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The rhizoma peanut (Arachis glabrata Benth., section Rhizomatosae) is a tetraploid perennial legume. Although several A. glabrata cultivars have been developed as forage and ornamental turf, the origin and genomic constitution of this species are still unknown. In this study, we evaluated the affinity between the genomes of A. glabrata and the probable diploid donors of the sections Rhizomatosae, Arachis, Erectoides and Procumbentes by genomic in situ hybridization (GISH). Single GISH analyses detected that species of the sections Erectoides (E2 subgenome) and Procumbentes (E3 subgenome) were the diploid species with the highest degree of genomic affinity with A. glabrata. Based on single GISH experiments and DNA sequence similarity, three species -A. duranensis, A. paraguariensis subsp. capibarensis, and A. rigonii-, which showed the most uniform and brightest hybridization patterns and lowest genetic distance, were selected as probes for double GISH experiments. Double GISH experiments showed that A. glabrata is constituted by four identical or very similar chromosome complements. In these assays, A. paraguariensis subsp. capibarensis showed the highest brightness onto A. glabrata chromosomes. Thus, our results support the autopolyploid origin of A. glabrata and show that the species with E2 subgenome are the most probable ancestors of this polyploid legume forage.
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Arachis , Genoma de Planta , Arachis/genética , Genoma de Planta/genética , Hibridación in Situ , Poliploidía , GenómicaRESUMEN
MAIN CONCLUSION: Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
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Diploidia , Fabaceae , Arachis/genética , ADN Satélite/genética , Evolución Molecular , Fabaceae/genética , Genoma de Planta/genética , Heterocromatina/genética , Filogenia , Retroelementos/genéticaRESUMEN
Liolaemus is the most specious genus of the Squamata lizards in South America, presenting exceptional evolutionary radiation and speciation patterns. This recent diversification complicates the formal taxonomic treatment and the phylogenetic analyses of this group, causing relationships among species to remain controversial. Here we used Next-Generation Sequencing to do a comparative analysis of the structure and organization of the complete mitochondrial genomes of three differently related species of Liolaemus and with different reproductive strategies and ploidy levels. The annotated mitochondrial genomes of ca. 17 kb are the first for the Liolaemidae family. Despite the high levels of sequence similarity among the three mitochondrial genomes over most of their lengths, the comparative analyses revealed variations at the stop codons of the protein coding genes and the structure of the tRNAs among species. The presence of a non-canonical dihydrouridine loop is a novelty for the pleurodonts iguanians. But the highest level of variability was observed in two repetitive sequences of the control region, which were responsible for most of the length heterogeneity of the mitochondrial genomes. These tandem repeats may be useful markers to analyze relationships of closely related species of Liolaemus and related genera and to conduct population and phylogenetic studies.
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Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.
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Arachis/genética , Arachis/clasificación , Argentina , Cromosomas de las Plantas/genética , Productos Agrícolas/genética , Metilación de ADN , ADN de Plantas/genética , Domesticación , Evolución Molecular , Regulación de la Expresión Génica de las Plantas , Variación Genética , Genoma de Planta , Hibridación Genética , Fenotipo , Poliploidía , Recombinación Genética , Especificidad de la Especie , TetraploidíaRESUMEN
MAIN CONCLUSION: The most conspicuous difference among chromosomes and genomes in Arachis species, the patterns of heterochromatin, was mainly modeled by differential amplification of different members of one superfamily of satellite DNAs. Divergence in repetitive DNA is a primary driving force for genome and chromosome evolution. Section Arachis is karyotypically diverse and has six different genomes. Arachis glandulifera (D genome) has the most asymmetric karyotype and the highest reproductive isolation compared to the well-known A and B genome species. These features make A. glandulifera an interesting model species for studying the main repetitive components that accompanied the genome and chromosome diversification in the section. Here, we performed a genome-wide analysis of repetitive sequences in A. glandulifera and investigated the chromosome distribution of the identified satellite DNA sequences (satDNAs). LTR retroelements, mainly the Ty3-gypsy families "Fidel/Feral" and "Pipoka/Pipa", were the most represented. Comparative analyses with the A and B genomes showed that many of the previously described transposable elements (TEs) were differently represented in the D genome, and that this variation accompanied changes in DNA content. In addition, four major satDNAs were characterized. Agla_CL8sat was the major component of pericentromeric heterochromatin, while Agla_CL39sat, Agla_CL69sat, and Agla_CL122sat were found in heterochromatic and/or euchromatic regions. Even though Agla_CL8sat belong to a different family than that of the major satDNA (ATR-2) found in the heterochromatin of the A, K, and F genomes, both satDNAs are members of the same superfamily. This finding suggests that closely related satDNAs of an ancestral library were differentially amplified leading to the major changes in the heterochromatin patterns that accompanied the karyotype and genome differentiation in Arachis.
