Organellar-genome analyses from the lycophyte genus Isoetes L. show one of the highest frequencies of RNA editing in land plants.

RNA editing is a post-transcriptional process that challenges the central dogma of molecular biology by modifying RNA sequences, introducing nucleotide changes at specific sites, and generating functional diversity beyond the genomic code, especially when it concerns organellar transcripts. In plants, this phenomenon is widespread, but its extent varies significantly among species and organellar genomes. Among land plants, the heterosporous lycophytes (i.e., Isoetes and Selaginella) stand out for their exceptionally high numbers of RNA-editing sites, despite their morphological stasis and ancient lineage. In this study, we explore the complete set of organellar protein-coding genes in the aquatic plant group Isoetes, providing a detailed analysis of RNA editing in both the mitochondrial and plastid genomes. Our findings reveal a remarkable abundance of RNA editing, particularly in the mitochondrial genome, with thousands of editing sites identified. Interestingly, the majority of these edits result in non-silent substitutions, suggesting a role in fine-tuning protein structure and function. Furthermore, we observe a consistent trend of increased hydrophobicity in membrane-bound proteins, supporting the notion that RNA editing may confer a selective advantage by preserving gene functionality in Isoetes. The conservation of highly edited RNA sequences over millions of years underscores the evolutionary significance of RNA editing. Additionally, the study sheds light on the dynamic nature of RNA editing, with shared editing sites reflecting common ancestry whereas exclusive edits matching more recent radiation events within the genus. This work advances our understanding of the intricate interplay between RNA editing, adaptation, and evolution in land plants and highlights the unique genomic features of Isoetes, providing a foundation for further investigations into the functional consequences of RNA editing in this enigmatic plant lineage.

Molecular analyses of carangid fish diets reveal inter-predation, dietary overlap, and the importance of early life stages in trophic ecology.

Carangid fishes are commercially important in fisheries and aquaculture. They are distributed worldwide in both tropical and subtropical marine ecosystems. Their role in food webs is often unclear since their diet cannot be easily identified by traditional gut content analysis. They are suspected to prey on pelagic and benthic species, with clupeiform fishes being important dietary items for some species, though it is unknown whether carangids share food resources or show trophic segregation. Here, we used metabarcoding to overcome traditional challenges of taxonomic approaches to analyze the diet of seven carangid species caught as bycatch in the Brazilian southwest Atlantic sardine fishery. Stomach contents were processed from the following species: Caranx crysos, Caranx latus, Chloroscombrus chrysurus, Hemicaranx amblyrhynchus, Oligoplites saliens, Selene setapinnis, and Trachinotus carolinus. Identified diets were dominated by teleost fishes. The C. latus diet was the most distinct among the seven species, preferentially consuming Engraulis anchoita, but H. amblyrhynchus, O. saliens, and S. setapinnis also showed a trend of predominantly consuming small pelagic fishes. Finally, we found evidence of inter-predation in carangids, especially strong between S. setapinnis and C. crysos, suggesting that consumption of early life stages may result in indirect competition through reduced recruitment in these fishes. These findings provide unprecedented insights into the biodiversity in marine ecosystems, especially the poorly known diet of carangid fishes.

Comparison of two acidophilic sulfidogenic consortia for the treatment of acidic mine water.

Sulfate-reducing bioreactors are a biotechnological alternative for the treatment of acid mine drainage (AMD). In this study, two separate bioreactors with pH and temperature-controlled (Bio I and II) were operated with two different acidophilic microbial consortia to determine their efficiencies in sulfate removal from a synthetic acidic mine water. The bioreactors were operated for 302 days in continuous flow mode under the same parameters: fed with a sulfate solution of ∼30 mM with a pH of 2.5, the temperature at 30°C, stirred gently at 40 rpm and using a continuous stream of nitrogen to help remove the H2S produced in the bioreactor. The glycerol consumption, acetate production, and sulfate removal were monitored throughout the course of the experiment. The community composition and potential metabolic functional groups were analyzed via 16S rRNA partial gene sequencing. Bio I consortium reduced the sulfate, achieving a range of sulfate concentration from 4.7 to 19 mM in the effluent liquor. The removal of sulfate in Bio II was between 5.6 and 18 mM. Both bioreactors' communities showed the presence of the genus De sulfosporosinus as the main sulfate-reducing bacteria (SRB). Despite differences in microbial composition, both bioreactors have similar potential metabolism, with a higher percentage of microorganisms that can use sulfate in respiration. Overall, both bioreactors showed similar performance in treating acidic mine water containing mostly sulfate using two different acidophilic sulfidogenic consortia obtained from different global locations.

