Browsing by Author "Carrasquinho, Isabel"
Now showing 1 - 8 of 8
Results Per Page
Sort Options
- An improved reference genome and first organelle genomes of Quercus suberPublication . Usié, Ana; Serra, Octávio; Barros, Pedro M.; Barbosa, Pedro; Leão, Célia; Capote, Tiago; Almeida, Tânia; Rodrigues, Leandra; Carrasquinho, Isabel; Guimarães, Joana B.; Mendoça, Diogo; Nóbrega, Filomena; Egas, Conceição; Chaves, Inês; Abreu, Isabel A.; Saibo, Nelson J. M.; Marum, Liliana; Varela, Maria Carolina; Matos, José; Simões, Fernanda; Miguel, Célia M.; Oliveira, M. Margarida; Ricardo, Cândido P.; Gonçalves, Sónia; Ramos, António MarcosCork oak (Quercus suber L.) is an ecologically and economically important evergreen tree species native to the Mediterranean region and widespread in southwest Europe and northwest Africa. An improved genome assembly of cork oak using a combination of Illumina and PacBio sequencing is presented in this study. The assembled genome contains 2351 scaffolds longer than 1000 bp, accounting for 765.7 Mbp of genome size, L90 of 755, and a N50 of 1.0 Mbp, with 40,131 annotated genes. The repetitive sequences constitute 53.6% of the genome. The genome sequences of chloroplast and mitochondrion were determined for the first time, with a genome size of 161,179 bp and 531,858 bp, respectively. Phylogenetic analysis based on complete chloroplast genome sequence showed that Q. suber is closely related to Quercus variabilis, two cork-producing species with commercial use. All data generated are available through the public databases, being ready to be used without restrictions. This study provides an improved nuclear genome assembly together with the organelle genomes of cork oak. These resources will be useful for further breeding strategies and conservation programs and for comparative genomic studies in oak species.
- Insights into the mechanisms implicated in Pinus pinaster resistance to pinewood nematodePublication . Modesto, Inês; Sterck, Lieven; Arbona, Vicent; Gómez-Cadenas, Aurelio; Carrasquinho, Isabel; Van de Peer, Yves; Miguel, Célia M.Pine wilt disease (PWD), caused by the plant–parasitic nematode Bursaphelenchus xylophilus, has become a severe environmental problem in the Iberian Peninsula with devastating effects in Pinus pinaster forests. Despite the high levels of this species’ susceptibility, previous studies reported heritable resistance in P. pinaster trees. Understanding the basis of this resistance can be of extreme relevance for future programs aiming at reducing the disease impact on P. pinaster forests. In this study, we highlighted the mechanisms possibly involved in P. pinaster resistance to PWD, by comparing the transcriptional changes between resistant and susceptible plants after infection. Our analysis revealed a higher number of differentially expressed genes (DEGs) in resistant plants (1,916) when compared with susceptible plants (1,226). Resistance to PWN is mediated by the induction of the jasmonic acid (JA) defense pathway, secondary metabolism pathways, lignin synthesis, oxidative stress response genes, and resistance genes. Quantification of the acetyl bromide-soluble lignin confirmed a significant increase of cell wall lignification of stem tissues around the inoculation zone in resistant plants. In addition to less lignified cell walls, susceptibility to the pine wood nematode seems associated with the activation of the salicylic acid (SA) defense pathway at 72 hpi, as revealed by the higher SA levels in the tissues of susceptible plants. Cell wall reinforcement and hormone signaling mechanisms seem therefore essential for a resistance response
- Molecular Defense Response of Pine Trees (Pinus spp.) to the Parasitic Nematode Bursaphelenchus xylophilusPublication . Modesto, Inês; Mendes, André; Carrasquinho, Isabel; Miguel, Célia M.Pine wilt disease (PWD) is a severe environmental problem in Eastern Asia andWestern Europe, devastating large forest areas and causing significant economic losses. This disease is caused by the pine wood nematode (PWN), Bursaphelenchus xylophilus, a parasitic migratory nematode that infects the stem of conifer trees. Here we review what is currently known about the molecular defense response in pine trees after infection with PWN, focusing on common responses in different species. By giving particular emphasis to resistance mechanisms reported for selected varieties and families, we identified shared genes and pathways associated with resistance, including the activation of oxidative stress response, cell wall lignification, and biosynthesis of terpenoids and phenylpropanoids. The role of post-transcriptional regulation by small RNAs in pine response to PWN infection is also discussed, as well as the possible implementation of innovative RNAinterference technologies, with a focus on trans-kingdom small RNAs. Finally, the defense response induced by elicitors applied to pine plants before PWN infection to prompt resistance is reviewed. Perspectives about the impact of these findings and future research approaches are discussed
