B chromosomes (Bs) are dispensable components of the genomes of numerous species. Thus far, there... more B chromosomes (Bs) are dispensable components of the genomes of numerous species. Thus far, there is a lack of evidence for any transcripts of Bs in plants, with the exception of some rDNA sequences. Here, we show that the Giemsa banding-positive heterochromatic subterminal domain of rye (Secale cereale) Bs undergoes decondensation during interphase. Contrary to the heterochromatic regions of A chromosomes, this domain is simultaneously marked by trimethylated H3K4 and by trimethylated H3K27, an unusual combination of apparently conflicting histone modifications. Notably, both types of B-specific high copy repeat families (E3900 and D1100) of the subterminal domain are transcriptionally active, although with different tissue type-dependent activity. No small RNAs were detected specifically for the presence of Bs. The lack of any significant open reading frame and the highly heterogeneous size of mainly polyadenylated transcripts indicate that the noncoding RNA may function as structural or catalytic RNA.
Fucosyltransferases catalyse fucose transfer onto oligosaccharides. Two fucosylated structures ha... more Fucosyltransferases catalyse fucose transfer onto oligosaccharides. Two fucosylated structures have been identified in plants: the alpha1,4-fucosylated Lewis-a epitope and the alpha1,3-fucosylated core. Here we report the cloning, genomic characterization, and physical mapping of two genes encoding proteins similar to alpha1,4-fucosyltransferase (EC 2.4.1.65, MtFUT1) and alpha1,3-fucosyltransferase (EC 2.4.1.214, MtFUT2) in Medicago truncatula. Analysis of the genomic organization of the fucosyltransferase genes in M. truncatula, revealed the presence of two genomic variants of the MtFUT1 gene coding sequence, one containing a single intron and the other intronless, whereas in MtFUT2, the gene coding region is interrupted by four introns. Using for the first time fluorescence in situ hybridization (FISH) to physically map fucosyltransferase genes in plants, this study reveals a high genomic dispersion of these genes in Medicago. The MtFUT1 genes are mapped on chromosomes 4, 7, and 8, colocalizing on three of the five MtFUT2 loci. Chromosomes 1 and 5 carry the additional MtFUT2 loci. Moreover, the intensity of the FISH signals reveals marked differences in the number of gene copies per locus for both genes. Simultaneous mapping of rRNA genes on chromosome 5 shows that several MTFUT2 gene loci are inserted within the rDNA array. Insertions of coding DNA sequences into the rDNA repeats were never reported to date.
The understanding of the molecular mechanisms responsible for the making of a unisexual flower ha... more The understanding of the molecular mechanisms responsible for the making of a unisexual flower has been a long-standing quest in plant biology. Plants with male and female flowers can be divided mainly into two categories: dioecious and monoecious, and both sexual systems co-exist in nature in ca of 10% of the angiosperms. The establishment of male and female traits has been extensively described in a hermaphroditic flower and requires the interplay of networks, directly and indirectly related to the floral organ identity genes including hormonal regulators, transcription factors, microRNAs, and chromatin-modifying proteins. Recent transcriptomic studies have been uncovering the molecular processes underlying the establishment of unisexual flowers and there are many parallelisms between monoecious, dioecious, and hermaphroditic individuals. Here, we review the paper entitled "Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber" publis...
Abstract: Nucleolar dominance is an enigma. The puzzle of differential amphiplasty has remained u... more Abstract: Nucleolar dominance is an enigma. The puzzle of differential amphiplasty has remained unresolved since it was first recognised and described in Crepis hybrids by Navashin in 1934. Here we review the body of knowledge that has grown out of the many models that have tried to find the genetic basis for differential rRNA gene expression in hybrids, and present a new interpretation. We propose and discuss a chromatin imprinting model which re-interprets differential amphiplasty in terms of two genomes of differing size occupying a common space within the nucleus, and with heterochromatin as a key player in the scenario. Difference in size between two parental genomes induces an inherited epigenetic mark in the hybrid that allows patterns of chromatin organization to have positional effects on the neighbouring domains. This chromatin imprinting model can be also used to explain complex genomic interactions which transcend nucleolar dominance and which can account for the overall...
The genus Eucalyptus encloses several species with high ecological and economic value, being the ... more The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype...
The standard rye cultivar 'Imperial' and a structural variant carrying an intact 1R chrom... more The standard rye cultivar 'Imperial' and a structural variant carrying an intact 1R chromosome and two telocentric 1R chromosomes (short and long arms) were used to investigate expression patterns of homologous rDNA loci, and the influence of chromosome structural change on their interphase organisation and relative disposition. Sequential silver staining and in situ hybridization with the rDNA probe pTa71, established a correspondence between the expression and organization patterns of rDNA domains in metaphase and interphase cells. In most cells of the cultivar Imperial, nucleolar organizer region (NOR) silver staining on metaphase chromosomes with equivalent numbers of rDNA genes revealed a size heteromorphism between homologous rDNA loci, resulting from their differential expression. NOR heteromorphism in the structural variant line was significantly reduced. The preferential activity of one NOR over its homologue was found to be random within cells and independent of pa...
