Biology subjects

Kalantidis, K.

Publications and source records attributed to Kalantidis, K..

4 recordsLinked to original sources

bioRxiv2026

The Cretan Carob Virome

Carob (Ceratonia siliqua) is an important yet often underestimated Mediterranean tree species. Historically used as a sweetener by ancient Greeks and Arabs, it also supported populations during periods of famine. Beyond its cultural value, carob exhibits notable agronomic traits, including drought and temperature tolerance, soil erosion prevention, and potential contributions to rural development. Although a Cretan carob genome assembly has recently become available, little is known about pathogens associated with this species, particularly viruses. Here, we characterized the virome of carob trees in Crete using high throughput sequencing (HTS) and targeted molecular validation. We collected 134 leaf samples from 34 growers across the island four prefectures. HTS analysis revealed novel isolates of two Secoviridae members (Artichoke yellow ringspot virus - AYRSV) and Strawberry latent ringspot virus - SLRSV), as well as Soybean ilarvirus 1 (SolV1), a putative and incompletely characterized jivivirus, and a previously undescribed coguvirus of the family Phenuiviridae, all confirmed by PCR screening. Phylogenetic and sequence analyses support the classification of the coguvirus as a distinct viral species, for which we propose the name Carob coguvirus 1 (CaCoV1). To our knowledge, this study provides the first comprehensive characterization of the carob virome. These findings expand current knowledge of viral diversity in carob and establish a foundation for future epidemiological studies, certification of propagation material, and the sustainable expansion of carob cultivation in Crete and other Mediterranean regions.

microbiology↗

bioRxiv2026

VIRP1 bromodomain shapes nuclear condensate formation and has a positive effect on PSTVd accumulation

O_LIViroids are small, non-coding RNAs that rely on host factors for replication, intracellular trafficking and systemic movement. VIRP1, a Bromodomain and Extra-terminal domain (BET) protein, has previously been implicated in Potato spindle tuber viroid (PSTVd) infection, yet its precise role and mode of action remain unresolved. C_LIO_LIIn this work, we highlight VIRP1 as the only Solanaceae BET protein containing a proline-rich domain, which overlaps with the PSTVd-binding site. VIRP1-deficient plants exhibit delayed flowering and increased ABA sensitivity, with differentially expressed genes enriched in stress-related pathways. C_LIO_LIVIRP1 forms condensates in planta and in vitro, consistent with phase-separation behaviour. Condensate morphology is altered by PSTVd RNA, deletion of the intrinsically disordered CTD and bromodomain mutations. C_LIO_LIVIRP1 is particularly important for the early establishment of PSTVd infection, while nuclear localization and bromodomain integrity are required for efficient viroid accumulation. By contrast, the disordered CTD region is dispensable for complementation of PSTVd accumulation. C_LIO_LIOur results support a model in which VIRP1 acts as a host nuclear factor that links stress-related functions, nuclear condensate formation and early viroid infection. C_LI

plant biology↗

bioRxiv2023

Genome sequencing, assembly and annotation of the carob tree, Ceratonia siliqua (Eudicots:Fabaceae)

The carob tree, Ceratonia siliqua, is an evergreen tree that belongs to the family of Fabaceae. It has been cultivated for thousands of years in Mediterranean countries and thus, has a considerable impact on the nutrition of humans as well as other animals of this region. Despite its importance, genomic resources are still scarce for this plant species. To fill this gap, we undertook the sequencing, assembly and annotation of the carob tree genome, which resulted in the first, nearly chromosome-level assembly for this plant species. The total assembly size is 492 Mbp which is close to the previously estimated genome size. The assembly N50 is 34.99 Mbp, thus showing a high contiguity, which is also evident from the fact that >98% of the assembly is contained in as few as 17 very large contigs. Moreover, both the genome sequence as well as the predicted gene set contain more than 96% of conserved, full-length BUSCOs. Finally, a comparative orthology analysis with 10 other plant species showed that the vast majority of the predicted carob tree genes have orthologs in the other plants and only a small fraction of them appears to be species-specific. Additional analyses are in progress for a more detailed study of the agronomic traits of this important legume.

genomics↗

bioRxiv2021

DNA Preparation In Vitis vinifera L. For Third Generation Sequencing

BackgroundThere have been several attempts to sequence the genome of Vitis vinifera L. (grapevine), utilizing low-resolution second-generation platforms. Nevertheless, the characterization of the grapevine genetic resources and its adaptation to vulnerable conditions could be better addressed through extensive and high-resolution genome sequencing. MinION is a third-generation sequencer preferred by many laboratories due to its relatively low cost, ease of use and small size. Even though this long-read technology has been rapidly improving, to reach its full potential requires high-quality DNA. ResultsHere we establish a workflow for DNA extraction suitable for MinION sequencing long reads from grapevine. This protocol was tested with leaf samples from different positions on annual growing branches of grapevine, Purified nuclei from fresh young leaves that led to high quality, long DNA fragments, suitable for long-read sequencing were successfully generated. It is evident that longer reads in grapevine associate with both fresh tissue and adjusted conditions used for nuclei purification. ConclusionsWe propose that this workflow presents a significant advancement for long-read quality DNA isolation for grapevine and likely other plant species.

genomics↗