Complete mitochondrial genome of Glomeridesmus spelaeus (Diplopoda, Glomeridesmida), a troglobitic species from iron-ore caves in Eastern Amazon.

We report the complete mitochondrial genome sequence of Glomeridesmus spelaeus, the first sequenced genome of the order Gomeridesmida. The genome is 14,825 pb in length and encodes 37 mitochondrial (13 PCGs, 2 rRNA genes, 22 tRNA) genes and contains a typical AT-rich region. The base composition of the mitogenome was A (40.1%), T (36.4%), C (15.8%), and G (7.6%), with an GC content of 23.5%. Our results indicated that G. spelaeus is only distantly related to the other Diplopoda species with available mitochondrial genomes in the public databases. As the broadest genetic characterization of a Glomeridesmida species available to date, the mitogenome of G. spelaeus will help understanding the evolution of such a little-known millipede group. Also, our data will be important for the characterization and conservation of the diverse invertebrate troglofauna of the Amazonian caves.

Quillworts from the Amazon: A multidisciplinary populational study on Isoetes serracarajensis and Isoetes cangae.

Isoetes are ancient quillworts members of the only genus of the order Isoetales. The genus is slow evolving but is resilient, and widespread worldwide. Two recently described species occur in the Eastern Brazilian Amazon, Isoetes serracarajensis and Isoetes cangae. They are found in the ironstone grasslands known as Canga. While I. serracarajensis is present mostly in seasonal water bodies, I. cangae is known to occur in a single permanent lake at the South mountain range. In this work, we undertake an extensive morphological, physiological and genetic characterization of both species to establish species boundaries and better understand the morphological and genetic features of these two species. Our results indicate that the morphological differentiation of the species is subtle and requires a quantitative assessment of morphological elements of the megaspore for diagnosis. We did not detect differences in microspore output, but morphological peculiarities may establish a reproductive barrier. Additionally, genetic analysis using DNA barcodes and whole chloroplast genomes indicate that although the plants are genetically very similar both approaches provide diagnostic characters. There was no indication of population structuring I. serracarajensis. These results set the basis for a deeper understanding of the evolution of the Isoetes genus.

PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly.

BACKGROUND: Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it's often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discovery and identification and have been widely used for taxonomic identification by targeting known gene regions that permit to discriminate these species. DNA barcode sequence analysis is usually carried out with processes and tools that still demand a high interaction with the user or researcher. To reduce at most such interaction, we proposed PIPEBAR, a pipeline for DNA chromatograms analysis of Sanger platform sequencing, ensuring high quality consensus sequences along with efficient running time. We also proposed a paired-end reads assembly tool, OverlapPER, which is used in sequence or independently of PIPEBAR. RESULTS: PIPEBAR is a command line tool to automatize the processing of large number of trace files. It is accurate as the proprietary Geneious tool and faster than most popular software for barcoding analysis. It is 7 times faster than Geneious and 14 times faster than SeqTrace for processing hundreds of barcoding sequences. OverlapPER is a novel tool for overlapping paired-end reads accurately that accepts both substitution and indel errors and returns both overlapped and non-overlapped regions between a pair of reads. OverlapPER obtained the best results compared to currently used tools when merging 1,000,000 simulated paired-end reads. CONCLUSIONS: PIPEBAR and OverlapPER run on most operating systems and are freely available, along with supporting code and documentation, at https://sourceforge.net/projects/PIPEBAR / and https://sourceforge.net/projects/overlapper-reads /.