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Herbarium DNA degradation -Falling to pieces non-randomly / Freet T. Bakker in Bauhinia, 29 (2023) 

Public Citation [article]  inBauhinia > 29 (2023) . - 63-74 Titre : Herbarium DNA degradation -Falling to pieces non-randomly Type de document : Imprimé Auteurs : Freet T. Bakker ; Lia Hemerik Année de publication : 2023 Article en page(s) : 63-74 Langues : Multilingue (mul) Catégories : [CBNPMP-Thématique] Collections-herbiers Résumé : Post-mortem damage in herbarium DNA, mostly from 18th and 19th century collections, and with specimens usually heat-treated for conservation, consists mainly of genome fragmentation (single- and double-stranded breaks) rather than miscoding lesions. With typical herbarium DNA fragment sizes encountered (20–200 6 https://www.jstor.org/stable/1220096 bp) this easily leads to insert sizes in library construction being smaller than Illumina read lengths applied (i.e. 100–250 bp). Using a previously-published series of 56 genome-skimmed herbarium DNA extracts representing 10 angiosperm families, overlapping read pairs were found to occur in roughly 80 % of all read pairs obtained. After merging such overlapping pairs, the resulting fragments and their length-distributions are considered to reflect actual DNA fragmentation. Similar to occurrence in ancient DNA, we found over-representation of purines at fragment-ends in herbarium material. Distributions of fragment lengths fit gamma rather than exponential distributions, without apparent correlation with specimen age. The observed gamma distributions would indicate higher-order degradation kinetics, implying multiple processes acting during degradation. Possibly, the genome skimming data used here, in which repetitive sequences or compartments are over-represented, has biased genomic fragment-length distributions and half-lives as compared to the non-repetitive fraction of plant genomes, but no data was available to test this hypothesis. Overall, our results imply that we cannot confirm whether a plant archival DNA half-live exists and what its rate would be. Lien pérenne : DOI : 10.12685/bauhinia.1378 Permalink : https://biblio.cbnpmp.fr/index.php?lvl=notice_display&id=152760 Bakker, Freet T., Hemerik, Lia 2023 Herbarium DNA degradation -Falling to pieces non-randomly. Bauhinia, 29: 63-74.

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Improving procedures for obtaining Sanger sequences from old herbarium specimens / Mika Bendiksby in Bauhinia, 29 (2023) 

Public Citation [article]  inBauhinia > 29 (2023) . - 75-84 Titre : Improving procedures for obtaining Sanger sequences from old herbarium specimens Type de document : Imprimé Auteurs : Mika Bendiksby ; Lisbeth Thorbek ; Charlotte Bjorå ; Rune Halvorsen Année de publication : 2023 Article en page(s) : 75-84 Langues : Multilingue (mul) Catégories : [CBNPMP-Thématique] Collections-herbiers Résumé : Because DNA degrades over time, extracting DNA of sufficient quality for sequencing is presumed to be more difficult from older than younger herbarium specimens. Although massive parallel sequencing techniques have clear advantages when it comes to sequencing ancient DNA, Sanger sequencing is still in frequent use, prompting us to test and improve its application on herbarium specimens. During molecular phylogenetic investigations of the subfamily Lamioideae (Lamiaceae) and subgroups, we extracted DNA from 651 herbarium specimens collected between 1826 and 2006 using regular mini-prep methods. The aim was to obtain DNA of sufficient quality for Sanger sequencing of various plastid and nuclear genetic markers. Here, we report successful Sanger sequencing of the commonly used plastid marker, rps16, as a conservative measure of DNA quality, and logistic regression to investigate the relationship between age of the material and DNA quality. Our result indicates that the upper age limit for obtaining DNA suitable for Sanger,sequencing from herbarium specimens using regular mini-prep DNA extraction methods has not been reached. After simple modifications to the regular DNA miniprep and PCR procedures, at least one genetic marker was successfully sequenced for about 90 % of the specimens tested, the oldest being 168 years old. Jointly, despite the technique’s drawbacks, these results demonstrate a high success rate of Sanger sequencing of herbarium specimens. Lien pérenne : DOI : 10.12685/bauhinia.1353 Permalink : https://biblio.cbnpmp.fr/index.php?lvl=notice_display&id=152763 Bendiksby, Mika, Thorbek, Lisbeth, Bjorå, Charlotte, Halvorsen, Rune 2023 Improving procedures for obtaining Sanger sequences from old herbarium specimens. Bauhinia, 29: 75-84.

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SNP genotyping and environmental niche modelling using herbarium specimens of the northern dragonhead, Dracocephalum ruyschiana (Lamiaceae) / Malene Nygaard in Bauhinia, 29 (2023) 

Public Citation [article]  inBauhinia > 29 (2023) . - 127-128 Titre : SNP genotyping and environmental niche modelling using herbarium specimens of the northern dragonhead, Dracocephalum ruyschiana (Lamiaceae) Type de document : Imprimé Auteurs : Malene Nygaard ; Alexander Kopatz ; James M.D. Speed ; Michael D. Martin ; Tommy Presto ; Kleven Oddmund Année de publication : 2023 Article en page(s) : 127-128 Langues : Multilingue (mul) Catégories : [CBNPMP-Thématique] Collections-herbiers Mots-clés : Dracocephalum ruyschiana Résumé : Maintenance of genetic diversity is a central aim of species conservation, given its positive effect on species survival and adaptation in a changing environment. Data from different time points is key for understanding how populations behave under various conditions. In this regard, herbarium specimens are an invaluable source of information from the past. Still, utilizing archived biological material for studying trends of genetic diversity offers challenges such as DNA degradation and the lack of standardized, cost- and time efficient methods. Lien pérenne : DOI : 10.12685/bauhinia.1375 Permalink : https://biblio.cbnpmp.fr/index.php?lvl=notice_display&id=152769 Nygaard, Malene, Kopatz, Alexander, Speed, James M.D., Martin, Michael D., Presto, Tommy, Oddmund, Kleven 2023 SNP genotyping and environmental niche modelling using herbarium specimens of the northern dragonhead, Dracocephalum ruyschiana (Lamiaceae). Bauhinia, 29: 127-128.

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Looking into 16th-century botanical history to understand the complex taxonomy of Tulipa sylvestris in Europe / Anastasia Stefanaki in Bauhinia, 29 (2023) 

Public Citation [article]  inBauhinia > 29 (2023) . - 137-138 Titre : Looking into 16th-century botanical history to understand the complex taxonomy of Tulipa sylvestris in Europe Type de document : Imprimé Auteurs : Anastasia Stefanaki ; Tilmann Walter ; Tinde R. van Andel (1967-) Année de publication : 2023 Article en page(s) : 137-138 Langues : Multilingue (mul) Catégories : [CBNPMP-Thématique] Collections-herbiers Mots-clés : Tulipa sylvestris L., 1753  Tulipa australis Link Résumé : Tulipa sylvestris is a small yellow tulip that was introduced to northern Europe in the 16th century. Unlike the tulips that came from the Ottoman empire and gave birth to modern cultivars, T. sylvestris came from the Mediterranean and became a garden escapee that successfully naturalized across Europe. Its taxonomy is complex due to morphological diversity, polyploidy and naturalization of cultivated plants. Two subspecies are provisionally accepted in Europe: subsp. australis, a diploid native in the Mediterranean (up to Central Asia) that grows on mountainous rocky grasslands, on poor soils; and subsp. sylvestris a tetraploid that is naturalized across Europe and grows in rich soils at low altitudes, mainly at field margins, vineyards and gardens. Sometimes these two subspecies are regarded as distinct species, but their taxonomic delimitation is unclear. Lien pérenne : DOI : 10.12685/bauhinia.1369 Permalink : https://biblio.cbnpmp.fr/index.php?lvl=notice_display&id=152772 Stefanaki, Anastasia, Walter, Tilmann, Andel, Tinde R. van (1967-) 2023 Looking into 16th-century botanical history to understand the complex taxonomy of Tulipa sylvestris in Europe. Bauhinia, 29: 137-138.

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