| 1. |
- Eriksson, J. S., et al.
(author)
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Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
- 2021
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In: BMC Ecology and Evolution. - : Springer Science and Business Media LLC. - 1472-6785 .- 2730-7182. ; 21:1
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Journal article (peer-reviewed)abstract
- Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult. © 2021, The Author(s).
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| 2. |
- Moiloa, Ntwai A., et al.
(author)
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Biogeographic origins of southern African Silene (Caryophyllaceae)
- 2021
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 162
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Journal article (peer-reviewed)abstract
- Silene (Caryophyllaceae) is distributed predominantly in the northern Hemisphere, where it is most diverse around the Mediterranean Basin. The genus is also well represented in North Africa, extending into tropical, subSaharan and southern Africa. Eight native species are recognized in southern Africa, taxonomically placed in two sections: Elisanthe and Silene s.l. Although the taxonomy of the southern African taxa has recently been revised, their phylogenetic relationships and biogeographic history remain unclear. This study aims to infer the phylogenetic position and geographic origins of the southern African taxa. We generated DNA sequences of nuclear and plastid loci from several individuals belonging to all eight species of Silene recognized from southern Africa, and combined our DNA sequences with existing data representing species from major clades (i.e. sections) based on the recently revised Silene infrageneric taxonomy. We used a Bayesian coalescent species tree continuous diffusion approach to co-estimate the species tree and the ancestral areas of representative members of the genus. Our results show that the perennial southern African members of section Elisanthe form a strongly-supported clade with the Eurasian annual S. noctiflora and the Central Asian perennial S. turkestanica. The rest of the perennial species form a strongly-supported clade together with the annual S. aethiopica, which is nested in a larger Mediterranean clade comprising mostly annual species classified in section Silene s.l. Estimates of ancestral areas indicate a late Pleistocene dispersal to southern Africa from central and East Africa for the sub-Saharan members of section Silene s.l. The Elisanthe clade is inferred to have colonized southern Africa through longdistance dispersal from Eurasia during the late Pleistocene. Our findings support the hypothesis of a relatively recent colonization into southern Africa resulting from two independent dispersal events during the Pleistocene.
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| 3. |
- Quatela, Anne-Sophie, et al.
(author)
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Retrieval of long DNA reads from herbarium specimens
- 2023
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In: AOB PLANTS. - 2041-2851. ; 15:6
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Journal article (peer-reviewed)abstract
- High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads>1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads>1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.
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| 4. |
- Saez, L., et al.
(author)
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Re-establishment of Silene neglecta Ten. (Caryophyllaceae) with taxonomic notes on some related taxa
- 2022
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In: Phytokeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; :195, s. 143-160
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Journal article (peer-reviewed)abstract
- Silene neglecta has been misunderstood and confused with S. nocturna, although several morphological characters (petal shape, calyx indumentum, hairiness of stamen filaments, seed size, seed-coat surface and shape) allow separation of these species. Moreover, S. mutabilis (which has been considered conspecific with S. neglecta) and S. martinolii (an alleged endemic species to south-western Sardinia) are considered here as taxonomic synonyms of S. nocturna and S. neglecta, respectively. These taxonomic conclusions are strongly supported by multivariate morphometric analyses of 21 characters.
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