The intergenic spacer region of the rDNA in Olea europaea L.

Maggini, F.; Gelati, M. T.; Spolverini, Michela; Frediani, M.

doi:10.1007/s11295-007-0109-x

Cited by 14 publications

(12 citation statements)

References 28 publications

(41 reference statements)

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“…The non‐transcribed region of the intergenic spacer (IGS) remains incomplete due to short repeated and inverted elements (e.g. Maggini et al ., ) making the assembly very difficult with our approach. Overall, 8281 paired‐end reads ( c. 0.08% of the total reads) matched to the nrDNA region including the complete sequence of the 18S, ITS1, 5.8S, ITS2 and 26S subregions (5822 bp) with an average size of inserts of 123 bp (see http://onlinelibrary.wiley.com/doi/10.1111/bij.12509/suppinfo).…”

Section: Resultssupporting

confidence: 87%

Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico

Zedane

Hong‐Wa

Murienne

et al. 2015

Biol. J. Linn. Soc.

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Museum collections are essential for understanding biodiversity and next-generation sequencing methods (NGS) offer new opportunities to generate genomic data on specimens of extinct species for phylogenetic and other studies. Hesperelaea is a monotypic Oleaceae genus that was collected only once, 140 years ago on Guadalupe Island, Mexico. This lineage is almost certainly extinct, and has been considered an insular paleoendemic of unknown relationship within subtribe Oleinae. Here, a genome skimming approach was attempted on the H. palmeri specimen to generate genomic data in order to interpret the biogeographic history of Hesperelaea in a phylogenetic framework. Despite highly degraded DNA, we obtained the complete plastome, the nuclear ribosomal DNA cluster (nrDNA), and partial sequences of low-copy genes. Six plastid regions and nrDNA internal transcribed spacers were used for phylogenetic estimations of subtribe Oleinae, including data from previous studies. Bayesian and maximum likelihood phylogenies strongly place Hesperelaea within an American lineage that includes Forestiera and Priogymnanthus. Molecular dating suggests an Early Miocene divergence between Hesperelaea and its closest relatives. Our study thus confirms that Hesperelaea was a paleoendemic lineage that likely predates Guadalupe Island, and provides a notable example of the high potential of NGS for analyzing historical herbarium specimens and revolutionizing systematics.

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Section: Resultssupporting

confidence: 87%

Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico

Zedane

Hong‐Wa

Murienne

et al. 2015

Biol. J. Linn. Soc.

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“…However, it shows resemblance to other putative, deviant angiosperm (Quercus petrae/ robur, TCTTTAGGGGGG; Hordeum bulbosum, CATATAGCGCT) and bryophyte promoters (Marchantia polymorpha, TATATGAGGGG; Funaria hygrometrica, TACTATGTGGGG/GATAGGGGG). Increasing evidence suggests that restrictions on the TIS primary sequence could be much more relaxed than previously thought (Fan et al, 1995;Capesius, 1997;Sone et al, 1999;Maggini et al, 2008;Bauer et al, 2009).…”

Section: Discussionmentioning

confidence: 96%

Early evolutionary colocalization of the nuclear ribosomal 5S and 45S gene families in seed plants: evidence from the living fossil gymnosperm Ginkgo biloba

2012

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In seed plants, the colocalization of the 5S loci within the intergenic spacer (IGS) of the nuclear 45S tandem units is restricted to the phylogenetically derived Asteraceae family. However, fluorescent in situ hybridization (FISH) colocalization of both multigene families has also been observed in other unrelated seed plant lineages. Previous work has identified colocalization of 45S and 5S loci in Ginkgo biloba using FISH, but these observations have not been confirmed recently by sequencing a 1.8 kb IGS. In this work, we report the presence of the 45S-5S linkage in G. biloba, suggesting that in seed plants the molecular events leading to the restructuring of the ribosomal loci are much older than estimated previously. We obtained a 6.0 kb IGS fragment showing structural features of functional sequences, and a single copy of the 5S gene was inserted in the same direction of transcription as the ribosomal RNA genes. We also obtained a 1.8 kb IGS that was a truncate variant of the 6.0 kb IGS lacking the 5S gene. Several lines of evidence strongly suggest that the 1.8 kb variants are pseudogenes that are present exclusively on the satellite chromosomes bearing the 45S-5S genes. The presence of ribosomal IGS pseudogenes best reconciles contradictory results concerning the presence or absence of the 45S-5S linkage in Ginkgo. Our finding that both ribosomal gene families have been unified to a single 45S-5S unit in Ginkgo indicates that an accurate reassessment of the organization of rDNA genes in basal seed plants is necessary.

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“…The typical structure of the region near the beginning of the 5′ IGS was also observed in P. viridis and P. canaliculus, even though the sequences were not totally identical. The core promoter contains TATA and GGGG boxes, which appear to be a general feature of rDNA transcription, and this site is immediately preceded by an AT-rich region, which is commonly found in both plants and animals (Vera et al, 2003;Wang et al, 2003;Maggini et al, 2008;Krawczyk et al, 2017) . However, the beginnings of the P. viridis and P. canaliculus IGS genes contained only two and one TATA-box sequences, respectively, and lacked AT-rich regions.…”

Section: Discussionmentioning

confidence: 99%

Peer Review #2 of "Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791) (v0.1)"

2019

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Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA unit (rDNA) sequences of these species were determined for the first time. The gene order, 18S rRNA-internal transcribed spacer (ITS) 1-5.8S rRNA-ITS2-28S rRNA-intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8432 to 8616 bp and from 7597 to 7610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. P. viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three CpG sites with sizes of 440, 1075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together.

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The intergenic spacer region of the rDNA in Olea europaea L.

Cited by 14 publications

References 28 publications

Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico

Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico

Early evolutionary colocalization of the nuclear ribosomal 5S and 45S gene families in seed plants: evidence from the living fossil gymnosperm Ginkgo biloba

Peer Review #2 of "Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791) (v0.1)"

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