Abstract: Tandem repeats often confound large genome assemblies. A survey of tandemly arrayed repetitive sequences was carried out in whole genome sequences of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, and papaya, in order to test how these assemblies deal with this fraction of DNA. Our results suggest that plant genome assemblies preferentially include tandem repeats composed of shorter monomeric units (especially dinucleotide and 9-30-bp repeats), while higher repetitive units pose more difficulties to assemble. Nevertheless, notwithstanding that currently available sequencing technologies struggle with higher arrays of repeated DNA, major well-known repetitive elements including centromeric and telomeric repeats as well as high copy-number genes, were found to be reasonably well represented. A database including all tandem repeat sequences characterized here was created to benefit future comparative genomic analyses.
Abstract: Here, we analyze the evolutionary dynamics of a satellite-DNA family in an attempt to understand the effect of factors such as location, organization, and repeat-copy number in the molecular drive process leading to the concerted-evolution pattern found in this type of repetitive sequences. The presence of RAE180 satellite-DNA in the dioecious species of the plant genus Rumex is a noteworthy feature at this respect, as RAE180 satellite repeats have accumulated differentially, showing a distinct distribution pattern in different species. The evolution of dioecious Rumex gave rise to two phylogenetic clades: one clade composed of species with an ancestral XX/XY sex chromosome system and a second, derived clade of species with a multiple sex–chromosome system XX/XY1Y2. While in the XX/XY dioecious species, the RAE180 satellite-DNA is located only in a small autosomal locus, the RAE180 repeats are present also in a small autosomal locus and additionally have been massively amplified in the Y chromosomes of XX/XY1Y2 species. Here, we have found that the RAE180 repeats of the autosomal locus of XX/XY species are characterized by intra-specific sequence homogeneity and inter-specific divergence and that the comparison of individual nucleotide positions between related species shows a general pattern of concerted evolution. On the contrary, both in the autosomal and the Y-linked loci of XX/XY1Y2 species, ancestral variability has remained with reduced rates of sequence homogenization and of evolution. Thus, this study demonstrates that molecular mechanisms of non-reciprocal exchange are key factors in the molecular drive process; the satellite DNAs in the non-recombining Y chromosomes show low rates of concerted evolution and intra-specific variability increase with no inter-specific divergence. By contrast, freely recombining loci undergo concerted evolution with genetic differentiation between species as occurred in the autosomal locus of XX/XY species. However, evolutionary periods of rapid sequence change might alternate with evolutionary periods of stasis with variability remaining by the reduced action of molecular mechanisms of non-reciprocal exchange as occurred in XX/XY1Y2 species, which could depend on repeat-copy number and the processes involved in their amplification.
Abstract: A satellite-DNA family (RUSI) has been isolated and characterized in Rumexinduratus Boiss and Reuter (Polygonaceae), an Iberian endemic polygamous sorrel. The RUSI repeats are 170 bp in length and approximately 68% AT-rich containing different variants of degenerate telomere motifs--(TT)(n)AN(GG)(n) -, a typical feature of subtelomeric DNA repeats adjacent to telomeres, which have been referred to as telomere-associated sequences or TASs. In fact, fluorescent in situhybridization showed that this satellite DNA is located in subtelomeric positions of most of the chromosomes of R. induratus, with some centromeric loci. PCR and Southern-blot hybridization assays for sequence conservation in the genus Rumex, indicated that the RUSI sequences are restricted to the genomes of R. induratus and R. scutatus, both species of the section Scutati, suggesting that they are recently evolved. Sequence variation within the two species is high (mean value of sequence differences between repeats of 15% for R. induratus and 7.5% for R. scutatus) and the degree of sequence differentiation between species is low with no species-specific variants, postulated to be due to slowed rates of spreading of sequence variants by molecular homogenizing mechanisms. Characteristics of RUSI sequences are discussed in the light of their chromosomal location and analyzed for their evolutionary and phylogenetic implications.
