De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina

Torales, Susana; Rivarola, Máximo Lisandro; González, Sergio; Inza, María Virginia; Pomponio, María Florencia; Fernández, Paula; Acuña, Cintia V.; Zelener, Noga; Fornes, Luis F.; Hopp, H. Esteban; Paniego, Norma; Poltri, Susana N. Marcucci

doi:10.1371/journal.pone.0203768

Cited by 7 publications

(4 citation statements)

References 34 publications

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“…The fasta_sample option of the Population module (Stacks v1.48) was used to obtain the sequences of the two haplotypes of each sample for each locus in FASTA format. Then, according to the same criterion used by Torales et al [19], SSRs with a minimum of five repeats for dinucleotide, four repeats for trinucleotide, and three repeats for tetra, penta and hexanucleotide motives were searched. The polymorphic SSRs were also analyzed.…”

Section: Ssr Identificationmentioning

confidence: 99%

“…A collateral application of this Next Generation Sequencing (NGS) technique in plants is the cost-effective discovery of other genetic variants like polymorphic SSR loci [18,19]. SSRs have numerous uses, including linkage map development, quantitative trait locus (QTL) mapping, marker-assisted selection, cultivar or clone fingerprinting, and population structure and genetic diversity studies, among others [20].…”

Section: Introductionmentioning

confidence: 99%

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Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

et al. 2019

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Restriction site-associated DNA sequencing (RADseq) and its derived protocols, such as double digest RADseq (ddRADseq), offer a flexible and highly cost-effective strategy for efficient plant genome sampling. This has become one of the most popular genotyping approaches for breeding, conservation, and evolution studies in model and non-model plant species. However, universal protocols do not always adapt well to non-model species. Herein, this study reports the development of an optimized and detailed ddRADseq protocol in Eucalyptus dunnii, a non-model species, which combines different aspects of published methodologies. The initial protocol was established using only two samples by selecting the best combination of enzymes and through optimal size selection and simplifying lab procedures. Both single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were determined with high accuracy after applying stringent bioinformatics settings and quality filters, with and without a reference genome. To scale it up to 24 samples, we added barcoded adapters. We also applied automatic size selection, and therefore obtained an optimal number of loci, the expected SNP locus density, and genome-wide distribution. Reliability and cross-sequencing platform compatibility were verified through dissimilarity coefficients of 0.05 between replicates. To our knowledge, this optimized ddRADseq protocol will allow users to go from the DNA sample to genotyping data in a highly accessible and reproducible way.

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Section: Ssr Identificationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

et al. 2019

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“…DC.) por ejemplo, microsatélites para estudios de diversidad genética con fines de conservación (Torales et al, 2018). Además, el avance en el estudio del transcriptoma puede ser dirigido en interacciones planta-patógeno y en respuestas a diversas condiciones ambientales como estrés calórico e hídrico o a la exposición a sustancias (Soto y López et al, 2012).…”

Section: Transcriptómica De áRboles Maderablesunclassified

ENFOQUES GENÓMICOS Y TRANSCRIPTÓMICOS PARA ESTUDIAR ÁRBOLES MADERABLES: PERSPECTIVAS PARA EL ESTUDIO DE CEDRO ROJO (Cedrela odorata L.)

