristina da Silva Andrade
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Evandro Marsola Moraes
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
| | - Fernando Faria Franco
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil.
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Alves FRR, Lira BS, Pikart FC, Monteiro SS, Furlan CM, Purgatto E, Pascoal GB, Andrade SCDS, Demarco D, Rossi M, Freschi L. Beyond the limits of photoperception: constitutively active PHYTOCHROME B2 overexpression as a means of improving fruit nutritional quality in tomato. Plant Biotechnol J 2020; 18:2027-2041. [PMID: 32068963 PMCID: PMC7540714 DOI: 10.1111/pbi.13362] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/28/2020] [Accepted: 02/10/2020] [Indexed: 05/30/2023]
Abstract
Photoreceptor engineering has recently emerged as a means for improving agronomically beneficial traits in crop species. Despite the central role played by the red/far-red photoreceptor phytochromes (PHYs) in controlling fruit physiology, the applicability of PHY engineering for increasing fleshy fruit nutritional content remains poorly exploited. In this study, we demonstrated that the fruit-specific overexpression of a constitutively active GAF domain Tyr252 -to-His PHYB2 mutant version (PHYB2Y252H ) significantly enhances the accumulation of multiple health-promoting antioxidants in tomato fruits, without negative collateral consequences on vegetative development. Compared with the native PHYB2 overexpression, PHYB2Y252H -overexpressing lines exhibited more extensive increments in transcript abundance of genes associated with fruit plastid development, chlorophyll biosynthesis and metabolic pathways responsible for the accumulation of antioxidant compounds. Accordingly, PHYB2Y252H -overexpressing fruits developed more chloroplasts containing voluminous grana at the green stage and overaccumulated carotenoids, tocopherols, flavonoids and ascorbate in ripe fruits compared with both wild-type and PHYB2-overexpressing lines. The impacts of PHYB2 or PHYB2Y252H overexpression on fruit primary metabolism were limited to a slight promotion in lipid biosynthesis and reduction in sugar accumulation. Altogether, these findings indicate that mutation-based adjustments in PHY properties represent a valuable photobiotechnological tool for tomato biofortification, highlighting the potential of photoreceptor engineering for improving quality traits in fleshy fruits.
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Affiliation(s)
- Frederico Rocha Rodrigues Alves
- Departamento de BotânicaUniversidade de São PauloSão PauloSPBrazil
- Departamento de BotânicaUniversidade Federal de GoiásGoiásGOBrazil
| | | | | | | | | | - Eduardo Purgatto
- Departamento de Alimentos e Nutrição ExperimentalUniversidade de São PauloSão PauloSPBrazil
| | - Grazieli Benedetti Pascoal
- Departamento de Alimentos e Nutrição ExperimentalUniversidade de São PauloSão PauloSPBrazil
- Curso de Graduação em NutriçãoUniversidade Federal de UberlândiaMinas GeraisMGBrazil
| | | | - Diego Demarco
- Departamento de BotânicaUniversidade de São PauloSão PauloSPBrazil
| | - Magdalena Rossi
- Departamento de BotânicaUniversidade de São PauloSão PauloSPBrazil
| | - Luciano Freschi
- Departamento de BotânicaUniversidade de São PauloSão PauloSPBrazil
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Rocha CC, da Silva Andrade SC, de Melo GD, Motta IG, Coutinho LL, Gonella-Diaza AM, Binelli M, Pugliesi G. Early pregnancy-induced transcripts in peripheral blood immune cells in Bos indicus heifers. Sci Rep 2020; 10:13733. [PMID: 32792605 PMCID: PMC7426272 DOI: 10.1038/s41598-020-70616-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/08/2020] [Indexed: 01/05/2023] Open
Abstract
Immune cells play a central role in early pregnancy establishment in cattle. We aimed to: (1) discover novel early-pregnancy-induced genes in peripheral blood mononuclear cells (PBMC); and (2) characterize the temporal pattern of early-pregnancy-induced transcription of select genes in PBMC and peripheral blood polymorphonuclear cells (PMN). Beef heifers were artificially inseminated on D0 and pregnancies were diagnosed on D28. On D10, 14, 16, 18, and 20, blood was collected for isolation of PBMC and PMN from heifers that were retrospectively classified as pregnant (P) or non-pregnant (NP). PBMC samples from D18 were submitted to RNAseq and 220 genes were differentially expressed between pregnant (P) and non-pregnant (NP) heifers. The temporal abundance of 20 transcripts was compared between P and NP, both in PBMC and PMN. In PBMC, pregnancy stimulated transcription of IFI6, RSAD2, IFI44, IFITM2, CLEC3B, OAS2, TNFSF13B, DMKN and LGALS3BP as early as D18. Expression of IFI44, RSAD2, OAS2, LGALS3BP, IFI6 and C1R in PMN was stimulated in the P group from D18. The novel early-pregnancy induced genes discovered in beef heifers will allow both the understanding of the role of immune cells during the pre-attachment period and the development of technologies to detect early pregnancies in beef cattle.
