Repetitive sequences in Eragrostis curvula cDNA EST libraries obtained from genotypes with different ploidy

Romero, José R.; Selva, Juan Pablo; Pessino, Silvina Claudia; Echenique, Viviana; Garbus, Ingrid

doi:10.1007/s10535-015-0569-z

Cited by 8 publications

(9 citation statements)

References 68 publications

(72 reference statements)

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“…Out of these, 63 were differentially represented between sexual and apomictic plants, but the differences were not conclusive. On the other hand, in a previous report on repetitive sequences expressed in cDNA libraries obtained from Eragrostis 21 , we showed differential expression for several members of the Gypsy retrotransposons family between inflorescences of sexual and apomictic genotypes. As already mentioned, our reference transcriptome covers all developmental stages.…”

Section: Resultscontrasting

confidence: 55%

Temporal and spatial expression of genes involved in DNA methylation during reproductive development of sexual and apomictic Eragrostis curvula

Selva

Siena

Rodrigo

et al. 2017

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Recent reports in model plant species have highlighted a role for DNA methylation pathways in the regulation of the somatic-to-reproductive transition in the ovule, suggesting that apomixis (asexual reproduction through seeds) likely relies on RdDM downregulation. Our aim was therefore to explore this hypothesis by characterizing genes involved in DNA methylation in the apomictic grass Eragrostis curvula. We explored floral transcriptomes to identify homologs of three candidate genes, for which mutations in Arabidopsis and maize mimic apomixis (AtAGO9/ZmAGO104, AtCMT3/ZmDMT102/ZmDMT105, and AtDDM1/ZmCHR106), and compared both their spatial and temporal expression patterns during reproduction in sexual and apomictic genotypes. Quantitative expression analyses revealed contrasting expression patterns for the three genes in apomictic vs sexual plants. In situ hybridization corroborated these results for two candidates, EcAGO104 and EcDMT102, and revealed an unexpected ectopic pattern for the AGO gene during germ line differentiation in apomicts. Although our data partially support previous results obtained in sexual plant models, they suggest that rather than an RdDM breakdown in the ovule, altered localization of AtAGO9/ZmAGO104 expression is required for achieving diplospory in E. curvula. The differences in the RdDM machinery acquired during plant evolution might have promoted the emergence of the numerous apomictic paths observed in plants.

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Section: Resultscontrasting

confidence: 55%

Temporal and spatial expression of genes involved in DNA methylation during reproductive development of sexual and apomictic Eragrostis curvula

Selva

Siena

Rodrigo

et al. 2017

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“…Previously reported ESTs related to repetitive elements present in E . curvula ´s floral and leaf libraries 25 were mapped onto the genome assembly. Using this scheme a LTR structure of a Gypsy superfamily of retrotransposons identified from the EST EH191456 was validated, since it was present in at least 16 scaffolds (Supplementary Table S4).…”

Section: Resultsmentioning

confidence: 99%

A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality

Carballo

Santos

Zappacosta

et al. 2019

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The Poaceae constitute a taxon of flowering plants (grasses) that cover almost all Earth’s inhabitable range and comprises some of the genera most commonly used for human and animal nutrition. Many of these crops have been sequenced, like rice, Brachypodium, maize and, more recently, wheat. Some important members are still considered orphan crops, lacking a sequenced genome, but having important traits that make them attractive for sequencing. Among these traits is apomixis, clonal reproduction by seeds, present in some members of the Poaceae like Eragrostis curvula . A de novo , high-quality genome assembly and annotation for E . curvula have been obtained by sequencing 602 Mb of a diploid genotype using a strategy that combined long-read length sequencing with chromosome conformation capture. The scaffold N50 for this assembly was 43.41 Mb and the annotation yielded 56,469 genes. The availability of this genome assembly has allowed us to identify regions associated with forage quality and to develop strategies to sequence and assemble the complex tetraploid genotypes which harbor the apomixis control region(s). Understanding and subsequently manipulating the genetic drivers underlying apomixis could revolutionize agriculture.

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“…For validation assays, total RNA was isolated from inflorescences from Tanganyika and OTA-S, following the protocol previously used for library construction. Reverse transcription was performed as described in [ 33 ]. Amplification of the cDNA was performed using specific primer pairs designed and synthesized through the Integrated DNA technology (IDT) webpage ( http://www.idtdna.com/Scitools/Applications/RealTimePCR/ ).…”

Section: Methodsmentioning

confidence: 99%

“…The ubiquitin conjugating enzyme transcript, used as housekeeping gene, was amplified with E . curvula -based primers (UBICE_F / R: / ) [ 33 ]. The isotig-based primers designed for validation were isotig27875_F / R: / ; isotig38926_F / R: / and isotig36655_F / R: / .…”

Section: Methodsmentioning

confidence: 99%

“…Analysis of these libraries, together with differential display studies conducted with these genotypes, allowed the identification of a set of genes differentially expressed between diplosporous and sexual E . curvula , including some coding for retrotransposon proteins [ 30 – 33 ]. However, the number of genes sequenced with these technologies was quite low compared to the number of genes that the Next-generation sequencing (NGS) technologies could provide.…”

Section: Introductionmentioning

confidence: 99%

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De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes

et al. 2017

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A long-standing goal in plant breeding has been the ability to confer apomixis to agriculturally relevant species, which would require a deeper comprehension of the molecular basis of apomictic regulatory mechanisms. Eragrostis curvula (Schrad.) Nees is a perennial grass that includes both sexual and apomictic cytotypes. The availability of a reference transcriptome for this species would constitute a very important tool toward the identification of genes controlling key steps of the apomictic pathway. Here, we used Roche/454 sequencing technologies to generate reads from inflorescences of E. curvula apomictic and sexual genotypes that were de novo assembled into a reference transcriptome. Near 90% of the 49568 assembled isotigs showed sequence similarity to sequences deposited in the public databases. A gene ontology analysis categorized 27448 isotigs into at least one of the three main GO categories. We identified 11475 SSRs, and several of them were assayed in E curvula germoplasm using SSR-based primers, providing a valuable set of molecular markers that could allow direct allele selection. The differential contribution to each library of the spliced forms of several transcripts revealed the existence of several isotigs produced via alternative splicing of single genes. The reference transcriptome presented and validated in this work will be useful for the identification of a wide range of gene(s) related to agronomic traits of E. curvula, including those controlling key steps of the apomictic pathway in this species, allowing the extrapolation of the findings to other plant species.

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Repetitive sequences in Eragrostis curvula cDNA EST libraries obtained from genotypes with different ploidy

Cited by 8 publications

References 68 publications

Temporal and spatial expression of genes involved in DNA methylation during reproductive development of sexual and apomictic Eragrostis curvula

Temporal and spatial expression of genes involved in DNA methylation during reproductive development of sexual and apomictic Eragrostis curvula

A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality

De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes

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