47 research outputs found
Different histories of two highly variable LTR retrotransposons in sunflower species
In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution
A survey of variability in LTR-retrotransposon abundance and proximity to genes between wild and cultivated sunflower genotypes
Sunflower (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
Variability in LTR-retrotransposon redundancy and proximity to genes between sunflower cultivars and wild accessions.
The 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
A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome
In 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
Repetitive DNA and plant domestication: variation in copy number and proximity to genes of LTR-retrotransposons among wild and cultivated sunflower (Helianthus annuus) genotypes.
The sunflower (Helianthus annuus) genome 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 15 genotypes - 7 wild accessions and 8 cultivars - of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis we mapped Illumina paired reads to two sets of sequences, i.e. long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was ascertained also for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower
An insight into structure and composition of the fig genome
Ficus carica L. is a diploid species, with a genome size of 0.36 pg/2C, still poorly characterized at genetic and genomic level. With the aim of analysing the fig genome structure, we used Illumina technology to produce 25.64 genome equivalents of 35-511 nt long MiSeq sequences and 12.96 genome equivalents of 25-100 nt long HiSeq paired-end reads. The two libraries were subject to a first assembly run separately, then a hybrid assembly was performed; finally, contigs and supercontigs were scaffolded. This first rough assembly is composed of 264,088 scaffolds, up to 41,760 nt in length, covering 323,708,138 nt, that corresponds to 87.5% of the fig genome, with N50 = 2,523. Masking the scaffolds with a transcriptome of Rosaceae, from which sequences related to repetitive elements were removed, allowed us to establish that coding genes account for at least 6.8% of the fig genome. Gene prediction analysis produced 44,419 putative genes. A sample of around 5,000 predicted genes were annotated with regard to gene ontology and function. Concerning the repetitive component, the fig genome resulted composed for 58.3% of repeated sequences, of which none was especially redundant. Among identified repeats, the most represented were LTR-retrotransposons, with Gypsy elements more frequent than Copia
Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study
Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species.
A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species
essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation
A molecular characterization of the invasive fig weevil Aclees taiwanensis in Italy
An economically important pest of Ficus carica L. is causing severe infestations in many fig nurseries and orchards in Italy. Belonging to the genus Aclees spp. (Coleoptera Curculionidae), this Asiatic species was accidentally introduced in Europe about 15
years ago, in a Tuscan nursery. Originally identified as Aclees cribratus Gyllenhal, it has been then reported as Aclees sp.cf. foveatus
Voss and, more recently, identified as Aclees taiwanensis Kono. A serious damage to fig plants is caused mainly by the larvae,
which drill tunnels into the wood and by adults that feed on buds, leaves and young fruits. The present survey applies molecular
genetics techniques to reconstruct the genetic profile of the species. To this purpose, the partial sequence of the 18S rRNA gene and
the hypervariable region ITS2 of the ribosomal cistron were used as molecular markers for specimens of A. taiwanensis collected
in Italy and Aclees hirayamai Kono from Philippines. The analysis of the partial sequences of the 18S rRNA allowed the distinction
of two haplotypes for each insect, except for a sample from Philippines, for which one haplotype does exist. The use of the ITS2
hypervariable region highlighted the existence of only one haplotype in the Italian accessions. Only in the sample collected in Lucca
(2LU) two haplotypes were highlighted in ITS2. These results are discussed with the occurrence of A. taiwanensis in Italy
Genome-wide identification and characterisation of exapted transposable elements in the large genome of sunflower (Helianthus annuus L.)
Transposable elements (TEs) are an important source of genome variability, playing many roles in the evolution of eukaryotic species. Besides well-known phenomena, TEs may undergo the exaptation process and generate the so-called exapted transposable element genes (ETEs). Here we present a genome-wide survey of ETEs in the large genome of sunflower (Helianthus annuus L.), in which the massive amount of TEs, provides a significant source for
exaptation.
A library of sunflower TEs was used to build TE-specific Hidden Markov Model profiles, to search for all available sunflower gene products. In doing so, 20,016 putative ETEs were identified and further investigated for the characteristics that distinguish TEs from genes, leading to the validation of 3,530 ETEs.
The analysis of ETEs transcription patterns under different stress conditions showed a differential regulation triggered by treatments mimicking biotic and abiotic stress; furthermore, the distribution of functional domains of differentially regulated ETEs revealed a relevant presence of domains involved in many aspects of cellular functions. A comparative genomic investigation was performed including species representative of Asterids and appropriate
outgroups: the bulk of ETEs resulted specific to the sunflower, while few ETEs presented orthologues in the genome of all analysed species, making the hypothesis of a conserved function.
This study highlights the crucial role played by exaptation, actively contributing to species evolution
The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)
Background
The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries, but shares numerous morphological and ecological characteristics with F. vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca
Findings
In this study, the Potentilla micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2,674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of BUSCO genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced
Conclusions
Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca. The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family