Abstract: Rumex papillaris Boiss, & Reut., an Iberian endemic, belongs to the section Acetosa of the genus Rumex whose main representative is R. acetosa L., a species intensively studied in relation to sex-chromosome evolution. Here, we characterize cytogenetically the chromosomal complement of R. papillaris in an effort to enhance future comparative genomic approaches and to better our understanding of sex chromosome structure in plants. Rumex papillaris, as is common in this group, is a dioecious species characterized by the presence of a multiple sex chromosome system (with females 2n = 12 + XX and males 2n = 12 + XY(1)Y(2)). Except for the X chromosome both Y chromosomes are the longest in the karyotype and appear heterochromatic due to the accumulation of at least two satellite DNA families, RAE180 and RAYSI. Each chromosome of pair VI has an additional major heterochromatin block at the distal region of the short arm. These supernumerary heterochromatic blocks are occupied by RAE730 satellite DNA family. The Y-related RAE180 family is also present in an additional minor autosomal locus. Our comparative study of the chromosomal organization of the different satellite-DNA sequences in XX/XY and XX/XY(1)Y(2) Rumex species demonstrates that of active mechanisms of heterochromatin amplification occurred and were accompanied by chromosomal rearrangements giving rise to the multiple XX/XY(1)Y(2) chromosome systems observed in Rumex. Additionally, Y(1) and Y(2) chromosomes have undergone further rearrangements leading to differential patterns of Y-heterochromatin distribution between Rumex species with multiple sex chromosome systems.
Abstract: Papaya (Carica papaya L.) is an important fruit crop cultivated in tropical and subtropical regions worldwide. A first draft of its genome sequence has been recently released. Together with Arabidopsis, rice, poplar, grapevine and other genomes in the pipeline, it represents a good opportunity to gain insight into the organization of plant genomes. Here we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly-arrayed sequences, and high copy number genes. These repetitive sequences account for \u223c56% of the papaya genome with TEs being the most abundant at 52%, tandem repeats at 1.3% and high copy number genes at 3%. Most common types of TEs are represented in the papaya genome with retrotransposons being the dominant class, accounting for 40% of the genome. The most prevalent retrotransposons are Ty3-gypsy (27.8%) and Ty1-copia (5.5%). Among the tandem repeats, microsatellites are the most abundant in number, but represent only 0.19% of the genome. Minisatellites and satellites are less abundant, but represent 0.68% and 0.43% of the genome, respectively, due to greater repeat length. Despite an overall smaller gene repertoire in papaya than many other angiosperms, a significant fraction of genes (>2%) are present in large gene families with copy number greater than 20. This repeat database clarified a major part of the papaya genome organization and partly explained the lower gene repertoire in papaya than in Arabidopsis.
Abstract: Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.
Abstract: Sex of dioecious and gynodioecious papayas is
controlled by two slightly different Y chromosomes, Y for
males and Yh for hermaphrodites. All combinations of the
Y and/or Yh chromosomes are lethal. We investigated the
features of paired dioecious X- and Y-specific bacterial
artificial chromosomes (BACs) and compared their sequences
to corresponding gynodioecious X- and Y-specific
BACs. Numerous chromosomal rearrangements were
detected between the X- and Y-specific BACs, including
inversions, deletions, insertions, and duplications. DNA
sequence expansion was documented on the Y BAC.
Dioecious and gynodioecious X-specific BACs were
virtually identical. The Y- and Yh-specific BACs shared
high degree of DNA sequence identity, but local chromosomal
rearrangements were detected, as the consequence of
suppression of recombination in the male specific region
and the isolation of Yand Yh chromosomes enforced by the
lethal effect. Analysis of sequence divergence between
three dioecious X and Y gene pairs resulted in the estimated
ages of divergence from 0.6 to 2.5 million years, reinforcing
the hypothesis of a recent origin of the papaya sex
chromosomes. The estimated age of divergence between Y
and Yh chromosomes was approximately 73,000 years for
Gene 5. Our findings indicate that Y and Yh chromosomes
evolved from a common ancestral Y chromosome, possibly
prior to the origin of agriculture. The existence of a
hermaphrodite Yh chromosome is less likely to have resulted
from human selection as once suggested.
Notes: First Volume of Tropical Plant Biology launched by Springer
Abstract: satDNA Analyzer is a program, implemented in C++, for the analysis of the patterns of variation at each nucleotide position considered independently amongst all units of a given satellite-DNA family when comparing it between a pair of species. The program classifies each site accordingly as monomorphic or polymorphic, discriminates shared from non-shared polymorphisms and classifies each non-shared polymorphism according to the model proposed by Strachan et al. in six different stages of transition during the spread of a variant repeat unit toward its fixation. Furthermore, this program implements several other utilities for satellite-DNA analysis evolution such as the design of the average consensus sequences, the average base pair contents, the distribution of variant sites, the transition to transversion ratio and different estimates of intra-specific variation and inter-specific variation. Aprioristic hypotheses on factors influencing the molecular drive process and the rates and biases of concerted evolution can be tested with this program. Additionally, satDNA Analyzer generates an output file containing a sequence alignment without shared polymorphisms to be used for further evolutionary analysis by using different phylogenetic softwares. AVAILABILITY: satDNA Analyzer is freely available at http://satdna.sourceforge.net/. SatDNA Analyzer has been designed to operate on Windows, Linux and Mac OS X.
Notes: *Equal contribution
Freely available at satdna.sourceforge.net
Abstract: In Oleaceae the most outstanding
biological issue is to clarify the taxonomic relationships
of cultivated and wild olives. To establish the
genetic relationships between the wild (Olea europaea
subsp. europaea var. sylvestris (Mill.) Lehr.), the
cultivated olive (Olea europaea subsp. europaea var.
europaea), and other taxa of the genus Olea (Olea
europaea subsp. cuspidata (Wall. ex G.Don)Cif., Olea
europaea subsp. cerasiformis G. Kunkel & Sunding,
Olea paniculata R. Br.) and other Oleaceae (represented
by Ligustrum vulgaris) we carried out the
amplification by polymerase chain reaction (PCR)
and the sequencing of the third nuclear intron of the
nitrate reductase gene (nia-i3). Sequence analyses
showed the presence of two different functional
variants of the intron (nia1 and nia2) in the Oleaceae,
in addition to a shorter non-functional one. Notably,
while the shortest and the nia1 variantswere present in
all the taxa analysed, the nia2 variant was present only
in thewild and the cultivatedolive.These data confirm
the close phylogenetic relationship between wild and
cultivated olives and suggest that this gene could be
duplicated in these two taxa after its divergence from
the remaining Oleaceae. The presence of a target for
AflII enzyme in nia2 and its absence in nia1 variant
enables easy distinction by PCR-RFLP between, on
the one hand, wild and cultivated olive, and on the
other the remaining subspecies of theOlea europaea L.
complex (O. e. subsp. cuspidata and O. e. subsp.
cerasiformis) as well as other Oleaceae (O. paniculata,
L. vulgaris L.). Additionally, nia1 sequences provide
useful information about phylogeny of the wild and
cultivated olives inside the genus Olea.
Abstract: The structural features and evolutionary state of the sex chromosomes of the XX/XY species of Rumex are unknown. Here, we report a study of the meiotic behaviour of the XY bivalent in Rumex acetosella and R. suffruticosus, a new species which we describe cytogenetically for the first time in this paper, and also that of the XY(1)Y(2) trivalent of R. acetosa by both conventional cytogenetic techniques and analysis of synaptonemal complex formation. Fluorescent in situ hybridization with satellite DNA and rDNA sequences as probes was used to analyse the degree of cytogenetic differentiation between the X and Y chromosomes in order to depict their evolutionary stage in the three species. Contrasting with the advanced state of genetic differentiation between the X and the Y chromosomes in R. acetosa, we have found that R. acetosella and R. suffruticosus represent an early stage of genetic differentiation between sex chromosomes. Our findings further demonstrate the usefulness of the genus Rumex as a model for analysing the evolution of sex chromosomes in plants, since within this genus it is now possible to study the different levels of genetic differentiation between the sex chromosomes and to analyse their evolutionary history from their origin.
Abstract: In this paper, we analyze a satellite-DNA family, the RAYSI family, which is specific of the Y chromosomes of Rumex acetosa, a dioecious plant species with a multiple sex-chromosome system in which the females are XX and the males are XY(1)Y(2). Here, we demonstrate that this satellite DNA is common to other relatives of R. acetosa, including Rumex papillaris, Rumex intermedius, Rumex thyrsoides and Rumex tuberosus that are also dioecious species with a multiple system of sex chromosomes. This satellite-DNA family is absent from the genomes of other dioecious Rumex species having an XX/XY sex-chromosome system. Our data confirm recent molecular phylogenies that support a unique origin for all dioecious species of Rumex and two separate lineages for species with single or complex sex-chromosome systems. Our data also support an accelerated degeneration of Y-chromosome in XX/XY(1)Y(2) species by the accumulation of satellite-DNA sequences. On the other hand, the particular non-recombining nature of the Y chromosomes of R. acetosa and their closest relatives lead to a particular mode of evolution of RAYSI sequences. Thus, mechanisms leading to the suppression of recombination between the Y chromosomes reduced the rate of concerted evolution and gave rise to the apparition of different RAYSI subfamilies. Thus, R. acetosa and R. intermedius have two subfamilies (the RAYSI-S and RAYSI-J subfamilies and the INT-A and INT-B subfamilies, respectively), while R. papillaris only has one, the RAYSI-J subfamily. The RAYSI-S and RAYSI-J subfamilies of R. acetosa differ in 83 fixed diagnostic sites and several diagnostic deletions while the INT-A and the INT-B of R. intermedius differ in 27 fixed diagnostic sites. Pairwise comparisons between RAYSI-S and RAYSI-J sequences or between INT-A and INT-B sequences revealed these sites to be shared mutations detectable in repeats of the same variant in same positions. Evolutionary comparisons suggest that the subfamily RAYSI-J has appeared in the common ancestor of R. acetosa and R. papillaris, in which RAYSI-J has replaced totally (R. papillaris) or almost totally the ancestral sequence (R. acetosa). This scenario assumes that RAYSI-S sequences should be considered ancestral sequences and that a secondary event of subfamily subdivision should be occurring in R. intermedius, with their RAYSI subfamilies more closely related to one another than with other RAYSI sequences. Our analysis suggests that the different subfamilies diverged by a gradual and cohesive way probably mediated by sister-chromatid interchanges while their expansion or contraction in number might be explained by alternating cycles of sudden mechanisms of amplification or elimination.
