Banca de DEFESA: Deborah Ribeiro Bambil
Uma banca de DEFESA de DOUTORADO foi cadastrada pelo programa.STUDENT : Deborah Ribeiro Bambil
DATE: 25/07/2023
TIME: 14:00
LOCAL: Auditório 2 do IB
TITLE:
KEY WORDS:
covariance models, data curation, pink ipê, Handroanthus impetiginosus, hidden Markov models, homology, pre-miRNAs, redundancy.
PAGES: 87
BIG AREA: Ciências Biológicas
AREA: Biologia Geral
SUMMARY:
microRNAs (miRNAs) are short non-coding RNA sequences that play a role in gene expression. The mature form consists of 20 to 24 nucleotides (nt), whereas the precursor structure (pre-miRNAs) has a maximum length of 300 nt (updated criteria). In recent years, studies related to pre-miRNAs and mature miRNAs have substantially increased, resulting in numerous annotations and increasing the challenge analysis. This work aimed to curate data and analyze the redundancy in the pre-miRNAs and mature miRNAs dataset to construct a computational tool to identify novel pre-miRNAs. premiRNA sequences are more informative for identifying mature miRNAs in experiments and evolutionary studies. The genome of a model plant (rice - Oryza sativa L.) and a wild species (ipê – Handroanthus impetiginosus Mart. ex DC. Mattos) were analyzed through the computational tool. This pipeline started from the curated dataset of premiRNAs (updated criteria). Redundancy was analyzed by the pre-miRNAs family, with identity ranging from 95% to 70% (in 5% intervals) using the T-Coffee tool. The alignments showed color-coded similarity matches (good – pink, average – yellow, bad – green and blue). Color characteristics were extracted from the alignments using the Inovtaxon tool and classified with the Deep Learning (DL) algorithm in the Weka tool. The resulting DL-measured F-score provided the color-based classification result, which was used for ANOVA, where the 80% threshold was significant compared to the other thresholds. The identification of novel pre-miRNAs in genomes used the covariance models (CMs), which were constructed using the Infernal tool from the curated dataset of pre-miRNAs. This approach utilizes homology search. The output of these results is organized in directories based on redundancy thresholds (identical, non-identical, 95% to 70%) using the skipRedundant tool. The outputs differentiated by thresholds facilitate the analysis of identical or highly similar copies, enabling a pre-selection of specimens for experimental validation. These routines are implemented in the computational tool PmiR-Select, which is open-source and comes with usage instructions. It is also registered as a software patent (No. BR512022001292). At miRBase, there are 8677 pre-miRNA plants from 2942 families. With a 300 nt length threshold, pre-miRNAs were reduced to 8304 (↓4.3%) in 2726 (↓7.3%) families. The angiosperms (Ang) have the highest number of pre-miRNA families (n=2294), followed by gymnosperms (Gym - n=281), bryophytes (Bry - n=121), and algae (n=80). The MIR169 family, involved with flowering timing and photosynthesis, had the highest number of pre-miRNAs (n=391) and occurred only in Ang and Gym. PmiR-Select was validated using the rice genome (388 Mb), where 4087 new pre-miRNAs homologous to 31 families were identified. Of these, sixteen existing families in the rice miRBase and fifteen new families. These pre-miRNAs are involved in growth, development, and responses to biotic and abiotic stresses. The miRBase currently registers 557 pre-miRNAs from 341 pre-miRNA families for rice, indicating an increase of 4.4% (n=15) in families compared to the total number of pre-miRNAs deposited in the miRBase. These new pre-miRNAs and families can assist in the design and results analysis of future bench or computational experiments. At pink ipê genome (503Mb) using a pipeline based on hidden Markov models (HMM) profiles, 5229 pre-miRNAs from 62 families were detected. Using PmiR-Select to identify new pre-miRNAs in the pink ipê genome, 912 were new homologous pre-miRNAs to 24 pre-miRNA families. While the RNA-Seq is being analyzed. These potential pre-miRNAs are involved in model plants’ growth, development, and responses to biotic and abiotic stresses. Handroanthus impetiginosus, commonly known as the pink ipê tree, is considered a native species of the Cerrado biome, and its genome was the first among the Bignoniaceae family to be annotated. Like the Handroanthus impetiginosus genome, over 90% of sequenced genomes have not yet been annotated for miRNA sequences in the databases. Using PmiR-Select opens up opportunities for the initial exploration of new pre-miRNAs from native and unique species across different clades, including specific strata of diverse biomes. During the validation of PmiR-Select using the rice and Handroanthus impetiginosus genomes, it was observed that some improvements could be added to enhance the application of the obtained results. Such as the localization of pre-miRNAs on chromosomes and identifying the pre-miRNAs as possible non-functional repetitive elements. In addition, it is essential to emphasize the importance of reaching a critical mass in this field, which is significant in agriculture and medicine.
COMMITTEE MEMBERS:
Presidente - 2241442 - LUCIO FLAVIO DE ALENCAR FIGUEIREDO
Externa à Instituição - PRISCILA GRYNBERG - EMBRAPA
Externo ao Programa - 2644635 - ROBERT NEIL GERARD MILLER - UnBExterno à Instituição - ROBERTO COITI TOGAWA - EMBRAPA
Externo ao Programa - 1143211 - THIAGO JOSE DE CARVALHO ANDRE - UnB