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Affiliation(s)
- Cecilia Constantino Rocha
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Gabriela Dalmaso de Melo
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Igor Garcia Motta
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Laboratory of Animal Biotechnology, School of Agriculture Luiz de Queiroz, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Angela Maria Gonella-Diaza
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Marianna, FL, USA
| | - Mario Binelli
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Guilherme Pugliesi
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil.
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Mercier H, Rodrigues MA, Andrade SCDS, Coutinho LL, Gobara BNK, Matiz A, Mioto PT, Gonçalves AZ. Transcriptional foliar profile of the C3-CAM bromeliad Guzmania monostachia. PLoS One 2019; 14:e0224429. [PMID: 31661510 PMCID: PMC6818958 DOI: 10.1371/journal.pone.0224429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 10/14/2019] [Indexed: 11/19/2022] Open
Abstract
Guzmania monostachia is an epiphytic tank bromeliad that displays the inducible CAM photosynthesis under stressful conditions and had the highest stomata density in the leaf apex, while the base portion has the highest density of trichomes, which are specialized structures used to acquire water and nutrients from the tank solution. In order to correlate the genetic factors behind these morpho-physiological characteristics along the leaf blade of G. monostachia, a comparative transcriptome analysis was performed to identify the functional enriched pathways and unigenes that could play a role in the apical, middle and basal leaf portions. A total of 653 million reads were used for de novo transcriptome assembly, resulting in 48,051 annotated unigenes. Analysis of differentially expressed genes (DEGs) among distinct leaf regions revealed that 806 DEGs were upregulated in the apex compared to the middle portion, while 9685 DEGs were upregulated in the apex and 9784 DEGs were upregulated in the middle portions compared to the base. Our outcomes correlated some DEGs and identified unigenes with their physiological functions, mainly suggesting that the leaf apex was related to the regulation of stomatal movement, production of chlorophyll, cellular response to stress, and H2O2 catabolic process. In contrast, the middle portion showed DEGs associated with the transport of amino acids. Furthermore, DEGs from the leaf base were mainly correlated with responses to nutrients and nitrogen compounds, regulation of potassium ion import, response to water deprivation, and trichome branching, indicating that, at least in part, this leaf portion can replace some of the root functions of terrestrial plants. Therefore, possibly candidate unigenes and enriched pathways presented here could be prospected in future experimental work, opening new possibilities to bioengineer non-inducible CAM plants and/or improve the fertilization use efficiency by increasing leaf nutrient acquisition of crop plants.
