1,721,006 research outputs found
Analysis of the repetitive component and retrotransposon population in the genome of a marine angiosperm, Posidonia oceanica (L.) Delile.
No full textPosidonia oceanica is amonocotyledonousmarine plant that plays a crucial role inmaintaining theMediterranean
environment.Despite its ecological importance, basic knowledge of the functional and structural genomics of this
species is still limited, as it is for the other seagrasses. Here, for the first time, we report data on the repetitive
component of the genome of this seagrass using a lowcoverage of Illumina sequences and different assembly approaches.
A dataset of 19,760 assembled sequences, mostly belonging to the repetitive fraction of the genome,
was produced and annotated. Based on mapping Illumina reads onto this dataset, the genome structure of
P. oceanica and its repetitive component was inferred. A very large proportion of the genome is represented by
long-terminal-repeat (LTR) retrotransposons of both the Copia and Gypsy superfamilies. Posidonia LTRretrotransposons
were classified and their sequences analysed. Gypsy elements belong to three main lineages,
while Copia ones belong to seven lineages. Gypsy elements were more represented than Copia ones in the set
of assembled sequences and in the genome. Analysis of sequence variability indicated that Gypsy lineages have
experienced amplification in more recent times compared to Copia ones
LTR-retrotransposons as major drivers of genome diversification across the genus Helianthus L.
No full textVariability in LTR-retrotransposon redundancy and proximity to genes between sunflower cultivars and wild accessions.
Full text linkThe sunflower (Helianthus annuus) genome contains a very large proportion of transposable
elements, especially long-terminal-repeat retrotransposons. Being knowledge on the
retrotransposon-related variability within this species still limited, we performed a quantitative and
qualitative survey of intraspecific variation of LTR-retrotransposon fraction of the genome across
different genotypes of H. annuus, using next generation sequencing technologies. First, we
characterized the repetitive component of a sunflower homozygous experimental line, using 454
reads, and prepared a library of retrotransposon-related sequences. Then, we analysed the LTRretrotransposon
fraction of 7 wild accessions and 8 cultivars of sunflowerby mapping Illumina reads
of the 15 genotypes onto the library. We observed large variations in redundancy among genotypes,
at both superfamily and family levels. In another analysis, we mapped Illumina paired reads of the
15 genotypes onto two sets of sequences, i.e. retrotransposons and protein-encoding sequences, and
evaluated the extent of retrotransposon proximity to genes in the 15 genomes by counting the
number of paired reads of which one mapped onto a retrotransposon and the other onto a gene.
Large variability among genotypes was ascertained also for retrotransposonproximity to genes.
Both retrotransposon redundancy and proximity to genes showed different behaviour among
retrotransposon families and also between cultivated and wild genotypes, indicating a possible
involvement in sunflower domestication
Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome
No full textShort Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most
eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE
identification has been carried out only in a limited number of plant species. This lack of information is apparent
especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific
bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying
SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one
of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362 bp in
length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority
of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis
of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive
tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to
SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon
expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids.
Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE
identification. Applying this pipeline will favour further structural and functional analyses on these relatively
unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will
allow establishing general evolutionary patterns for this kind of repeats in plants
Retrotransposon copy number variation between wild and cultivated sunflowers
No full textSunflower (Helianthus annuus) is an important crop species of the Asteraceae family. Despite its economic relevance, a detailed structural analysis of its genome is still missing. We have investigated the repetitive fraction of the sunflower genome, especially transposable elements, which constitute a major driver of genome size increasing, are able to cause lethal mutations, and may also play a role in the epigenetic setting of the genome.
We first characterized the repetitive component of a sunflower homozygous experimental line, using 454 reads, then extended our studies to 7 wild accessions and 8 cultivars using Illumina reads.
Using RepeatExplorer, we obtained 288 clusters representing the most representative repeat families in a random sample of sunflower reads. The annotated clusters were collected in a library, and a phylogenetic analysis of conserved regions of LTR-retroelement protein domains was performed. This library was used as reference to be mapped with reads of all the accessions. We identified 19 clusters belonging to Gypsy and Copia superfamilies showing different redundancy between cultivars and wild accessions, possibly involved in sunflower domestication
A survey of variability in LTR-retrotransposon abundance and proximity to genes between wild and cultivated sunflower genotypes
Full text linkSunflower (Helianthus annuus) is an important crop species of the Asteraceae family. Recent
characterization of sunflower repetitive fraction has shown that the genome of this species contains
a very large proportion of transposable elements, especially long-terminal-repeat retrotransposons.
However, knowledge on the retrotransposon-related variability within this species is still limited.
We used next generation sequencing technologies to perform a quantitative and qualitative survey
of intraspecific variation of the retrotransposon fraction of the genome across different genotypes of
H. annuus. First, we characterized the repetitive component of a sunflower homozygous
experimental line, using 454 reads, and prepared a library of retrotransposon-related sequences.
Then, we analysed the retrotransposon fraction of 7 wild accessions and 8 cultivars of H. annuus by
mapping Illumina reads of the 15 genotypes onto the library. We observed large variations in
redundancy among genotypes, at both superfamily and family levels. In another analysis, we
mapped Illumina paired reads of the 15 genotypes onto two sets of sequences, i.e. retrotransposons
and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in
the 15 genomes by counting the number of paired reads of which one mapped onto a
retrotransposon and the other onto a gene. Large variability among genotypes was ascertained also
for retrotransposon proximity to genes. Both retrotransposon redundancy and proximity to genes
showed different behaviour among retrotransposon families and also between cultivated and wild
genotypes, indicating a possible involvement in sunflower domestication
A comparison of methods for LTR-retrotransposon insertion time profiling in the Populus trichocarpa genome
No full textTwo different methods of calculating insertion profiles of long terminal repeat (LTR)
retrotransposons in the genome are compared, analysing six retrotransposon lineages in Populus
trichocarpa. The first method consists of aligning the two long terminal repeats of an element
and translating nucleotide differences into years, based on nucleotide synonymous substitution
rate. The second method infers proliferation time profile of a group of retrotransposons by
analysing pairwise genetic distances between reverse transcriptase (RT)-encoding sequences
that belong to paralogous elements of the same group and translating them into insertion dates
using the same mutation rate as for the first method. The two methods gave quite different
results, probably because they are related to different populations of retrotransposons. The RTbased
method can provide reliable insertion profiles; the method based on LTRs can be used to
date individual elements and to obtain reliable profiles related to the most recent evolutionary
periods. We suggest that both methods should be used to evaluate the dynamics of the
retrotransposon component of a genome
LTR-retrotransposons as major drivers of genome diversification across the genus Helianthus L.
No full textTransposons play a key role in the evolution of species leading to rapid
genome remodeling. Herein, we study the variability of the repetitive
fraction of the genome in the genus Helianthus which recently
has emerged as model for studying the genetics of speciation and
adaptation. After determining the relative genome size of ten species
and one subspecies of Helianthus, different assembling and clustering
approaches were carried on by using next generation sequencing
techniques to explore the repetitive component of the genomes. On
average, repetitive DNA in Helianthus species represented more than
75% of the genome, with long terminal repeat retrotransposons (LTRREs)
being the vast majority of repetitive sequences. Prevalence of Gypsy
over Copia superfamily was observed; and, among Gypsy lineages,
Chromovirus was by far the most represented in each analyzed species.
