Biology subjects

Gazizova, G. R.

Publications and source records attributed to Gazizova, G. R..

3 recordsLinked to original sources

bioRxiv2025

Full-length isoform constructor (FLIC) - a tool for isoform discovery based on long reads

Advances in high-throughput sequencing have illuminated a complexity of transcriptome landscape in eukaryotes. An inherent part of this complexity is the presence of multiple isoforms generated by the alternative splicing and the use of alternative transcription start and polyadenylation sites. However, currently available tools have limited capacity to infer full-length isoforms. To address this problem, we developed a new pipeline, FLIC (Full-Length Isoform Constructor). FLIC is based on the long-read transcriptome data and integrates several key features: 1) utilizing biological replicate concordance to filter out noise and artifacts; 2) employing peak calling to precisely identify transcription start and polyadenylation sites; 3) enabling robust isoform reconstruction with minimal reliance on existing annotations. We evaluated FLIC using a dedicated set of real and simulated data of Arabidopsis thaliana cDNA sequencing. Results demonstrate that FLIC accurately reconstructs known and novel isoforms, outperforming existing tools, especially in the absence of reference annotations. A direct comparison with CAGE, currently regarded as golden standard for TSS identification shows that FLIC is equally accurate, while being much less time-consuming. Thus FLIC provides a valuable tool for comprehensive transcript characterization, particularly for non-model organisms or when dealing with incomplete or inaccurate annotations.

bioinformatics↗

bioRxiv2023

Expanded Expression of Pro-Neurogenic Factor SoxB1 during Larval Development of gastropod Lymnaea stagnalis Suggests Preadaptation to Prolonged Neurogenesis in Mollusca

The diversity in the organization of the nervous system in mollusks raises intriguing questions about its development and evolution. Our study aims to gain a deeper understanding of how the nervous system forms in Mollusca by examining the involvement of SoxB-family transcription factors in the early development of neurogenic zones. Specifically, we explore the expression patterns of two SoxB genes in the gastropod Lymnaea stagnalis, namely Ls-SoxB1 and Ls-SoxB2, across various developmental stages. Through a combination of in situ hybridization chain reaction, immunohistochemistry, and proliferation assays, we examine the dynamic spatial distribution of Ls- SoxB1 and Ls-SoxB2, with a particular emphasis on the formation of central ring ganglia and the identification of active proliferative zones. Our findings reveal that Ls-SoxB1 exhibits expanded ectodermal expression from the gastrula to the postmetamorphic stage, evident at both transcriptional and translational levels. Throughout larval development, Ls-SoxB1 is expressed in the ectoderm of the head, foot, and visceral complex, as well as in ganglia anlagen and sensory cells. In contrast, the expression of Ls-SoxB2 in the ectoderm is observed until the veliger stage, after which it persists in subepithelial layer cells and ganglia rudiments. Proliferation assay reveals a uniform distribution of dividing cells in the ectoderm at all developmental stages, indicating the absence of distinct neurogenic zones with increased proliferation in gastropods. Our findings highlight that Ls-SoxB1 exhibit widespread expression patterns in both location and time compared to other Lophotrochozoa species. This prolonged expression of SoxB genes in gastropods can be interpreted as a form of transcriptional neoteny, playing a crucial role in the diversification of nervous systems. Thus, it serves as a preadaptation to prolonged neurogenesis and an increase in the central nervous system complexity in Mollusca.

developmental biology↗

bioRxiv2020

Population genomics of two closely related anhydrobiotic midges reveals differences in adaptation to extreme desiccation

The sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with the emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process are protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, a closely related anhydrobiotic midge from Malawi, P. pembai, showing the ability to tolerate complete desiccation similar to that of P. vanderplanki, but experiences more frequent desiccation-rehydration cycles due to differences in ecology, was discovered. Here, we sequenced and assembled the genome of P. pembai and performed a population genomics analysis of several populations of P. vanderplanki and a population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including multiple duplication events in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity ({pi}) of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with post-duplication adaptation in the former. Overall, our results suggest an extensive recent and likely ongoing, adaptation of the mechanisms of anhydrobiosis.

evolutionary biology↗