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Oltehua-López O, Arteaga-Vázquez MA, Sosa V. Stem transcriptome screen for selection in wild and cultivated pitahaya ( Selenicereus undatus): an epiphytic cactus with edible fruit. PeerJ 2023; 11:e14581. [PMID: 36632141 PMCID: PMC9828283 DOI: 10.7717/peerj.14581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/28/2022] [Indexed: 01/09/2023] Open
Abstract
Dragon fruit, pitahaya or pitaya are common names for the species in the Hylocereus group of Selenicereus that produce edible fruit. These Neotropical epiphytic cacti are considered promising underutilized crops and are currently cultivated around the world. The most important species, S. undatus, has been managed in the Maya domain for centuries and is the focus of this article. Transcriptome profiles from stems of wild and cultivated plants of this species were compared. We hypothesized that differences in transcriptomic signatures could be associated with genes related to drought stress. De novo transcriptome assembly and the analysis of differentially expressed genes (DEGs) allowed us to identify a total of 9,203 DEGs in the Hunucmá cultivar relative of wild Mozomboa plants. Of these, 4,883 represent up-regulated genes and 4,320, down-regulated genes. Additionally, 6,568 DEGs were identified from a comparison between the Umán cultivar and wild plants, revealing 3,286 up-regulated and 3,282 down-regulated genes. Approximately half of the DEGs are shared by the two cultivated plants. Differences between the two cultivars that were collected in the same region could be the result of differences in management. Metabolism was the most representative functional category in both cultivars. The up-regulated genes of both cultivars formed a network related to the hormone-mediated signaling pathway that includes cellular responses to auxin stimulus and to hormone stimulus. These cellular reactions have been documented in several cultivated plants in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates.
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Affiliation(s)
| | | | - Victoria Sosa
- Biologia Evolutiva, Instituto de Ecologia AC, Xalapa, Veracruz, Mexico
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De novo assembly and annotation of the transcriptome of the endangered seagrass Zostera capensis: Insights from differential gene expression under thermal stress. Mar Genomics 2022; 66:100984. [PMID: 36116404 DOI: 10.1016/j.margen.2022.100984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022]
Abstract
Seagrasses are important marine ecosystem engineers but anthropogenic impacts and climate change have led to numerous population declines globally. In South Africa, Zostera capensis is endangered due to fragmented populations and heavy anthropogenic pressures on estuarine ecosystems that house the core of the populations. Addressing questions of how pressures such as climate change affect foundational species, including Z. capensis are crucial to supporting their conservation and underpin restoration efforts. Here we use ecological transcriptomics to study key functional responses of Z. capensis through quantification of gene expression after thermal stress and present the first reference transcriptome of Z. capensis. Four de novo reference assemblies (Trinity, IDBA-tran, RNAspades, SOAPdenovo) filtered through the EvidentialGene pipeline resulted in 153,755 transcripts with a BUSCO score of 66.1% for completeness. Differential expression analysis between heat stressed (32 °C for three days) and pre-warming plants identified genes involved in photosynthesis, oxidative stress, translation, metabolic and biosynthetic processes in the Z. capensis thermal stress response. This reference transcriptome is a significant contribution to the limited available genomic resources for Z. capensis and represents a vital tool for addressing questions around the species restoration and potential functional responses to warming marine environments.
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Enríquez-González C, Garcidueñas-Piña C, Castellanos-Hernández OA, Enríquez-Aranda S, Loera-Muro A, Ocampo G, Pérez-Molphe Balch E, Morales-Domínguez JF. De Novo Transcriptome of Mammillaria bombycina (Cactaceae) under In Vitro Conditions and Identification of Glyoxalase Genes. PLANTS 2022; 11:plants11030399. [PMID: 35161380 PMCID: PMC8838482 DOI: 10.3390/plants11030399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
Mammillaria bombycina is a cactus distributed in the central region of Mexico. Cactaceae have the particularity of surviving drought and high temperatures, which is why in vitro propagation studies have been carried out successfully to preserve this species and use it as a study model in cacti. In this contribution, a de novo transcriptome of M. bombycina was produced under in vitro conditions for the identification and expression of genes related to abiotic stress. Samples were sequenced using an Illumina platform, averaging 24 million clean readings. From assembly and annotation, 84,975 transcripts were generated, 55% of which were unigenes. Among these, the presence of 13 isoforms of genes belonging to glyoxalase I, II and III were identified. An analysis of the qRT-PCR expression of these genes was performed under in vitro and ex vitro conditions and dehydration at 6 and 24 h. The highest expression was observed under greenhouse conditions and dehydration at 24 h, according to the control. The de novo assembly of the M. bombycina transcriptome remains a study model for future work in cacti.
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Affiliation(s)
- Carolina Enríquez-González
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Cristina Garcidueñas-Piña
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Osvaldo Adrián Castellanos-Hernández
- Centro de Investigación en Biología Molecular Vegetal, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad, 1115, Linda Vista, Ocotlán 47810, Mexico
| | - Sergio Enríquez-Aranda
- Centro de Ciencias Básicas, Departamento de Sistemas de la Información, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Abraham Loera-Muro
- CONACyT Centro de Investigaciones Biológicas del Noroeste S.C., Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, Mexico
| | - Gilberto Ocampo
- Centro de Ciencias Básicas, Departamento de Biología, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Eugenio Pérez-Molphe Balch
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - José Francisco Morales-Domínguez
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
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Narum S, News JK, Fountain-Jones N, Hooper Junior R, Ortiz-Barrientos D, O'Boyle B, Sibbett B. Editorial 2022. Mol Ecol Resour 2021; 22:1-8. [PMID: 34919782 DOI: 10.1111/1755-0998.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Considerations for Initiating a Wildlife Genomics Research Project in South and South-East Asia. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00243-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lataretu M, Hölzer M. RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow. Genes (Basel) 2020; 11:E1487. [PMID: 33322033 PMCID: PMC7763471 DOI: 10.3390/genes11121487] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data's computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus. We evaluated the DEG detection functionality while using qRT-PCR data serving as a reference and observed a very high correlation of the logarithmized gene expression fold changes.
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Affiliation(s)
- Marie Lataretu
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany;
| | - Martin Hölzer
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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