Biology subjects

Trubanova, N.

Publications and source records attributed to Trubanova, N..

3 recordsLinked to original sources

bioRxiv2026

GENE-FAM: An automated pipeline for mining gene families and its application to MADS-box genes in Cannabis sativa

Understanding how gene families evolve can offer great insight into adaptation at the phenotypic and ecological levels. This is particularly true in plants, where transcription factor gene families are often targeted for breeding programs to improve the agronomic traits of economically important crops. While recent advances in next generation sequencing have accelerated the wealth of genomics data, there remains a lack of accessible and reproducible genome mining pipelines tailored for gene family characterisation. Here, we address this gap by developing GENE-FAM, an automated, scalable and open-source pipeline designed to mine and predict gene families based on conserved domains and motifs. To illustrate its application, we apply GENE-FAM to annotate MADS-box transcription factor genes across multiple Cannabis sativa genomes. A comprehensive set of MADS-box genes was identified across three C. sativa cultivars, including both previously annotated and newly predicted genes. Through phylogenetic analyses, we confirm that all type II MADS-box gene subfamilies represented in flowering plants are present in C. sativa. Comparing our annotations with those of Arabidopsis thaliana and Solanum lycopersicum revealed that while most MADS type II families are highly conserved, SEPALLATA-like genes have undergone diversification in C. sativa. Together, these results demonstrate the application of GENE-FAM for genome-wide identification and characterisation of gene families in non-model species, revealing novel insights into MADS-box gene family evolution in C. sativa.

genomics↗

bioRxiv2023

Best Paper awards lack transparency, inclusivity, and support for Open Science

Awards can propel academic careers. They also reflect the culture and values of the scientific community. But, do awards incentivise greater transparency, diversity, and openness in science? Our cross-disciplinary survey of 222 awards for the "best" journal articles across all 27 SCImago subject areas revealed that journals and learned societies administering such awards generally publish little detail on their procedures and criteria. Award descriptions are brief, rarely including contact details or information on the nominations pool. Nominations of underrepresented groups are not explicitly encouraged and concepts that align with Open Science are almost absent from the assessment criteria. Instead, such awards increasingly rely on article-level impact metrics. USA-affiliated researchers dominated the winners pool (48%), while researchers from the Global South and developing countries were uncommon (11%). Sixty-one-percent of individual winners were men. Thus, Best Paper awards miss the global calls for greater transparency and equitable access to academic recognition.

scientific communication and education↗

bioRxiv2023

Exploring phenotypic and genetic variability in hemp (Cannabis sativa)

Hemp (Cannabis sativa L.) is a high-value multi-purpose crop with applications ranging from the medicinal use of its secondary metabolites to carbon-sequestering building materials. To fully capitalise on the potential of hemp as a crop for more sustainable agriculture, detailed phenotypic and genotypic characterizations are required in order to inform targeted breeding programmes. Here, we present a detailed morphological and genomic analysis of 10 hemp cultivars. We found high variability in agronomically important traits such as flowering time, plant height, and biomass in most of the hemp cultivars tested. Additionally, genotyping by sequencing demonstrates that genetic differences are pervasive, both between hemp cultivars as well as between individuals of a single cultivar. The significant genetic and phenotypic variability we observe in hemp contrasts with other crops, where cultivars are often phenotypically and genetically relatively uniform. We argue that the variability of hemp is an asset for breeding and increases the potential for further improvement of the crop but is also a challenge for todays highly automated agriculture that relies on phenotypic uniformity. Author summaryHemp (Cannabis sativa L.) stands as one of the earliest domesticated crops. This remarkable plant is a sustainable crop with high carbon sequestration capacity which can be cultivated for soil remediation. Furthermore, hemp oil and fibre are used for many applications ranging from cooking to manufacturing bioplastics, textiles, or building materials of superb characteristics, and its secondary metabolites are sought after because of their medicinal properties. However, in contrast to many modern crops, hemp exhibits extensive variability in key agricultural traits, such as plant height and flowering time. This variability presents a challenge for both farmers and processors. To unravel the fundamentals of hemp diversity we conducted a comprehensive study of phenotypic and genetic characterisation of ten diverse hemp cultivars. We present findings confirming substantial variability not only among individuals of different cultivars but also within the same cultivar. Additionally, we explore heterozygosity in the context of other hemp studies and other crops. Understanding this variability in the context of a single hemp cultivar and across multiple cultivars is paramount for breeding novel, more uniform hemp varieties which will allow us to unlock the full potential of hemp as a crop of the future.

plant biology↗