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Affiliation(s)
- Helenice Mercier
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Luiz Lehmann Coutinho
- Departamento de Zootecnia, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, São Paulo, Brazil
| | | | - Alejandra Matiz
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Paulo Tamaso Mioto
- Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Santa Catarina, Brazil
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Silva DAD, Tsai SM, Chiorato AF, da Silva Andrade SC, Esteves JADF, Recchia GH, Morais Carbonell SA. Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use. PLoS One 2019; 14:e0210428. [PMID: 30657755 PMCID: PMC6338380 DOI: 10.1371/journal.pone.0210428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/21/2018] [Indexed: 12/05/2022] Open
Abstract
Common bean is a highly important food in tropical regions, where most production occurs on small farms with limited use of technology and, consequently, greater vulnerability to abiotic stresses such as nutritional stress. Usually phosphorus (P) is the most limiting nutrient for crop growth in these regions. The aim of this study was to characterize the gene expression profiles of the genotypes of common bean IAC Imperador (P-responsive) and DOR 364 (P-unresponsive) under different P concentrations using RNA-seq transcriptome sequencing technology. Plants were grown hydroponically, with application of two P concentrations (4.00 mg L-1 restrictive level and 8.00 mg L-1 control level). Differential expression analyses, annotation, and functional classification were performed comparing genotypes within each P rate administered and comparing each genotype response to the different P levels. Considering differential expression analyses within genotypes, IAC Imperador exhibited 1538 up-regulated genes under P restriction and 1679 up-regulated genes in the control, while DOR 364 exhibited 13 up-regulated genes in the control and only 2 up-regulated genes under P restriction, strongly corroborating P-unresponsiveness of this genotype. Genes related to phosphorus restriction were identified among the differentially expressed genes, including transcription factors such as WRKY, ERF, and MYB families, phosphatase related genes such as pyrophosphatase, acid phosphatase, and purple acid phosphatase, and phosphate transporters. The enrichment test for the P restriction treatment showed 123 enriched gene ontologies (GO) for IAC Imperador, while DOR 364 enriched only 24. Also, the enriched GO correlated with P metabolism, compound metabolic processes containing phosphate, nucleoside phosphate binding, phosphorylation, and also response to stresses. Thus, this study proved to be informative to phosphorus limitation in common bean showing global changes at transcript level.
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Affiliation(s)
- Daiana Alves da Silva
- Instituto Agronômico (IAC)-Centro de Grãos e Fibras-Fazenda Santa Elis, Campinas, SP, Brazil
| | - Siu Mui Tsai
- Centro de Energia Nuclear na Agricultura (CENA)-Av. Centenário, São Dimas-CEP-Piracicaba, SP, Brazil
| | | | - Sónia Cristina da Silva Andrade
- Universidade de São Paulo (USP)-Departamento de Genética e Biologia Evolutiva-Instituto de Biociências-Rua do Matão, Cidade Universitária-Cep-São Paulo, SP, Brazil
| | | | - Gustavo Henrique Recchia
- Centro de Energia Nuclear na Agricultura (CENA)-Av. Centenário, São Dimas-CEP-Piracicaba, SP, Brazil
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Gonçalves TM, de Almeida Regitano LC, Koltes JE, Cesar ASM, da Silva Andrade SC, Mourão GB, Gasparin G, Moreira GCM, Fritz-Waters E, Reecy JM, Coutinho LL. Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle. Front Genet 2018; 9:441. [PMID: 30344530 PMCID: PMC6182065 DOI: 10.3389/fgene.2018.00441] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/14/2018] [Indexed: 12/13/2022] Open
Abstract
Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer’s palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle.
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Affiliation(s)
| | | | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | | | - Sónia Cristina da Silva Andrade
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil.,Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | | | - Gustavo Gasparin
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | | | - Elyn Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
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Sá Filho MFD, Gonella-Diaza AM, Sponchiado M, Mendanha MF, Pugliesi G, Ramos RDS, Andrade SCDS, Gasparin G, Coutinho LL, Goissis MD, Mesquita FS, Baruselli PS, Binelli M. Impact of hormonal modulation at proestrus on ovarian responses and uterine gene expression of suckled anestrous beef cows. J Anim Sci Biotechnol 2017; 8:79. [PMID: 29118976 PMCID: PMC5664832 DOI: 10.1186/s40104-017-0211-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/04/2017] [Indexed: 11/24/2022] Open
Abstract
