bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/615328

cT-DNA in Linaria vulgaris L. is multicopy, inverted and homogenized.

Vladimirov, I.·Pavlova, O.·Polev, D.·Bogomaz, D.
View original source ↗Export metadata ↓

Abstract

The phenomenon of evolutionary fixation of agrobacterial sequences (cT-DNA or cellular transferred DNA) in plant genomes is well known in nature. It was previously considered, that all of cT-DNA-containing species, except Linaria vulgaris, have multiple inverted cT-DNA repeats. Deep studying of general features of cT-DNA brings us closer to understanding the causes and mechanisms of its fixation in plants genomes. We combined multiple long-range PCR with genome walking for studying extended structure of cT-DNA. Using digital PCR method, we estimated copy number of cT-DNA elements. NGS with low covering allows us to develop a set of microsatellite markers, also used for copy number estimation. According to new data, cT-DNA elements in L. vulgaris form an inverted complex repeat of two simple direct repeats. After cT-DNA integration, cT-DNA sequence duplication events took place at least two times. The phenomenon of concerted evolution of cT-DNA sequences as well as some details of this process have been shown for the first time.\n\nWe have shown, that L. vulgaris, as well as other cT-DNA containing species, has inverted structure of repeats. This fact indicates possible existence of some general causes and mechanisms of cT-DNA fixation in plant genomes during evolution.

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Vladimirov, I., Pavlova, O., Polev, D., Bogomaz, D.. 2019-04-23. cT-DNA in Linaria vulgaris L. is multicopy, inverted and homogenized.. https://doi.org/10.1101/615328

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Secondary growth in the tomato stem is suppressed by the flowering regulators FUL2 and STM3

Herbaceous eudicot crops such as tomato accumulate substantial amounts of secondary xylem in their stems, particularly in the basal part. As plants progress from the vegetative phase to flowering and fruit development, secondary growth continues to provide mechanical support and facilitate transport. To uncover how secondary growth is regulated in the tomato stem, we used laser capture microdissection RNA-seq to establish tissue-specific transcriptomic profiles. This revealed that key regulators associated with wood formation in poplar are also acting in tomato. Furthermore, we found that the flowering regulators FUL2 and STM3 are substantially expressed in xylem tissue. Subsequent functional analysis identified FUL2 and STM3 as key repressors of secondary growth, with ful2 or stm3 knock-out mutants exhibiting strongly increased secondary growth in older tomato stems. Notably, a higher order mutant in which both ful2 and stm3 were knocked out displays a similar non-additive phenotype, indicating, together with yeast two-hybrid data showing physical interaction, that FUL2 and STM3 act together in a complex. The expression levels of both genes remain low until after the floral transition but strongly rise during subsequent stem development. Transcriptomic analyses in ful2, stm3, and wild-type stems at stages before and after detectable anatomical differences, showed that the FUL2-STM3 complex represses distinct sets of NAC and MYB candidate regulators associated with xylem development. Interestingly, FUL2 and STM3 control these regulators in a stage- and position-dependent way, with candidates showing upregulation only at later stages in mid-height stems being already upregulated at earlier stages in basal stem regions. Our findings provide a tissue-resolved transcriptomic resource for tomato stems and reveal a role for FUL2 and STM3 in limiting secondary xylem accumulation as stem development progresses.

plant biology↗
bioRxiv2026

Geometric Morphometrics of Pistillate Flowers in Astrocaryum sect. Huicungo (Arecaceae): Taxonomic Implications for the Peruvian Species

The taxonomy of the Amazonian palm clade Astrocaryum sect. Huicungo remains controversial due to deep discordances between traditional classifications based on qualitative floral traits and recent phylogenomic evidence. To address this, landmark-based two-dimensional geometric morphometrics (4 landmarks, 16 semilandmarks) was applied to evaluate the symmetric component of shape variation in calyx and corolla structures across 549 pistillate flowers from the 11 Peruvian species. Although multivariate analyses (PCA, CVA) revealed continuous morphological variation and extensive phenotypic overlap, perianth geometry retained a significant diagnostic signal. Cross-validated classification rates demonstrated that the corolla exhibited higher discriminatory power than the calyx, while the combined perianth analysis (calyx + corolla) maximized taxonomic assignment accuracy. Furthermore, Mahalanobis distance-based clustering did not replicate traditional subsections: A. chonta and A. ulei exhibited divergent architectures, whereas A. carnosum, A. faranae, and A. huicungo shared profound geometric similarity. This study demonstrates that quantitative perianth morphometrics is a valuable tool for species delimitation in Astrocaryum, supporting the re-evaluation of traditional taxonomic boundaries through an integrative approach.

plant biology↗
bioRxiv2026

Multi-Criteria Evaluation of Hibiscus mutabilis Cultivars for Food Development Using Delphi and Analytic Hierarchy Process

This study evaluated 11 Hibiscus mutabilis cultivars from Chengdu Botanical Garden to assess their quality for food use and identify promising cultivars. An evaluation framework was developed using the Delphi method to select indicators and the analytic hierarchy process (AHP) to determine their weights. Overall scores ranged from 2.5785 to 3.6043, and the cultivars were classified into three grades. Grade I included Hibiscus mutabilis 'Bairi Huacai', Hibiscus mutabilis 'Chongbanbai' and Hibiscus mutabilis 'Jinqiusong'; Grade II included Hibiscus mutabilis 'Jinqiuhong', Hibiscus mutabilis 'Zuifurong', Hibiscus mutabilis 'Danbanhong', Hibiscus mutabilis 'Jinxiuzi', Hibiscus mutabilis 'Jinbiyu' and Hibiscus mutabilis 'Caixia'; whereas Grade III included Hibiscus mutabilis 'Mudanfen' and Hibiscus mutabilis 'Jinrui'. In summary, Hibiscus mutabilis 'Bairi Huacai', Hibiscus mutabilis 'Chongbanbai' and Hibiscus mutabilis 'Jinqiusong' are the preferred cultivars for food processing and development. The framework provides a basis for cultivar screening and further evaluation of H. mutabilis flowers for food use.

plant biology↗