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Arachis/genética , Elementos Transponibles de ADN/genética , Genoma de Planta/genética , Heterocromatina/genética , Evolución Molecular , Estudio de Asociación del Genoma Completo , Comunicaciones por SatéliteRESUMEN
Rhizomatosae is a taxonomic section of the South American genus Arachis, whose diagnostic character is the presence of rhizomes in all its species. This section is of particular evolutionary interest because it has three polyploid (A. pseudovillosa, A. nitida and A. glabrata, 2n = 4x = 40) and only one diploid (A. burkartii, 2n = 2x = 20) species. The phylogenetic relationships of these species as well as the polyploidy nature and the origin of the tetraploids are still controversial. The present study provides an exhaustive analysis of the karyotypes of all rhizomatous species and six closely related diploid species of the sections Erectoides and Procumbentes by cytogenetic mapping of DAPI/CMA heterochromatin bands and 5S and 18-26S rDNA loci. Chromosome banding showed variation in the DAPI heterochromatin distribution pattern, which, together with the number and distribution of rDNA loci, allowed the characterization of all species studied here. The bulk of chromosomal markers suggest that the three rhizomatous tetraploid species constitute a natural group and may have at least one common diploid ancestor. The cytogenetic data of the diploid species analyzed evidenced that the only rhizomatous diploid species-A. burkartii-has a karyotype pattern different from those of the rhizomatous tetraploids, showing that it is not likely the genome donor of the tetraploids and the non-monophyletic nature of the section Rhizomatosae. Thus, the tetraploid species should be excluded from the R genome, which should remain exclusively for A. burkartii. Instead, the karyotype features of these tetraploids are compatible with those of different species of the sections Erectoides and Procumbentes (E genome species), suggesting the hypothesis of multiple origins of these tetraploids. In addition, the polyploid nature and the group of diploid species closer to the tetraploids are discussed.
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Arachis/genética , Genoma de Planta/genética , Heterocromatina/genética , Arachis/citología , Evolución Biológica , Mapeo Cromosómico , Cromosomas de las Plantas/genética , ADN de Plantas/genética , ADN Ribosómico/genética , Diploidia , Cariotipo , Cariotipificación , Filogenia , Poliploidía , TetraploidíaRESUMEN
Notolathyrus is a section of South American endemic species of the genus Lathyrus. The origin, phylogenetic relationship and delimitation of some species are still controversial. The present study provides an exhaustive analysis of the karyotypes of approximately half (10) of the species recognized for section Notolathyrus and four outgroups (sections Lathyrus and Orobus) by cytogenetic mapping of heterochromatic bands and 45S and 5S rDNA loci. The bulk of the parameters analyzed here generated markers to identify most of the chromosomes in the complements of the analyzed species. Chromosome banding showed interspecific variation in the amount and distribution of heterochromatin, and together with the distribution of rDNA loci, allowed the characterization of all the species studied here. Additionally, some of the chromosome parameters described (st chromosomes and the 45S rDNA loci) constitute the first diagnostic characters for the Notolathyrus section. Evolutionary, chromosome data revealed that the South American species are a homogeneous group supporting the monophyly of the section. Variation in the amount of heterochromatin was not directly related to the variation in DNA content of the Notolathyrus species. However, the correlation observed between the amount of heterochromatin and some geographical and bioclimatic variables suggest that the variation in the heterochromatic fraction should have an adaptive value.