ABSTRACT As a major part of most plant genomes, retrotransposons are distributed throughout the p... more ABSTRACT As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities. We had performed in silico analysis of the Vitis vinifera 'Pinot Noir' genome to search for gypsy type retroelements homologues to the one identified in Finns radiata (IFG7) and P pinaster (PpRT1) and in Quercus suber (Corky). We intended to see the existence and structure of gypsy-like retroelements homologues in the Vitis genome as well as the existence of integration site preference. From all data and to perform a deeper analysis we chose 36 complete sequences copies in the Vitis genome. We used three genetic distance corrections, additional to p-distance to estimate retroelements insertion time and reverse transcriptase, integrase and LTR (Long Terminal Repeat) sequences to establish a phylogeny and to see the contributions of different regions according to the evolutionary rates. We found three elements with identical LTRs and two old elements that revealed recent and very old insertions as well as insertions inside other retroelements. Additionally, we found no preference for the integration site as shown by the different target site repeat for each element
Probes for B chromosome-specific sequences in the distal region of the long arm of the rye B have... more Probes for B chromosome-specific sequences in the distal region of the long arm of the rye B have been used to investigate the interphase arrangement of the Bs in rye and in hexaploid wheat. The Lindström strain of wheat carries the rye Bs as additions. The number of in situ signals in nuclei with two, three and four Bs is often less than the maximum B number, and it seems that the Bs may be grouped together in various ways rather than being randomly dispersed throughout the nucleus. The degree of physical association is greater in rye than in the allen wheat background. The results are discussed in relation to the pairing and recombination preferences of the Bs in rye and in Lindström wheat.
EXPRESSION OF 1R rDNA loci IN TRITICALE: GENETIC AND DEVELOPMENTAL CONTROLS Wanda Viegas1, Manuel... more EXPRESSION OF 1R rDNA loci IN TRITICALE: GENETIC AND DEVELOPMENTAL CONTROLS Wanda Viegas1, Manuela Silva1, Nuno Neves1, Alexandra Castilho1, Augusta Barao1, Alvaro Queiroz1, JS (Pat) Heslop-Harrison2, Leonor Morais-Cecilio1, Luis Amado1, Margarida ...
B chromosomes (Bs) are dispensable components of the genomes of numerous species. Thus far, there... more B chromosomes (Bs) are dispensable components of the genomes of numerous species. Thus far, there is a lack of evidence for any transcripts of Bs in plants, with the exception of some rDNA sequences. Here, we show that the Giemsa banding-positive heterochromatic subterminal domain of rye (Secale cereale) Bs undergoes decondensation during interphase. Contrary to the heterochromatic regions of A chromosomes, this domain is simultaneously marked by trimethylated H3K4 and by trimethylated H3K27, an unusual combination of apparently conflicting histone modifications. Notably, both types of B-specific high copy repeat families (E3900 and D1100) of the subterminal domain are transcriptionally active, although with different tissue type-dependent activity. No small RNAs were detected specifically for the presence of Bs. The lack of any significant open reading frame and the highly heterogeneous size of mainly polyadenylated transcripts indicate that the noncoding RNA may function as structural or catalytic RNA.
Fucosyltransferases catalyse fucose transfer onto oligosaccharides. Two fucosylated structures ha... more Fucosyltransferases catalyse fucose transfer onto oligosaccharides. Two fucosylated structures have been identified in plants: the alpha1,4-fucosylated Lewis-a epitope and the alpha1,3-fucosylated core. Here we report the cloning, genomic characterization, and physical mapping of two genes encoding proteins similar to alpha1,4-fucosyltransferase (EC 2.4.1.65, MtFUT1) and alpha1,3-fucosyltransferase (EC 2.4.1.214, MtFUT2) in Medicago truncatula. Analysis of the genomic organization of the fucosyltransferase genes in M. truncatula, revealed the presence of two genomic variants of the MtFUT1 gene coding sequence, one containing a single intron and the other intronless, whereas in MtFUT2, the gene coding region is interrupted by four introns. Using for the first time fluorescence in situ hybridization (FISH) to physically map fucosyltransferase genes in plants, this study reveals a high genomic dispersion of these genes in Medicago. The MtFUT1 genes are mapped on chromosomes 4, 7, and 8, colocalizing on three of the five MtFUT2 loci. Chromosomes 1 and 5 carry the additional MtFUT2 loci. Moreover, the intensity of the FISH signals reveals marked differences in the number of gene copies per locus for both genes. Simultaneous mapping of rRNA genes on chromosome 5 shows that several MTFUT2 gene loci are inserted within the rDNA array. Insertions of coding DNA sequences into the rDNA repeats were never reported to date.