Abstract: Rumex acetosa is characterized by a multiple chromosome system (2n = 12 + XX for females, and 2n = 12 + XY1Y2 for males), in which sex is determined by the ratio between the number of X chromosomes and autosome sets. For a better understanding of the molecular structure and evolution of plant sex chromosomes, we have generated a sex chromosome specific library of R. acetosa by microdissection. The screening of this library has allowed us to identify 5 repetitive DNA families that have been characterized in detail. One of these families, DOP-20, has shown no homology with other sequences in databases. Nevertheless, the putative proteins encoded by the other 4 families, DOP-8, DOP-47, DOP-60, and DOP-61, show homology with proteins from different plant retroelements, including poly proteins from Ty3-gypsy- and Ty1-copia-like long terminal repeat (LTR) retroelements, and reverse transcriptase from non-LTR retro elements. Results indicate that sequences from these 5 families are dispersed throughout the genome of both males and females, but no appreciable accumulation or differentiation of these types of sequences have been found in the Y chromosomes. These repetitive DNA sequences are more conserved in the genome of other dioecious species such as Rumex papillaris, Rumex intermedius, Rumex thyrsoides, Rumex hastatulus, and Rumex suffruticosus, than in the polygamous, gynodioecious, or hermaphrodite species Rumex induratus, Rumex lunaria, Rumex con glom er atus, Rumex crispus, and Rumex bucephalo phorus, which supports a single origin of dioecious species in this genus. The implication of these transposable elements in the origin and evolution of the heteromorphic sex chromosomes of R. acetosa is discussed.
Abstract: One characteristic of sex chromosomes is
the accumulation of a set of different types of repetitive
DNA sequences in the Y chromosomes. However,
little is known about how this occurs or about
how the absence of recombination affects the subsequent
evolutionary fate of the repetitive sequences
in the Y chromosome. Here we compare the evolutionary
pathways leading to the appearance of three
different families of satellite-DNA sequences within
the genomes of Rumex acetosa and R. papillaris, two
dioecious plant species with a complex XX/XY1Y2
sex-chromosome system. We have found that two of
these families, one autosomic (the RAE730 family)
and one Y-linked (the RAYSI family), arose independently
from the ancestral duplication of the same
120-bp repeat unit. Conversely, a comparative analysis
of the three satellite-DNA families reveals no
evolutionary relationships between these two and the
third, RAE180, also located in the Y chromosomes.
However, we have demonstrated that, regardless of
the mechanisms that gave rise to these families, satellite-
DNA sequences have different evolutionary
fates according to their location in different types of
chromosomes. Specifically, those in the Y chromosomes
have evolved at half the rate of those in the
autosomes, our results supporting the hypothesis that satellite DNAs in nonrecombining Y chromosomes undergo lower rates of sequence evolution and homogenization than do satellite DNAs in autosomes.
Abstract: The genus Rumex includes hermaphroditic, polygamous, gynodioecious, monoecious, and dioecious species, with the dioecious species being represented by different sex-determining mechanisms and sex-chromosome systems. Therefore, this genus represents an exceptional case study to test several hypotheses concerning the evolution of both mating systems and the genetic control of sex determination in plants. Here, we compare nuclear intergenic transcribed spacers and chloroplast intergenic sequences of 31 species of Rumex. Our phylogenetic analysis supports a systematic classification of the genus, which differs from that currently accepted. In contrast to the current view, this new phylogeny suggests a common origin for all Eurasian and American dioecious species of Rumex, with gynodioecy as an intermediate state on the way to dioecy. Our results support the contention that sex determination based on the balance between the number of X chromosomes and the number of autosomes (X/A balance) has evolved secondarily from male-determining Y mechanisms and that multiple sex-chromosome systems, XX/XY1Y2, were derived twice from an XX/XY system. The resulting phylogeny is consistent with a classification of Rumex species according to their basic chromosome number, implying that the evolution of Rumex species might have followed a process of chromosomal reduction from x = 10 toward x = 7 through intermediate stages (x = 9 and x = 8).