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ADN Ribosómico/genética , Evolución Molecular , Heterocromatina/genética , Cariotipo , Lathyrus/genética , Cromomicina A3/química , Mapeo Cromosómico , ADN de Plantas/genética , Hibridación Fluorescente in Situ , Indoles/química , Lathyrus/clasificación , América del SurRESUMEN
The genome size was surveyed in 13 Notolathyrus species endemic to South America by flow cytometry and analyzed in an evolutionary and biogeographic context. A DNA content variation of 1.7-fold was registered, and four groups of species with different DNA content were determined. Although, the 2C values were correlated with the total chromosome length and intrachromosomal asymmetry index (A1), the karyotype formula remained almost constant. The conservation of the karyotype formula is in agreement with proportional changes of DNA in the chromosome arms. Species with annual life cycle and shorter generation time had the lowest DNA content and the data suggest that changes in DNA content involved reductions of genome size in the perennial to annual transitions. The variation of 2C values was correlated with precipitation of the coldest quarter and, to some extent, with altitude. Additional correlations with other variables were observed when the species were analyzed separately according to the biogeographic regions. In general, the species with higher DNA content were found in more stable environments. The bulk of evidence suggests that changes on genome size would have been one of the most important mechanisms that drove or accompanied the diversification of Notolathyrus species.
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ADN de Plantas/análisis , ADN de Plantas/genética , Tamaño del Genoma , Genoma de Planta/genética , Cariotipo , Lathyrus/genética , Evolución Biológica , Núcleo Celular/genética , Citometría de Flujo , Geografía , América del SurRESUMEN
The cytogenetic characterization of Arachis species is useful for assessing the genomes present in this genus, for establishing the relationship among their representatives and for understanding the variability in the available germplasm. In this study, we used fluorescence in situ hybridization (FISH) to examine the distribution patterns of heterochromatin and rDNA genes in 12 Brazilian accessions of five species of the taxonomic section Arachis. The heterochromatic pattern varied considerably among the species: complements with centromeric bands in all of the chromosomes (A. hoehnei) and complements completely devoid of heterochromatin (A. gregoryi, A. magna) were observed. The number of 45S rDNA loci ranged from two (A. gregoryi) to eight (A. glandulifera), while the number of 5S rDNA loci was more conserved and varied from two (in most species) to four (A. hoehnei). In some species one pair of 5S rDNA loci was observed adjacent to 45S rDNA loci. The chromosomal markers revealed polymorphism in the three species with more than one accession (A. gregoryi, A. magna and A. valida) that were tested. The previous genome assignment for each of the species studied was confirmed, except for A. hoehnei. The intraspecific variability observed here suggests that an exhaustive cytogenetic and taxonomic analysis is still needed for some Arachis species.
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BACKGROUND AND AIMS: Peanut (Arachis hypogaea) is an allotetraploid (AABB-type genome) of recent origin, with a genome of about 2·8 Gb and a high repetitive content. This study reports an analysis of the repetitive component of the peanut A genome using bacterial artificial chromosome (BAC) clones from A. duranensis, the most probable A genome donor, and the probable consequences of the activity of these elements since the divergence of the peanut A and B genomes. METHODS: The repetitive content of the A genome was analysed by using A. duranensis BAC clones as probes for fluorescence in situ hybridization (BAC-FISH), and by sequencing and characterization of 12 genomic regions. For the analysis of the evolutionary dynamics, two A genome regions are compared with their B genome homeologues. KEY RESULTS: BAC-FISH using 27 A. duranensis BAC clones as probes gave dispersed and repetitive DNA characteristic signals, predominantly in interstitial regions of the peanut A chromosomes. The sequences of 14 BAC clones showed complete and truncated copies of ten abundant long terminal repeat (LTR) retrotransposons, characterized here. Almost all dateable transposition events occurred <3·5 million years ago, the estimated date of the divergence of A and B genomes. The most abundant retrotransposon is Feral, apparently parasitic on the retrotransposon FIDEL, followed by Pipa, also non-autonomous and probably parasitic on a retrotransposon we named Pipoka. The comparison of the A and B genome homeologous regions showed conserved segments of high sequence identity, punctuated by predominantly indel regions without significant similarity. CONCLUSIONS: A substantial proportion of the highly repetitive component of the peanut A genome appears to be accounted for by relatively few LTR retrotransposons and their truncated copies or solo LTRs. The most abundant of the retrotransposons are non-autonomous. The activity of these retrotransposons has been a very significant driver of genome evolution since the evolutionary divergence of the A and B genomes.