Background This study evaluated the impact of hormonal modulation at the onset of proestrus on ovarian response and uterine gene expression of beef cows. Methods A total of 172 anestrous beef cows were assigned to one of four groups according to the treatment with estradiol cypionate (ECP) and/or equine chorionic gonadotropin (eCG) [CON (n = 43), ECP (n = 43), eCG (n = 44) and ECP + eCG (n = 42)]. Results ECP-treated cows (ECP and ECP + eCG groups) presented greater occurrence of estrus (44.6% vs. 65.4%; P = 0.01) and pregnancy per AI [47.1% vs. 33.3%; P = 0.07], but similar progesterone (P4) concentration at subsequent diestrus than cows not treated with ECP (CON and eCG groups). Nonetheless, eCG-treated cows (eCG and ECP + eCG groups) presented larger follicle at timed AI (12.6 ± 0.3 vs. 13.5 ± 0.3 mm; P = 0.03), greater ovulation rate (96.5% vs. 82.6%; P = 0.008) and greater P4 concentration at d 6 (3.9 ± 0.2 vs. 4.8 ± 0.2 ng/mL; P = 0.001) than cows not treated with eCG (CON and ECP groups). Next, cows with a new corpus luteum 6 d after TAI were submitted to uterine biopsy procedure. Uterine fragments [CON (n = 6), ECP (n = 6)] were analyzed by RNA-Seq and a total of 135 transcripts were differentially expressed between groups (73 genes up-regulated by ECP treatment). Subsequently, uterine samples were analyzed by qPCR (genes associated with cell proliferation). ECP treatment induced greater abundance of PTCH2 (P = 0.07) and COL4A1 (P = 0.02), whereas suppressed EGFR (P = 0.09) expression. Conversely, eCG treatment increased abundance of HB-EGF (P = 0.06), ESR2 (P = 0.09), and ITGB3 (P = 0.05), whereas it reduced transcription of ESR1 (P = 0.05). Collectively, supplementation with ECP or eCG at the onset of proestrous of anestrous beef cows influenced ovarian responses, global and specific endometrial gene expression. Conclusion Proestrus estradiol regulate the endometrial transcriptome, particularly stimulating proliferative activity in the endometrium. Electronic supplementary material The online version of this article (10.1186/s40104-017-0211-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Gustavo Gasparin
- Laboratório de Biotecnologia Animal, ESALQ-USP, Av Pádua Dias, Piracicaba, SP 11 Brazil
| | - Luiz Lehmann Coutinho
- Laboratório de Biotecnologia Animal, ESALQ-USP, Av Pádua Dias, Piracicaba, SP 11 Brazil
| | | | | | | | - Mario Binelli
- Departamento de Reprodução Animal, FMVZ-USP, São Paulo, SP Brazil.,Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Avenida Duque de Caxias Norte, 225, Pirassununga, SP Zip Code 13635900 Brazil
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Gonella-Diaza AM, da Silva Andrade SC, Sponchiado M, Pugliesi G, Mesquita FS, Van Hoeck V, de Francisco Strefezzi R, Gasparin GR, Coutinho LL, Binelli M. Oviductal transcriptional profiling of a bovine fertility model by next-generation sequencing. Genom Data 2017; 13:27-29. [PMID: 28664146 PMCID: PMC5480813 DOI: 10.1016/j.gdata.2017.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 11/22/2022]
Abstract
In cattle, the oviduct plays a fundamental role in the reproductive process. Oviductal functions are controlled by the ovarian sex steroids: estradiol and progesterone. Here, we tested the hypothesis that the exposure to contrasting sex steroid milieus differentially impacts the oviductal transcriptional profile. We manipulated growth of the pre-ovulatory follicle to obtain cows that ovulated a larger (LF group) or a smaller (SF group) follicle. The LF group presented greater proestrus/estrus concentrations of estradiol and metaestrus concentrations of progesterone (Gonella-Diaza et al. 2015 [1], Mesquita et al. 2014 [2]). Also, the LF group was associated with greater fertility in timed-artificial insemination programs (Pugliesi et al. 2016 [3]). Cows were slaughtered on day 4 of the estrous cycle and total RNA was extracted from ampulla and isthmus fragments and analyzed by RNAseq. The resulting reads were mapped to the bovine genome (Bos taurus UMD 3.1, NCBI). The differential expression analyses revealed that 325 and 367 genes in ampulla and 274 and 316 genes in the isthmus were up-regulated and down-regulated in LF samples, respectively. To validate the RNAseq results, transcript abundance of 23 genes was assessed by qPCR and expression patterns were consistent between the two techniques. A functional enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) software. Processes enriched in the LF group included tissue morphology changes (extracellular matrix remodeling), cellular changes (proliferation), and secretion changes (growth factors, ions and metal transporters). An overview of the gene expression data was deposited in the NCBI's Gene Expression Omnibus (GEO) and is accessible through the accession number GSE65681. In conclusion, differences in the peri-ovulatory sex steroid milieu modify the oviductal gene expression profiles. Such differences may be associated with the greater fertility of the LF cows. This dataset is useful for further investigations of the oviductal biology and the impact of sex-steroid on the female reproductive tract.
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Affiliation(s)
- Angela Maria Gonella-Diaza
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Mariana Sponchiado
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Guilherme Pugliesi
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Veerle Van Hoeck
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Gustavo R Gasparin
- Laboratório de Biotecnologia Animal, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av Pádua Dias, 11, Piracicaba, SP, Brazil
| | - Luiz L Coutinho
- Laboratório de Biotecnologia Animal, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av Pádua Dias, 11, Piracicaba, SP, Brazil
| | - Mario Binelli
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
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Leasi F, Andrade SCDS, Norenburg J. At least some meiofaunal species are not everywhere. Indication of geographic, ecological and geological barriers affecting the dispersion of species of Ototyphlonemertes
(Nemertea, Hoplonemertea). Mol Ecol 2016; 25:1381-97. [DOI: 10.1111/mec.13568] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/08/2015] [Accepted: 01/25/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Francesca Leasi
- Department of Invertebrate Zoology; Smithsonian National Museum of Natural History; PO Box 37012, NMNH Washington DC 20013-7012 USA
| | | | - Jon Norenburg
- Department of Invertebrate Zoology; Smithsonian National Museum of Natural History; PO Box 37012, NMNH Washington DC 20013-7012 USA
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Gonella-Diaza AM, da Silva Andrade SC, Sponchiado M, Pugliesi G, Mesquita FS, Van Hoeck V, de Francisco Strefezzi R, Gasparin GR, Coutinho LL, Binelli M. Size of the Ovulatory Follicle Dictates Spatial Differences in the Oviductal Transcriptome in Cattle. PLoS One 2015; 10:e0145321. [PMID: 26699362 PMCID: PMC4689418 DOI: 10.1371/journal.pone.0145321] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/01/2015] [Indexed: 12/12/2022] Open
Abstract
In cattle, molecular control of oviduct receptivity to the embryo is poorly understood. Here, we used a bovine model for receptivity based on size of the pre-ovulatory follicle to compare oviductal global and candidate gene transcript abundance on day 4 of the estrous cycle. Growth of the pre-ovulatory follicle (POF) of Nelore (Bos indicus) cows was manipulated to produce two groups: large POF large corpus luteum (CL) group (LF-LCL; greater receptivity) and small POF-small CL group (SF-SCL). Oviductal samples were collected four days after GnRH-induced ovulation. Ampulla and isthmus transcriptome was obtained by RNA-seq, regional gene expression was assessed by qPCR, and PGR and ERa protein distribution was evaluated by immunohistochemistry. There was a greater abundance of PGR and ERa in the oviduct of LF-LCL animals thus indicating a greater availability of receptors and possibly sex steroids stimulated signaling in both regions. Transcriptomic profiles indicated a series of genes associated with functional characteristics of the oviduct that are regulated by the periovulatory sex steroid milieu and that potentially affect oviductal receptivity and early embryo development. They include tissue morphology changes (extra cellular matrix remodeling), cellular changes (proliferation), and secretion changes (growth factors, ions and metal transporters), and were enriched for the genes with increased expression in the LF-LCL group. In conclusion, differences in the periovulatory sex steroid milieu lead to different oviductal gene expression profiles that could modify the oviductal environment to affect embryo survival and development.
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Affiliation(s)
- Angela María Gonella-Diaza
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Sónia Cristina da Silva Andrade
- Laboratório de Biotecnologia Animal, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av Pádua Dias, 11, Piracicaba, SP, Brazil
| | - Mariana Sponchiado
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Guilherme Pugliesi
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Veerle Van Hoeck
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Gustavo R. Gasparin
- Laboratório de Biotecnologia Animal, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av Pádua Dias, 11, Piracicaba, SP, Brazil
| | - Luiz L. Coutinho
- Laboratório de Biotecnologia Animal, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av Pádua Dias, 11, Piracicaba, SP, Brazil
| | - Mario Binelli
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
- * E-mail:
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