Notes: Recommended by Faculty of 1000 Biology (http://www.f1000biology.com/article/id/1027433/evaluation)
Abstract: The molecular structure of the exceptional telomeres
of six plant species belonging to the order Asparagales
and two species of the order Liliales was analyzed using Southern
blot and fluorescence in situ hybridization. Three different
situations were found, namely: i) In the two Liliales species,
Tulipa australis (Liliaceae) and Merendera montana (Colchicaceae),
the chromosome ends display hybridization signals with
oligonucleotides resembling telomere repeats of both plants
(TTTAGGG)n and vertebrates (TTAGGG)n. ii) Asparagales
species such as Phormium tenax (Hemerocallidaceae), Muscari
comosum (Hyacinthaceae), Narcissus jonquilla (Amaryllidaceae)
and Allium sativum (Alliaceae) lack both the plant telomere
repeats and the vertebrate telomere repeats. iii) Two other
Asparagales species, Aloe vera (Asphodelaceae) and an Iris
hybrid (Iridaceae), display positive hybridization with the vertebrate
telomere repeats but not with the plant telomere
repeats. Southern blot hybridization revealed concurring results.
On this basis, the composition of the telomere structure in
this plant group is discussed.
Abstract: In a previous paper [1] we showed that Y-linked satellite-DNA
sequences of Rumex (Polygonaceae) present reduced rates of evolution in
relation to other autosomal satellite-DNA sequences. In the present paper, we
re-analyze the same set of sequences by using the satDNA Analyzer 1.2
software, specifically developed by us for analysis of satellite DNA evolution.
We do not only confirm our previous findings but also prove that the satDNA
Analyzer 1.2 package constitutes a powerful tool for users interested in
evolutionary analysis on satellite-DNA sequences. In fact, we are able to gather
more accurate calculations regarding location of Strachan positions and
evolutionary rates calculations, among others useful statistics. All results are
displayed in a very comprehensive multicoloured graphic representation easy to
use as an html file. Furthermore, satDNA Analyzer 1.2 is a time saving feature
since every utility is automatized and collected in a single software package, so
the user does not need to use different programs. Additionally, it significantly
reduces the rate of data miscalculations due to human errors, very prone to
occur specially in large files.
Abstract: One characteristic feature of the sex chromosomes is the accumulation of a sort of repetitive DNA
sequences in the Y chromosomes. However little is known about how this occurs and about how the
absence of recombination affects the subsequent evolutionary fate of the repetitive sequences in the Y
chromosome. Here, we compare the evolutionary pathways leading to the accumulation of three families
of satellite DNA sequences within the genomes of Rumex acetosa and Rumex papillaris, two dioecious
plant species with a complex XX/XY1Y2
sex-chromosome system. We have found that two of these
families, one autosomic and one Y-linked, shared a common origin. Conversely, they are not related in
origin with the third one, also located in the Y chromosomes. However, we have demonstrated that the
two satellite DNA families in the Y chromosomes of these species have reduced rates of evolution and
sequence homogenisation, in relation to those found for the satellite DNAs in autosome.
Abstract: Although satellite DNAs normally evolve concertedly, resulting in intra-specific sequence
homogenization and inter-specific divergence, the existence of several mechanisms leading to satellite
DNA subfamilies formation has been largely reported. Among the proposed causes, the existence of
higher-order repeats, the population size and recombination disruptions are supposed to be the major
factors.
Sex chromosomes represent good examples not only of repetitive sequence accumulation sites, but also of
systems with an almost complete lack of recombination, and as such, they are ideal candidates for
subfamily formation.
Specifically, in this study we analysed the sex-chromosome system of the dioecious species Rumex
acetosa (Polygonaceae) paying special attention to a Y-specific satellite DNA family, RAYSI. Rumex
acetosa is a classical model in sex-determining mechanisms research due to the presence of a complex
sex system comprising of females 2n=14 (XX + 12 autosomes) and males 2n=15 (XY1Y2 + 12
autosomes). The two Y chromosomes appear not to recombine during male meiosis and both of them will
only pair with the ends of each X chromosome arm. In this study, by means of molecular as well as
fluorescent in situ hibridization techniques, we demonstrate the existence of two subfamilies of the
RAYSI family (called RAYSI-S and RAYSI-J) looking at both fixed positions (homogenizated positions)
and also their differential chromosome location. Causes and implications are discussed as well.