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Arachis/genética , ADN Intergénico , Evolución Molecular , Genoma de Planta , Cromosomas Artificiales Bacterianos/genética , Hibridación Fluorescente in Situ , Filogenia , Secuencias Repetitivas de Ácidos Nucleicos , Retroelementos/fisiologíaRESUMEN
BACKGROUND AND AIMS: Polyploidy is a dominant feature of flowering-plant genomes, including those of many important crop species. Arachis is a largely diploid genus with just four polyploid species. Two of them are economically important: the cultivated peanut and A. glabrata, a tropical forage crop. Even though it is usually accepted that polyploids within papilionoid legumes have arisen via hybridization and further chromosome doubling, it has been recently suggested that peanut arose through bilateral sexual polyploidization. In this paper, the polyploid nature of the recent, spontaneously originated triploid cytotype of the tropical lucerne, A. pintoi, was analysed, and thereby the mechanism by which polyploids may arise in the genus. METHODS: Chromosome morphology of 2x and 3x A. pintoi was determined by the Feulgens technique and the rDNA sites were mapped by FISH. To investigate whether polyploidization occurred by means of unreduced gametes, a detailed analysis of the microsporogenesis and pollen grains was made. KEY RESULTS: The 2x and 3x plants presented 9m + 1sm and a satellited chromosome type 2 in each haploid genome. Physical mapping revealed a cluster of 18S-26S rDNA, proximally located on chromosome 6, and two 5S rDNA loci on chromosomes 3 and 5. Diploid plants presented 10II in meiosis while trivalents were observed in all triploids, with a maximum of 10III by cell. Diploid A. pintoi produced normal tetrads, but also triads, dyads and monads. Two types of pollen grains were detected: (1) normal-sized with a prolate shape and (2) large ones with a tetrahedral morphology. CONCLUSIONS: Karyotype and meiotic analysis demonstrate that the 3x clone of A. pintoi arose by autopolyploidy. The occurrence of unreduced gametes strongly supports unilateral sexual polyploidization as the most probable mechanism that could have led to the origin of the triploid cytotype. This mechanism of polyploidization would probably be one of the most important mechanisms involved in the origin of economically important species of Arachis, either by triploid bridge or bilateral sexual polyploidization.
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Arachis/genética , Evolución Biológica , Genoma de Planta/genética , Meiosis , Triploidía , Arachis/citología , Arachis/fisiología , Emparejamiento Cromosómico , Cromosomas de las Plantas/genética , ADN Ribosómico/genética , Células Germinativas de las Plantas/fisiología , Hibridación Genética , Hibridación Fluorescente in Situ , Cariotipificación , Meiosis/genética , Microscopía Electrónica de Rastreo , Polen/fisiología , Polen/ultraestructura , Poliploidía , Colorantes de RosanilinaRESUMEN
Arachis hypogaea is an allotetraploid species with low genetic variability. Its closest relatives, all of the genus Arachis, are important sources of alleles for peanut breeding. However, a better understanding of the genome constitution of the species and of the relationships among taxa is needed for the effective use of the secondary gene pool of Arachis. In the present work, we focused on all 11 non-A genome (or B genome sensu lato) species of Arachis recognized so far. Detailed karyotypes were developed by heterochromatin detection and mapping of the 5S and the 18S-25S rRNA using FISH. On the basis of outstanding differences observed in the karyotype structures, we propose segregating the non-A genome taxa into three genomes: B sensu stricto (s.s.), F and K. The B genome s.s. is deprived of centromeric heterochromatin and is homologous to one of the A. hypogaea complements. The other two genomes have centromeric bands on most of the chromosomes, but differ in the amount and distribution of heterochromatin. This organization is supported by previously published data on molecular markers, cross compatibility assays and bivalent formation at meiosis in interspecific hybrids. The geographic structure of the karyotype variability observed also reflects that each genome group may constitute lineages that have evolved through independent evolutionary pathways. In the present study, we confirmed that Arachis ipaensis was the most probable B genome donor for A. hypogaea, and we identified a group of other closely related species. The data provided here will facilitate the identification of the most suitable species for the development of prebreeding materials for further improvement of cultivated peanut.
