Biology subjects

Pedrosa, F. d. O.

Publications and source records attributed to Pedrosa, F. d. O..

3 recordsLinked to original sources

bioRxiv2025

Atypical plastid genome evolution: Cereus Mill. from distinct environments harbor one of the largest plastid genomes in Cactaceae

BackgroundCactaceae has successfully radiated in xeric habitats across the Americas, presenting very distinct morphologies and evolutionary patterns within tribes. This study presents the complete plastomes of C. jamacaru subsp. jamacaru and C. hildmannianus subsp. hildmannianus, which inhabit distinct habitats, providing insights into their genomic structure and evolutionary history, with implications for conservation. Methods and ResultsChloroplast genomes of the two Cereus were assembled and analyzed to investigate plastome evolution in Cactoideae. Fresh cladodes were collected and their mesophyll manually extracted, chloroplasts were extracted from the mesophyll, and cpDNA sequenced using Illumina MiSeq. De novo assembly and annotation were conducted using BLAST, Expasy, and tRNAScan as validation tools. We compared the genome structure, gene content, codon usage, and RNA editing predictions between tribes. The genome was 141.884 and 141.600 bp for C. jamacaru and C. hildmannianus, respectively, and dotplot analysis confirmed highly syntenic plastomes. The genes trnV-GAC, trnV-UAC, rpl23, ndhA, ndhE, ndhG, ndhI, and ndhK were lost, and ndhB, ndhC, ndhF, and rpl33 are pseudogenes. The tRNAval losses indicate putative superwobbling or nuclear-coded tRNA import from cytosol. We identified an insertion in rps18 for both Cereus, suggesting that intron retention may be in course for these species. We identified [~]190 single sequence repeats and 50 tandem repeats for each species, and eight exclusive RNA editing sites. Synteny analysis revealed rearrangements distinguishing taxa within Cactoideae. Phylogenetic results supported Cereus monophyly, corroborating existing classifications, and clarifies unresolved relationships, enhancing understanding of phylogenetic relationships within Cactaceae. ConclusionsOur results provide evidence on the evolutionary patterns and putative signatures of adaptation to distinct environments, providing insights into genomic evolution and conservation of Cereus.

evolutionary biology↗

bioRxiv2020

Genome-wide Association Studies Reveal Important Candidate Genes for the Bacillus pumilus TUAT-1-Arabidopsis thaliana Interaction

The plant growth promoting bacterium (PGPB) Bacillus pumilus TUAT-1 is an indole acetic acid producer that can increase plant growth. Inoculation with this strain has been shown to confer greater plant tolerance to drought and saline conditions. Although the ability of TUAT-1 to enhance plant growth is well documented, little is known about what mechanisms underlie the plant response to this bacterium. Applying genome-wide association study (GWAS), we evaluated the interaction between TUAT-1 and Arabidopsis thaliana, screening 288 plant ecotypes for root architecture traits comparing non-inoculated and inoculated plants. Most of the ecotypes were significantly affected by TUAT-1 inoculation (66.7%) for at least one of the root traits measured. For example, some ecotypes responded positively increasing root growth while others showed reduced growth upon inoculation. A total of 96 ecotypes (33.3%) did not respond significantly to PGPB inoculation. These results are consistent with the widely reported strain-genotype specificity shown in many plant-microbe interactions. The GWAS analysis revealed significant SNPs associated to specific root traits leading to identification of several genes putatively involved in enabling the Bacillus pumilus TUAT-1 and A. thaliana association and contributing to plant growth promotion. Our results show that root architecture features are genetic separable traits associated with plant growth in association with TUAT-1. Our findings validate previous reported genes involved in Bacillus spp.-plant interaction, growth promotion and highlight potential genes involved in plant microbe interaction. We suggest that plant-bacterial interaction and the plant growth promotion are quantitative and multigenic traits. This knowledge expands our understanding of the functional mechanisms driving plant growth promotion by PGPB.

plant biology↗

bioRxiv2018

RAFTS3G - An efficient and versatile clustering software to analyses in large protein datasets

The need to develop computational tools and techniques that can predict efficiently consistent groups of family proteins in large volume of biological information is still a great perspective in Bioinformatic studies. Besides that, it is difficult to increase speed demanding low computational processing to minimize the information complexity. Tools already consolidated as the CD-HIT and UCLUST generates very compact data that makes the Data Mining difficult and have low efficiency when used for detect homology among proteins requiring manual intervention, therefore it is necessary a tool that is also efficient in low similarity. Here we present a new approach for the Data Mining and analysis of homology in large dataset of protein sequences, the RAFTS3G. We used the UniProtKB/Swiss-Prot database with the most popular clustering tools and RAFTS3G proved to be more than 10 times faster than CD-HIT and its strategy increases the performance in low similarity to detect protein families.\n\nContact: raittz@ufpr.br

bioinformatics↗