- Pinus pinaster early hormonal defence responses to pinewood nematode (Bursaphelenchus xylophilus) infectionPublication . Rodrigues, Ana M.; Langer, Swen; Carrasquinho, Isabel; Bergstrom, Ed; Larson, Tony; Thomas-Oates, Jane; António, CarlaThe pinewood nematode (PWN) is the causal agent of pine wilt disease, a pathology that affects conifer forests, mainly Pinus spp. PWN infection can induce the expression of phytohormonerelated genes; however, changes at the early phytohormone level have not yet been explored. Phytohormones are low-abundance metabolites, and thus, difficult to quantify. Moreover, most methodologies focus mainly on Arabidopsis or crop species. This work aimed to validate a fast (run time 6.6 min) liquid chromatography-triple quadrupole tandem mass spectrometry (LC-QqQ-MS/MS) analytical method to quantify 14 phytohormones in Pinus pinaster stem tissues. This method was further applied to evaluate, for the first time, early phytohormone changes in susceptible and resistant phenotypes of P. pinaster 24, 48 and 72 h after inoculation (HAI) with PWN. A significant increase in salicylic acid (SA, 48 and 72 HAI) and jasmonic acid methyl ester (JA-ME, 72 HAI) was observed in susceptible phenotypes. Results indicate that the higher susceptibility of P. pinaster to PWN infection might result from an inefficient trigger of hypersensitive responses, with the involvement of JA and SA pathways. This work provides an important update in forest research, and adds to the current knowledge of Pinus spp. defence responses to PWN infection
- Primary Metabolite Adjustments Associated With Pinewood Nematode Resistance in Pinus pinasterPublication . Rodrigues, Ana M.; Carrasquinho, Isabel; António, CarlaThe pinewood nematode (PWN) Bursaphelenchus xylophilus is the causal agent of the pine wilt disease (PWD) and represents one of the major threats to conifer forests. The detection of the PWN in Portugal, associated with Pinus pinaster, increased the concern of its spread to European forests. Despite its susceptibility to PWD, genetic variability found among P. pinaster populations has been associated with heritable PWD resistance. Understanding the mechanisms underlying tree resistance constitutes a valuable resource for breeding programs toward more resilient forest plantations. This study investigated changes in anatomy, chlorophyll a fluorescence (ChlF), and primary metabolism in susceptible and resistant P. pinaster half-sib plants, after PWN inoculation. Susceptible plants showed a general shutdown of central metabolism, osmolyte accumulation, photosynthetic inhibition, and a decrease in the plant water status. The ChlF transient rise (OJIP curve) revealed the appearance of L- and K-bands, indicators of environmental stress. In contrast, resistant plants revealed a regulated defense response and were able to restrict PWN migration and cellular damage. Furthermore, the accumulation of g-aminobutyric acid (GABA) and succinate suggested a role of these metabolites in PWD resistance and the possible activation of the GABA shunt. Altogether, these results provide new insights to the role of primary metabolism in PWD resistance and in the selection of resistant phenotypes for disease mitigation
- Quantificação da biomassa florestal residual em povoamentos de pinheiro manso na Mata Nacional do EscaroupimPublication . Tomé, Margarida; Soares, Paula; Cardoso, Sónia; Carvalho, José Luis; Carrasquinho, IsabelO projecto Gestão Multifuncional do Pinheiro Manso (Pinus pinea L.) Para a Produção de Fruto, Diminuição de Riscos de Incêndio, Utilização de Biomassa e Recuperação Ambiental, financiado pelo Fundo Florestal Permanente, resulta de uma parceria entre instituições públicas e privadas e tem como um dos objectivos quantificar o material removido em desbastes e desramações tendo em vista a produção de estilha. Aproveitou-se a oportunidade para se instalar um ensaio de desbaste na Mata Nacional do Escaroupim em povoamentos nunca desbastados. Das árvores a desbastar seleccionou-se uma sub-amostra para determinação de biomassa por componentes (folhas, ramos, casca, lenho, pinhas, ramos e folhas secas) o que nos permitiu quantificar, em termos de biomassa seca, as quantidades de estilha obtidas nos respectivos talhões.
- SNP Detection in Pinus pinaster Transcriptome and Association with Resistance to Pinewood NematodePublication . Modesto, Inês; Inácio, Vera; Novikova, Polina; Carrasquinho, Isabel; Van de Peer, Yves; Miguel, Célia M.Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studies
- The draft genome sequence of cork oakPublication . Ramos, António Marcos; Usié, Ana; Barbosa, Pedro; Barros, Pedro M.; Capote, Tiago; Chaves, Inês; Simões, Fernanda; Abreu, Isabl; Carrasquinho, Isabel; Faro, Carlos; Guimarães, Joana B.; Mendonça, Diogo; Nóbrega, Filomena; Rodrigues, Leandra; Saibo, Nelson J. M.; Varela, Maria Carolina; Egas, Conceição; Matos, José; Miguel, Célia M.; Oliveira, M. Margarida; Ricardo, Cândido P.; Gonçalves, SóniaCork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.