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Arachis/genética , Mapeo Cromosómico , ADN Ribosómico/genética , Genoma de Planta , Heterocromatina/genética , Alelos , Arachis/clasificación , Centrómero , Cromosomas de las Plantas , ADN de Plantas , ADN Recombinante , Hibridación Genética , Hibridación Fluorescente in Situ , Cariotipificación , Especificidad de la EspecieRESUMEN
In this paper, we describe a Ty3-gypsy retrotransposon from allotetraploid peanut (Arachis hypogaea) and its putative diploid ancestors Arachis duranensis (A-genome) and Arachis ipaënsis (B-genome). The consensus sequence is 11,223 bp. The element, named FIDEL (Fairly long Inter-Dispersed Euchromatic LTR retrotransposon), is more frequent in the A- than in the B-genome, with copy numbers of about 3,000 (+/-950, A. duranensis), 820 (+/-480, A. ipaënsis), and 3,900 (+/-1,500, A. hypogaea) per haploid genome. Phylogenetic analysis of reverse transcriptase sequences showed distinct evolution of FIDEL in the ancestor species. Fluorescent in situ hybridization revealed disperse distribution in euchromatin and absence from centromeres, telomeric regions, and the nucleolar organizer region. Using paired sequences from bacterial artificial chromosomes, we showed that elements appear less likely to insert near conserved ancestral genes than near the fast evolving disease resistance gene homologs. Within the Ty3-gypsy elements, FIDEL is most closely related with the Athila/Calypso group of retrovirus-like retrotransposons. Putative transmembrane domains were identified, supporting the presence of a vestigial envelope gene. The results emphasize the importance of FIDEL in the evolution and divergence of different Arachis genomes and also may serve as an example of the role of retrotransposons in the evolution of legume genomes in general.
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Arachis/genética , Genoma de Planta , Retroelementos , Secuencia de Aminoácidos , Variaciones en el Número de Copia de ADN , Datos de Secuencia Molecular , Filogenia , Alineación de SecuenciaRESUMEN
The karyotype structure of Arachis trinitensis was studied by conventional Feulgen staining, CMA/DAPI banding and rDNA loci detection by fluorescence in situ hybridization (FISH) in order to establish its genome status and test the hypothesis that this species is a genome donor of cultivated peanut. Conventional staining revealed that the karyotype lacked the small "A chromosomes" characteristic of the A genome. In agreement with this, chromosomal banding showed that none of the chromosomes had the large centromeric bands expected for A chromosomes. FISH revealed one pair each of 5S and 45S rDNA loci, located in different medium-sized metacentric chromosomes. Collectively, these results suggest that A. trinitensis should be removed from the A genome and be considered as a B or non-A genome species. The pattern of heterochromatic bands and rDNA loci of A. trinitensis differ markedly from any of the complements of A. hypogaea, suggesting that the former species is unlikely to be one of the wild diploid progenitors of the latter.
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The karyotype structure of Arachis trinitensis was studied by conventional Feulgen staining, CMA/DAPI banding and rDNA loci detection by fluorescence in situ hybridization (FISH) in order to establish its genome status and test the hypothesis that this species is a genome donor of cultivated peanut. Conventional staining revealed that the karyotype lacked the small "A chromosomes" characteristic of the A genome. In agreement with this, chromosomal banding showed that none of the chromosomes had the large centromeric bands expected for A chromosomes. FISH revealed one pair each of 5S and 45S rDNA loci, located in different medium-sized metacentric chromosomes. Collectively, these results suggest that A. trinitensis should be removed from the A genome and be considered as a B or non-A genome species. The pattern of heterochromatic bands and rDNA loci of A. trinitensis differ markedly from any of the complements of A. hypogaea, suggesting that the former species is unlikely to be one of the wild diploid progenitors of the latter.
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Chromosome markers were developed for Arachis glandulifera using fluorescence in situ hybridization (FISH) of the 5S and 45S rRNA genes and heterochromatic 4'-6-diamidino-2-phenylindole (DAPI) positive bands. We used chromosome landmarks identified by these markers to construct the first Arachis species ideogram in which all the homologous chromosomes were precisely identified. The comparison of this ideogram with those published for other Arachis species revealed very poor homeologies with all A and B genome taxa, supporting the special genome constitution (D genome) of A. glandulifera. Genomic affinities were further investigated by dot blot hybridization of biotinylated A. glandulifera total DNA to DNA from several Arachis species, the results indicating that the D genome is positioned between the A and B genomes.