Gómez-Godínez,

Cruz-Cárdenas,

Rojas-Anaya

et al. 2023

Trop Subtrop Agroecosyst

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Introduction: The high-throughput genomic and transcriptomic approach has been developed and implemented to address the main challenges that the timber forestry sector faces, such as population growth, climate change, deforestation and the loss of forest ecosystem services. Objective: To carry out a bibliographic review focused on the genomes and transcriptomes of timber trees reported in the databases, with special attention to red cedar (Cedrela odorata L.), due to its importance as precious wood in Mexico. Methodology: A literature review was carried out, directed at studying timber trees with genomic and transcriptomic strategies in different databases such as Pubmed, Scopus, Google Scholar, ScienceDirect, Wiley Online Library, MDPI and Scielo to identify the timber species that have been reported genomes and transcriptomes. The structure of the review was the genomics of timber trees, the transcriptomics of wood, and the potential species for study due to their importance and finally, the databases for consultation. Subsequently, a bibliometric study was carried out with the bibliometrix library in R Studio. Main results: The first genome to be assembled at the chromosome level was the black cottonwood. Among the timber trees, the genomes of black cottonwood, desert poplar, eucalyptus and oak with a length of 392, 496, 691 and 789 Mb have been reported. Through study of the transcriptome, it has been possible to identify genes related to formation of the wood in a hybrid poplar (Populus alba L. × P. glandulosa) and P. tremula L. and with drought tolerance in Pinus massoniana and Pinus pinaster Aiton. In red cedar (Cedrela odorata L.), the transcriptome was obtained by sequencing a single leaf, identifying 52,181 gene models. In the NCBI, EMBL-EBI, TreeGenes, PLAZA databases and the hardwood genomics website it is possible to find information related to the genomics and transcriptomics of timber species. Implications: More research is required in omics in timber, particularly in red cedar, since the search on these topics yielded little information. Conclusion: Through the bibliographic review in databases, the timber trees that have a described genome and transcriptome were identified. This information can be used for the assembly and annotation of new genomes, identification of genes and molecular markers, among other applications.

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“…RNA sequencing (RNA-seq) analysis and subsequent SSR loci discovery in transcripts are promising approaches for producing molecular tools for minor crops. With the development of High Throughput Sequencing (HTS) technology, RNA-seq data production and abundant number of SSR loci discovery became possible for the minor plants such as Cedar (Cedrela balansae) (Torales et al 2018); Lei bamboo (Phyllostachys violascens) (Cai et al 2019), tropical chestnut (Sterculia lanceolata) (Eum et al 2019), chrysanthemum (Chrysanthemum ×morifolium) (Fan et al 2019), Capsicum species (Jaiswal et al 2020), broadleaf lilac (Syringa oblata) (Yang et al 2020), and Carexspecies (Liu et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysisand development of SSR markers in Sumac (Rhus coriariaL.), and population structure analysis of sumac in Turkey

Gürcan

Kılınçer

Khanyile

2022

Preprint

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Sumac ( Rhus coriaria L.) is known for medicinal properties since at least the time of Theophrastus in the ancient Graeco-Roman time. Indeed, in the last decade, vast number of scientific papers demonstrated the benefits of multifunctional sumac in pharmaceutical, food, and textile industries. However, genetic and genomic information is scarce for sumac. In this study, RNA-seq transcriptome data consisting of 72,554 unigenes with an average length of 869 nt was produced for sumac. The transcripts were considered for further downstream analysis of GO, COG, and KEGG. The sumac transcripts showed highest mapping rate to pistachio genome (97%) followed by poison ivy (95%) and mango (91%). In total, 11.177 SSR loci di-, tri- tetra-, penta-, and hexa-nucleotide motif loci with minimum of 5 repeats were identified. Phylogenetic and structure analysis of 64 sample collected from a wide geographic region in Turkey were studied with eight polymorphic SSR loci. Structure analysis showed existence of two sub-populations in sumac in Turkey. The bushes located in residential areas and used for sumac production were found to be genetically unique as so non-residential bushes. This demonstrates that sumac growing since ancient time has not resulted in selection of superior cultivar, followed by clonal propagation and transfer of clones between territories.

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De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina

Cited by 7 publications

References 34 publications

Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

ENFOQUES GENÓMICOS Y TRANSCRIPTÓMICOS PARA ESTUDIAR ÁRBOLES MADERABLES: PERSPECTIVAS PARA EL ESTUDIO DE CEDRO ROJO (Cedrela odorata L.)

Transcriptome analysisand development of SSR markers in Sumac (Rhus coriariaL.), and population structure analysis of sumac in Turkey

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