The understanding of the molecular mechanisms responsible for the making of a unisexual flower ha... more The understanding of the molecular mechanisms responsible for the making of a unisexual flower has been a long-standing quest in plant biology. Plants with male and female flowers can be divided mainly into two categories: dioecious and monoecious, and both sexual systems co-exist in nature in ca of 10% of the angiosperms. The establishment of male and female traits has been extensively described in a hermaphroditic flower and requires the interplay of networks, directly and indirectly related to the floral organ identity genes including hormonal regulators, transcription factors, microRNAs, and chromatin-modifying proteins. Recent transcriptomic studies have been uncovering the molecular processes underlying the establishment of unisexual flowers and there are many parallelisms between monoecious, dioecious, and hermaphroditic individuals. Here, we review the paper entitled "Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber" publis...
Abstract: Nucleolar dominance is an enigma. The puzzle of differential amphiplasty has remained u... more Abstract: Nucleolar dominance is an enigma. The puzzle of differential amphiplasty has remained unresolved since it was first recognised and described in Crepis hybrids by Navashin in 1934. Here we review the body of knowledge that has grown out of the many models that have tried to find the genetic basis for differential rRNA gene expression in hybrids, and present a new interpretation. We propose and discuss a chromatin imprinting model which re-interprets differential amphiplasty in terms of two genomes of differing size occupying a common space within the nucleus, and with heterochromatin as a key player in the scenario. Difference in size between two parental genomes induces an inherited epigenetic mark in the hybrid that allows patterns of chromatin organization to have positional effects on the neighbouring domains. This chromatin imprinting model can be also used to explain complex genomic interactions which transcend nucleolar dominance and which can account for the overall...
The genus Eucalyptus encloses several species with high ecological and economic value, being the ... more The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype...
The standard rye cultivar 'Imperial' and a structural variant carrying an intact 1R chrom... more The standard rye cultivar 'Imperial' and a structural variant carrying an intact 1R chromosome and two telocentric 1R chromosomes (short and long arms) were used to investigate expression patterns of homologous rDNA loci, and the influence of chromosome structural change on their interphase organisation and relative disposition. Sequential silver staining and in situ hybridization with the rDNA probe pTa71, established a correspondence between the expression and organization patterns of rDNA domains in metaphase and interphase cells. In most cells of the cultivar Imperial, nucleolar organizer region (NOR) silver staining on metaphase chromosomes with equivalent numbers of rDNA genes revealed a size heteromorphism between homologous rDNA loci, resulting from their differential expression. NOR heteromorphism in the structural variant line was significantly reduced. The preferential activity of one NOR over its homologue was found to be random within cells and independent of pa...
ABSTRACT As a major part of most plant genomes, retrotransposons are distributed throughout the p... more ABSTRACT As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities. We had performed in silico analysis of the Vitis vinifera 'Pinot Noir' genome to search for gypsy type retroelements homologues to the one identified in Finns radiata (IFG7) and P pinaster (PpRT1) and in Quercus suber (Corky). We intended to see the existence and structure of gypsy-like retroelements homologues in the Vitis genome as well as the existence of integration site preference. From all data and to perform a deeper analysis we chose 36 complete sequences copies in the Vitis genome. We used three genetic distance corrections, additional to p-distance to estimate retroelements insertion time and reverse transcriptase, integrase and LTR (Long Terminal Repeat) sequences to establish a phylogeny and to see the contributions of different regions according to the evolutionary rates. We found three elements with identical LTRs and two old elements that revealed recent and very old insertions as well as insertions inside other retroelements. Additionally, we found no preference for the integration site as shown by the different target site repeat for each element
Probes for B chromosome-specific sequences in the distal region of the long arm of the rye B have... more Probes for B chromosome-specific sequences in the distal region of the long arm of the rye B have been used to investigate the interphase arrangement of the Bs in rye and in hexaploid wheat. The Lindström strain of wheat carries the rye Bs as additions. The number of in situ signals in nuclei with two, three and four Bs is often less than the maximum B number, and it seems that the Bs may be grouped together in various ways rather than being randomly dispersed throughout the nucleus. The degree of physical association is greater in rye than in the allen wheat background. The results are discussed in relation to the pairing and recombination preferences of the Bs in rye and in Lindström wheat.
EXPRESSION OF 1R rDNA loci IN TRITICALE: GENETIC AND DEVELOPMENTAL CONTROLS Wanda Viegas1, Manuel... more EXPRESSION OF 1R rDNA loci IN TRITICALE: GENETIC AND DEVELOPMENTAL CONTROLS Wanda Viegas1, Manuela Silva1, Nuno Neves1, Alexandra Castilho1, Augusta Barao1, Alvaro Queiroz1, JS (Pat) Heslop-Harrison2, Leonor Morais-Cecilio1, Luis Amado1, Margarida ...
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