Moreover, considerable variability in the abundance of diverse LTR-RE
lineages was found across the genus, showing differences especially
between annual and perennial species. In some cases, such variation
produced relevant effects on species genome size which was only partly
related to the ploidy level
A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome
Full text linkIn this work, we report a comprehensive study of long terminal repeat retrotransposons of Populus trichocarpa. Our research group studied the retrotransposon component of the poplar genome in 2012, isolating 1479 putative full-length elements. However, in that study, it was not possible to identify the superfamily to which the majority of isolated full-length elements belonged. Moreover, during recent years, the genome sequence of P. trichocarpa has been updated, deciphering thek sequences of a number of previously unresolved loci. In this work, we performed a complete scan of the updated version of the genome sequence to isolate full-length retrotransposons based on sequence and structural features. The new dataset showed a reduced number of elements (958), and 21 fulllength elements were discovered for the first time. The majority of retroelements belonged to the Gypsy superfamily (57%), while Copia elements amounted to 41.1% of the dataset. Fulllength elements were dispersed throughout the chromosomes. However, Gypsy and, to a lesser extent, Copia elements accumulated preferentially at putative centromeres. Gypsy elements were more active in retrotransposition than Copia elements, with the exception of during the past million years, in which Copia elements were the most active. Improved annotation procedures also allowed us to determine the specific lineages to which isolated elements belonged. The three Gypsy lineages, Athila, OGRE, and Chromovirus (in the decreasing order), were by far the most abundant. On the other hand, each identified Copia lineage represented less than 1 % of the genome. Significant differences in the insertion age were found among lineages, suggesting specific activation mechanisms. Moreover, different chromosomal regions were affected by retrotransposition in different ages. In all chromosomes, putative
pericentromeric regions were filled with elements older than themean insertion age. Overall, results demonstrate structural and functional differences among plant retrotransposon lineages and further support the view of retrotransposons as a community of different organisms in the genome
CHARACTERIZATION OF THE REPETITIVE COMPONENT OF THE FIG (FICUS CARICA) GENOME
Full text linkThe fig tree (Ficus carica L.) is an ancient crop with promising perspectives for Italian
Mediterranean agriculture. Fig is widely grown throughout the temperate world, both for its fruit
and as an ornamental plant. In recent years, large interest arose on the nutraceutical properties of fig
fruit, especially dried.
Considering the low level of genetic improvement of the present fig cultivars, a genomic
approach can be useful to speed up the development of new cultivars. Despite its economic, cultural
and ecological importance in many areas of the world, fig is however still poorly characterized at
genetic and genomic level compared to other fruit tree crops.
Ficus is one of the thirty-seven genera of the Moraceae family. Ficus carica L. is a diploid
species, with a small/medium genome size. The aim of this work was to gain an insight into fig
genome structure.
After DNA isolation, Illumina sequencing was carried out using both HiSeq2000 and MiSeq
platforms. Different assembling and clustering approaches were performed for characterizing the
repetitive component of the genome. The fig genome resulted composed for around 60% of
repeated sequences, of which none was especially redundant. All types of repeats already described
in plants were found, however the majority of assembled repeats were not identified. Among
identified repeats, ribosomal DNA constituted around 5% of the genome. The most represented
repeats were LTR-retrotransposons (20% of the genome), with Gypsy elements much more frequent
than Copia. LTR-retrotransposons were also characterized with regard to their age of insertion in
the genome.
A comparative analysis of Ficus carica, Morus notabilis and Malus domestica was carried out
using RepeatExplorer, performing a hybrid clustering of Illumina sequence reads. These species all
belong to the Rosales order: F. carica and M. notabilis to the Moraceae family while M. domestica
to the Rosaceae family. Results highlighted a large diversification among the repetitive component
of the genomes of these related species, even within the Moraceae family. In fact, excluding
ribosomal DNA related clusters, only 15 out of 227 hybrid repeat clusters were found across all the
species, while fig and M. notabilis shared only 96/227 clusters. Finally, 29 clusters were specific to
the fig, 24 to M. notabilis and 45 to M. domestica.
This comparison was complemented by means of phylogenetic analysis. Paralogs of the
reverse transcriptase coding domain were identified in the three aforementioned species and used to
build Neighbor-Joining trees for both Ty1-Copia and Ty3-Gypsy elements.
Studies are in progress to extend the characterization of fig genome to its gene component,
leading to the identification of important genes involved in agronomic and productive traits as fruit
production and quality, biotic and abiotic stress resistance, and synthesis and accumulation of
metabolites. These data will offer a first start for new opportunities of fig breeding
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