Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

Lopes, Fabrício Ramon; Carazzolle, Marcelo Falsarella; Pereira, Gonçalo Amarante Guimarães; Colombo, Carlos Augusto; Carareto, Claudia M. A.

doi:10.1007/s00438-008-0319-4

Cited by 22 publications

(24 citation statements)

References 89 publications

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“…2F), indicating the presence of substantially active TEs or TE fragments in maize seed development. Although it remains to be determined whether these NTRs have any biological function, some evidence has shown that TE-related regions are widely active and have acquired specific cell functions during their evolution (Vicient et al, 2001;de Araujo et al, 2005;Ohtsu et al, 2007;Lopes et al, 2008;Picault et al, 2009), and we did observe 46 TE-associated NTRs with EST evidence in addition to the support of our RNA-seq data (Fig. 2F).…”

Section: Discovery Of Ntrssupporting

confidence: 79%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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Transcriptome analysis of early-developing maize (Zea mays) seed was conducted using Illumina sequencing. We mapped 11,074,508 and 11,495,788 paired-end reads from endosperm and embryo, respectively, at 9 d after pollination to define gene structure and alternative splicing events as well as transcriptional regulators of gene expression to quantify transcript abundance in both embryo and endosperm. We identified a large number of novel transcribed regions that did not fall within maize annotated regions, and many of the novel transcribed regions were tissue-specifically expressed. We found that 50.7% (8,556 of 16,878) of multiexonic genes were alternatively spliced, and some transcript isoforms were specifically expressed either in endosperm or in embryo. In addition, a total of 46 trans-splicing events, with nine intrachromosomal events and 37 interchromosomal events, were found in our data set. Many metabolic activities were specifically assigned to endosperm and embryo, such as starch biosynthesis in endosperm and lipid biosynthesis in embryo. Finally, a number of transcription factors and imprinting genes were found to be specifically expressed in embryo or endosperm. This data set will aid in understanding how embryo/endosperm development in maize is differentially regulated.Maize (Zea mays) seeds are one of the most important crop materials that provide resources for food, feed, biofuel, and raw material for processing. Maize seed development initiates from double fertilization, in which two of the pollen sperms fuse with an egg cell and a central cell to produce embryo and endosperm, respectively (Randolph, 1936;Chaudhury et al., 2001). The main function of endosperm is to provide nutrient for the developing embryo and germinating embryo.After fertilization, the zygote undergoes an asymmetric division into a small apical cell and a large basal cell, giving rise to the embryo proper and the suspensor, respectively. The radial symmetry of the proembryo is shifted to a bilateral symmetry at the transition stage, which is characterized by protoderm formation. The shoot apical meristem and the root apical meristem can be distinguished at the onset of the coleoptile stage, and then the position of the future coleoptile is marked by a small protuberance. The mature embryo is composed of the embryo axis, which is formed by the plumule with five or six short internodes, and leaf primordia and primary root surrounded by the coleoptile and the coleorhiza, respectively, and the scutellum (Randolph, 1936;Abbe and Stein, 1954;Diboll, 1968;Lammeren, 1986;Vernoud et al., 2005).Maize endosperm follows the nucleus-type endosperm development, where the fertilized central cell undergoes several rounds of synchronous division in the absence of cell wall formation and cytokinesis to produce a syncytium (Lopes and Larkins, 1993;Olsen, 2004). Cellularization allows the formation of the internuclear radial microtubule systems and open-ended alveolation from the periphery of the endosperm toward the central vacuole (Olsen et al., ...

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Section: Discovery Of Ntrssupporting

confidence: 79%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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“…These two retrotransposons were found to be common in species of Coffea and in Psilanthus ebracteolatus Hiern but with different activity rates, which has permitted the differentiation of species and accessions as well. Lopes et al (2008) annotated coding regions of ESTs and unigenes from Coffea arabica, C. canephora and C. racemosa, and suggested that many transposable element insertions involve diverse elements, such as LTR-retrotransposons, transposons, MITEs and Helitrons. In relation to LTRretrotransposons, representatives of Ty1-copia-like are preferentially inserted in the antisense orientation in the three species, while those of Ty3-gypsy-like are inserted in the sense orientation in C. arabica.…”

Section: Introductionmentioning

confidence: 99%

FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species

Yuyama

Pereira

Santos

et al. 2012

Genome

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The genus Coffea possesses about 100 species, and the most economically important are Coffea canephora and Coffea arabica. The latter is predominantly self-compatible with 2n = 4x = 44, while the others of the genus are diploid with 2n = 2x = 22 and mostly self-incompatible. Studies using molecular markers have been useful to detect differences between genomes in Coffea; however, molecular and cytogenetic studies have produced only limited information on the karyotypes organization. We used DOP-PCR to isolate repetitive elements from genome of Coffea arabica var. typica. The pCa06 clone, containing a fragment of 775 bp length, was characterized by sequencing and used as a probe in chromosomes of C. arabica and six other species: C. canephora, Coffea eugenioides, Coffea kapakata, Coffea liberica var. dewevrei, Coffea racemosa, and Coffea stenophylla. This insert shows similarities with a gag protein of the Ty3-gypsy-like super-family. Dot blot and FISH analyses demonstrated that pCa06 is differentially accumulated between species and chromosomes. Signals appeared scattered and clustered on the chromosomes and were also associated with heterochromatic regions. While the literature shows that there is a high karyotype similarity between Coffea species, our results point out differences in the accumulation and dispersion of this Ty3-gypsy-like retrotransposon during karyotype differentiation of Coffea.

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“…(11,17,18) Com o propósito de investigar em maiores detalhes as possíveis contribuições dos elementos móveis em sequências codificantes, foi realizada a busca por ESTs que validassem os modelos gênicos preditos que sugeriram a utilização de sequências de TEs na codificação de proteínas do genoma hospedeiro, possibilitando a análise mais rigorosa destes casos. Esta inspeção confirmou a ocorrência de TEs na região codificante de 4 genes ortólogos para C. reinhardtii (Figura 5.3) e 8 em V. carteri ( Figura 5.4).…”

Section: Resultsunclassified

“…O conhecimento acerca do potencial de TEs em eventos evolutivos, juntamente com o aumento do número de genomas sequenciados, tem incentivado o estudo da associação entre elementos de transposição e estruturas gênicas. (11,17,18,25) Quando genomas apresentam divergência recente, é esperado que características relativas ao conteúdo gênico dos mesmos -como número de genes e estrutura destes, a exemplo da organização de éxons e íntrons -permaneçam altamente conservadas. (56) Este fato é importante para estudos que almejam identificar modificações introduzidas por TEs, uma vez que estabelece um cenário adequado em que podem ser realizadas comparações de contextos gênicos.…”

Section: Genes Ortólogos E Associação Destes Com Tesunclassified

“…(11,84) No entanto, cópias que passam a integrar sequências codificantes podem conduzir a efeitos evolutivos positivos, embora estes eventos sejam raros, o que motiva estudos acerca da participação dos TEs em parcelas codificantes dos genes. (11,17,18) O efeito da integração de TEs nestas regiões têm sido explorado em genes de plantas como o arroz (18) e o café (17), assim como em mamíferos, a exemplo da espécie humana e de camundongos. (11) …”

Section: Introductionunclassified

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Estudo da influência de elementos transponíveis nos genomas das algas C. reinhardtii e V. carteri

Philippsen¹

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Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

Cited by 22 publications

References 89 publications

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species

Estudo da influência de elementos transponíveis nos genomas das algas C. reinhardtii e V. carteri

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