With the expansion of molecular techniques, the historical collections have become widely used. The last boom started with using next- and second-generation sequencing in which massive parallel sequencing replaced targeted sequencing and third-generation technology involves single molecule technology. Studying plant DNA using these modern molecular techniques plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for taxonomic long-standing issues, specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. The result of these applications is often fragmented DNA. The reason new sequencing approaches have been so successful is that the template DNA needs to be fragmented for proper library building, and herbarium DNA is exactly that. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods, microsatellites, AFLP or next-generation sequencing).
- MeSH
- analýza polymorfismu délky amplifikovaných restrikčních fragmentů MeSH
- chemická frakcionace metody MeSH
- DNA rostlinná genetika izolace a purifikace MeSH
- listy rostlin genetika MeSH
- mikrosatelitní repetice MeSH
- orgánová specificita MeSH
- polymerázová řetězová reakce MeSH
- reagenční diagnostické soupravy MeSH
- rostliny klasifikace genetika MeSH
- sekvenční analýza DNA MeSH
- taxonomické DNA čárové kódování metody MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Callose is a plant-specific polysaccharide (β-1,3-glucan) playing an important role in angiosperms in many developmental processes and responses to biotic and abiotic stresses. Callose is synthesised at the plasma membrane of plant cells by callose synthase (CalS) and, among others, represents the main polysaccharide in the callose wall surrounding the tetrads of developing microspores and in the growing pollen tube wall. CalS proteins involvement in spore development is a plesiomorphic feature of terrestrial plants, but very little is known about their evolutionary origin and relationships amongst the members of this protein family. We performed thorough comparative analyses of callose synthase family proteins from major plant lineages to determine their evolutionary history across the plant kingdom. A total of 1211 candidate CalS sequences were identified and compared amongst diverse taxonomic groups of plants, from bryophytes to angiosperms. Phylogenetic analyses identified six main clades of CalS proteins and suggested duplications during the evolution of specialised functions. Twelve family members had previously been identified in Arabidopsis thaliana. We focused on five CalS subfamilies directly linked to pollen function and found that proteins expressed in pollen evolved twice. CalS9/10 and CalS11/12 formed well-defined clades, whereas pollen-specific CalS5 was found within subfamilies that mostly did not express in mature pollen vegetative cell, although were found in sperm cells. Expression of five out of seven mature pollen-expressed CalS genes was affected by mutations in bzip transcription factors. Only three subfamilies, CalS5, CalS10, and CalS11, however, formed monophyletic, mostly conserved clades. The pairs CalS9/CalS10, CalS11/CalS12 and CalS3 may have diverged after angiosperms diversified from lycophytes and bryophytes. Our analysis of fully sequenced plant proteins identified new evolutionary lineages of callose synthase subfamilies and has established a basis for understanding their functional evolution in terrestrial plants.
BACKGROUND: Bryophytes represent a very diverse group of non-vascular plants such as mosses, liverworts and hornworts and the oldest extant lineage of land plants. Determination of endogenous phytohormone profiles in bryophytes can provide substantial information about early land plant evolution. In this study, we screened thirty bryophyte species including six liverworts and twenty-four mosses for their phytohormone profiles in order to relate the hormonome with phylogeny in the plant kingdom. METHODOLOGY: Samples belonging to nine orders (Pelliales, Jungermanniales, Porellales, Sphagnales, Tetraphidales, Polytrichales, Dicranales, Bryales, Hypnales) were collected in Central and Northern Bohemia. The phytohormone content was analysed with a high performance liquid chromatography electrospray tandem-mass spectrometry (HPLC-ESI-MS/MS). PRINCIPAL FINDINGS: As revealed for growth hormones, some common traits such as weak conjugation of both cytokinins and auxins, intensive production of cisZ-type cytokinins and strong oxidative degradation of auxins with abundance of a major primary catabolite 2-oxindole-3-acetic acid were pronounced in all bryophytes. Whereas apparent dissimilarities in growth hormones profiles between liverworts and mosses were evident, no obvious trends in stress hormone levels (abscisic acid, jasmonic acid, salicylic acid) were found with respect to the phylogeny. CONCLUSION: The apparent differences in conjugation and/or degradation strategies of growth hormones between liverworts and mosses might potentially show a hidden link between vascular plants and liverworts. On the other hand, the complement of stress hormones in bryophytes probably correlate rather with prevailing environmental conditions and plant survival strategy than with plant evolution.
- MeSH
- Bryophyta klasifikace metabolismus MeSH
- cyklopentany analýza metabolismus MeSH
- cytokininy analýza metabolismus MeSH
- fylogeneze MeSH
- hmotnostní spektrometrie s elektrosprejovou ionizací MeSH
- kyselina abscisová analýza metabolismus MeSH
- kyselina salicylová analýza metabolismus MeSH
- kyseliny indoloctové analýza metabolismus MeSH
- oxylipiny analýza metabolismus MeSH
- regulátory růstu rostlin analýza metabolismus MeSH
- vysokoúčinná kapalinová chromatografie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
DNA barcoding is a technique of species identification by using standardized DNA sequence. This technique represents a challenge in the taxonomic approaches avoiding the need of exact knowledge of morphology, particularly when diagnostic morphological features are absent. There has been a considerable debate regarding a locus choice for standard barcode of land plants. Two-locus plastome sequences have been recommended by Plant working group of CBOL for plant barcode: rbcL and matK. The future purposes of this technique suggest using it instead of simple replacement of morphological data to identification of newly found species, recognizing species boundaries and cryptic species, or determination illegally obtained organisms and material even in cases where diagnostic features have been artificially modified.
The genus Luzula consists of 115 species distributed throughout the world. Luzula is monophyletic, but species relationships within the genus are difficult to determine primarily due to the similar morphology even within geographically remote taxa (especially within the section Luzula). The plastome trnL intron, trnL-F intergenic spacer and the nuclear ribosomal ITS1-5.8S-ITS2 regions were analysed using maximum parsimony and maximum likelihood reconstruction in 93 species of Luzula. The incongruent phylogenetic signals obtained from the chloroplast and the nuclear genomes point to incomplete lineage sorting as well as recent hybridisation in this group. Although tree-building analyses revealed several well-supported lineages, the outcomes for many groups were ambiguous. In the total evidence tree, Luzula species were grouped within six main clades (1. subgenus Marlenia, 2. subgenus Pterodes except for L. pilosa, 3. sections Anthelaea and Nodulosae, 4. sections Diprophyllatae and Thyrsanochlamydeae, 5. section Alpinae except for a few species and 6. section Luzula). The subgenus Marlenia occupies the early derived lineage within the genus Luzula. The traditionally accepted subgenera Pterodes and Luzula (and its sections) appear to be non-monophyletic. A statistical parsimony network approach showed that ancient haplotypes and ribotypes co-occur with their descendants in Luzula. Furthermore, many haplotypes are shared among different species. Within the Luzula section Luzula, both recent hybridisation and incomplete lineage sorting of ancestral polymorphisms may represent potential sources of the incongruence between chloroplast and nuclear data.
- MeSH
- DNA chloroplastová genetika MeSH
- DNA rostlinná genetika MeSH
- fylogeneze MeSH
- Magnoliopsida klasifikace genetika MeSH
- polymerázová řetězová reakce MeSH
- pravděpodobnostní funkce MeSH
- ribozomální DNA genetika MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
