Cytological evidence for gametophytic self-incompatibility in the genus Veronica

The self-incompatibility (SI) of 3 Middle East Veronica species (V. filiformis, V. gentianoides, V. teucrium) is studied, for the first time, by pollination and pollen tube growth experiments. Cytological observations of the self-pollen tubes within the pistils permit a conclusion about the presence of a gametophytic SI system in the first 2 species. The investigated population of the third is self-compatible and confirms the facultative trait of its self-sterility. The presence of a gametophytic SI system in 2 of them suggests the putative conservation of this SI system within the genus Veronica (Plantaginaceae) and could be related to the well-known gametophytic SI system present in the other Plantaginaceae genus, Antirrhinum

Exploring the intricate evolutionary history of the diploid-polyploid complexVeronica subsection Pentasepalae(Plantaginaceae)

[EN]Veronica subsection Pentasepalae is a diploid–polyploid complex of c. 20 species distributed in Eurasia and North Africa, in which species boundaries are difficult to determine. Here, we present the first comprehensive phylogenetic analysis of V. subsection Pentasepalae based on nucleotide sequences [internal transcribed spacer (ITS) and the plastid trnH-psbA and ycf6-psbM spacers] combined with ploidy estimations. Our results support the monophyly of the subsection. Five well-supported clades are recovered in the ITS sequence analyses, corresponding to broad geographical areas. The causes of the extensive incongruence found between the ITS and plastid DNA datasets, namely incomplete lineage sorting and/or hybridization and polyploidization, are discussed. Most of the diploids traditionally recognized based on morphological characters and one tetraploid are each recovered as monophyletic by the ITS sequence analyses. The Balkan species V. kindlii is resurrected. DNA ploidy level for V. teucrioides is reported here for the first time (2x). Diploid populations have been found for V. orbiculata, which was previously thought to be only tetraploid. Past contact in the amphi-Adriatic area between V. orsiniana and V. orbiculata is suggested. Finally, molecular analyses show that diploid V. jacquinii and diploid V. orbiculata are unrelated. This study contributes to our understanding of the evolutionary history of polyploid complexes, especially those in southern Europe, and highlights the importance of using multiple lines of evidence to investigate species boundaries in such actively diversifying groups

High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

Siadjeu C, Pucker B, Viehöver P, Albach DC, Weisshaar B. High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing. Genes. 2020;11(3): 274.Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9941 non-coding RNA genes were predicted, and functional annotations were assigned

DNA extraction from old herbarium material of Veronica subgen. Pseudolysimachium (Plantaginaceae)

Herbarium specimens have become a major source of information in molecular biodiversity research, framing the term "herbarium genomics". However, obtaining good DNA from old herbarium specimens is still a challenge. Currently, DNA extraction methods from old herbarium material often yield highly degraded and fragmented DNA. A number of studies have discussed such methods, especially how to avoid further DNA fragmentation. This study aims to compare different DNA extraction methods applied to old herbarium material from Veronica subg. Pseudolysimachium. One such method is a CTABbased DNA extraction followed by a clean-up with paramagnetic beads that is used in the Jodrell Laboratory, Royal Botanic Gardens Kew, UK. This method was compared to a modified NucleoSpin Plant II protocol, based on silica columns, as used at the Technical University Munich-Freising, which was already successfully used for extracting DNA from a Linnean type specimen. Further tests were conducted on the influence of incubation time on the CTAB DNA extraction protocol with a subsample of specimens. Our preliminary results suggest that CTAB DNA extraction might have some advantages in specific cases but also that silica column-based methods have fewer problems with contamination by polysaccharides and polyphenolic compounds. Regarding the incubation time, we did not observe a clear pattern, but we developed several ideas on how to proceed with tests to find an optimal DNA extraction protocol to deal with highly fragmented DNA. Taking practical considerations into account, the column-based method proves to be preferable, especially when trying to reduce the amount of leaf tissue used, but further modifications of both methods should be explored

Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

<p>Abstract</p> <p>Background</p> <p>In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarifying borders of and relationships among lamialean families, has been hindered by largely unresolved trees in the past.</p> <p>Results</p> <p>Our analysis of the rapidly evolving <it>trnK/matK</it>, <it>trnL-F </it>and <it>rps16 </it>chloroplast regions enabled us to infer more precise phylogenetic hypotheses for the Lamiales. Relationships among the nine first-branching families in the Lamiales tree are now resolved with very strong support. Subsequent to Plocospermataceae, a clade consisting of Carlemanniaceae plus Oleaceae branches, followed by Tetrachondraceae and a newly inferred clade composed of Gesneriaceae plus Calceolariaceae, which is also supported by morphological characters. Plantaginaceae (incl. Gratioleae) and Scrophulariaceae are well separated in the backbone grade; Lamiaceae and Verbenaceae appear in distant clades, while the recently described Linderniaceae are confirmed to be monophyletic and in an isolated position.</p> <p>Conclusions</p> <p>Confidence about deep nodes of the Lamiales tree is an important step towards understanding the evolutionary diversification of a major clade of flowering plants. The degree of resolution obtained here now provides a first opportunity to discuss the evolution of morphological and biochemical traits in Lamiales. The multiple independent evolution of the carnivorous syndrome, once in Lentibulariaceae and a second time in Byblidaceae, is strongly supported by all analyses and topological tests. The evolution of selected morphological characters such as flower symmetry is discussed. The addition of further sequence data from introns and spacers holds promise to eventually obtain a fully resolved plastid tree of Lamiales.</p

Is genome downsizing associated with diversification in polyploid lineages of Veronica?

[EN] The study of genome size evolution in a phylogenetic context in related polyploid and diploid lineages can help us to understand the advantages and disadvantages of genome size changes and their effect on diversification. Here, we contribute 199 new DNA sequences and a nearly threefold increase in genome size estimates in polyploid and diploid Veronica (Plantaginaceae) (to 128 species, c. 30% of the genus) to provide a comprehensive baseline to explore the effect of genome size changes. We reconstructed internal transcribed spacer (ITS) and trnL-trnL-trnF phylogenetic trees and performed phylogenetic generalized least squares (PGLS), ancestral character state reconstruction, molecular dating and diversification analyses. Veronica 1C-values range from 0.26 to 3.19 pg. Life history is significantly correlated with 1C-value, whereas ploidy and chromosome number are strongly correlated with both 1C- and 1Cx-values. The estimated ancestral Veronica 1Cx-value is 0.65 pg, with significant genome downsizing in the polyploid Southern Hemisphere subgenus Pseudoveronica and two Northern Hemisphere subgenera, and significant genome upsizing in two diploid subgenera. These genomic downsizing events are accompanied by increased diversification rates, but a ‘core shift’ was only detected in the rate of subgenus Pseudoveronica. Polyploidy is important in the evolution of the genus, and a link between genome downsizing and polyploid diversification and species radiations is hypothesized

Polyploidy on Islands: Its Emergence and Importance for Diversification.

Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa

Polyploidy on Islands: Its Emergence and Importance for Diversification.

Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa