The Neotropical fish genus Prochilodus includes five species occurring in the main drainages of the eastern Brazilian Shield: P. argenteus, P. costatus, P. lineatus, P. harttii, and P. vimboides. Multi and single locus phylogenies have questioned the monophyly of P. costatus and P. lineatus, and the biogeographic history of these species in the Brazilian Shield has never been explored. We characterized new mitogenomes for these species to reconstruct their evolutionary history, estimated the timing of Prochilodus cladogenesis, and discussed the implications of past geologic events on species diversification. The phylogeny supports the monophyly of both P. costatus and P. lineatus, and indicates a Miocene divergence of P. vimboides, much earlier than subsequent species diversification. The Early Pleistocene split of P. argenteus and P. harttii (~2.1 million years ago—MYA) is hypothesized to be related to recent Quaternary reactivations of the Rio Araçuaí Fault that promoted river captures between the eastern tributaries of the São Francisco basin and the upper Rio Jequitinhonha in the Serra do Espinhaço mountain range. The time‐calibrated phylogeny also indicated a subsequent split of P. costatus and P. lineatus (~1.1 MYA) likely due to Quaternary activities of the Upper Rio São Francisco crustal discontinuity and Estrela Fault that catalyzed river captures between the upper Rio São Francisco and the Rio Grande of the Paraná basin in the Serra da Canastra mountain range. These results provide a temporal context for the diversification of Prochilodus and bring new insights to further study the historical biogeography of other riverine fish groups along the upland basins of the eastern Brazilian Shield.

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Trypanosoma cruzi, the causative agent of Chagas disease, is extremely resistant to ionizing radiation, enduring up to 1.5 kGy of gamma rays. Ionizing radiation can damage the DNA molecule both directly, resulting in double-strand breaks, and indirectly, as a consequence of reactive oxygen species production. After a dose of 500 Gy of gamma rays, the parasite genome is fragmented, but the chromosomal bands are restored within 48 hours. Under such conditions, cell growth arrests for up to 120 hours and the parasites resume normal growth after this period. To better understand the parasite response to ionizing radiation, we analyzed the proteome of irradiated (4, 24, and 96 hours after irradiation) and non-irradiated T. cruzi using two-dimensional differential gel electrophoresis followed by mass spectrometry for protein identification. A total of 543 spots were found to be differentially expressed, from which 215 were identified. These identified protein spots represent different isoforms of only 53 proteins. We observed a tendency for overexpression of proteins with molecular weights below predicted, indicating that these may be processed, yielding shorter polypeptides. The presence of shorter protein isoforms after irradiation suggests the occurrence of post-translational modifications and/or processing in response to gamma radiation stress. Our results also indicate that active translation is essential for the recovery of parasites from ionizing radiation damage. This study therefore reveals the peculiar response of T. cruzi to ionizing radiation, raising questions about how this organism can change its protein expression to survive such a harmful stress.

Yeast communities associated with cacti were studied in three ecosystems of Southeast, Central and North Brazil. A total of 473 yeast strains belonging to 72 species were isolated from 190 samples collected. Cactophilic yeast species were prevalent in necrotic tissues, flowers, fruits and insects of cacti collected in Southeast and North Brazil. Pichia cactophila, Candida sonorensis and species of the Sporopachydermia complex were the most prevalent cactophilic species in Southeast and Central regions. Kodamaea nitidulidarum, Candida restingae and Wickerhamiella cacticola were frequently associated with cactus flowers and fruits. The diversity of yeasts associated with the substrates studied was high. Twenty-one novel species were found. One is described here as Kluyveromyces starmeri sp. nov. based on 21 isolates obtained from necrotic tissues, flowers, fruits and associated insects of the columnar cacti Cereus saddianus, Micranthocereus dolichospermaticus and Pilosocereus arrabidae in two different ecosystems in Brazil. Phylogenetic analyses of sequences encoding the gene of the small subunit (SSU) rRNA gene, the internal transcribed spacer, the 5.8S rRNA gene and the D1/D2 domains of the large subunit (LSU) rRNA showed that the species is related to Kluyveromyces dobzhanskii, Kluyveromyces lactis and Kluyveromyces marxianus. Phylogenomic analyses based on 1264 conserved genes shared among the new species and 19 other members of the Saccharomycetaceae confirmed this phylogenetic relationship. The holotype is K. starmeri sp. nov. CBS 16103 T (=UFMG-CM-Y3682 T). The Mycobank number is MB 836817.

Here we report the draft genome sequence of Metschnikowia australis strain UFMG-CM-Y6158, a yeast endemic to Antarctica. We isolated the strain from the marine seaweed Acrosiphonia arcta (Chlorophyta). The genome is 14.3 Mb long and contains 4,442 predicted protein-coding genes.

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Despite the increasing popularity of DNA metabarcoding in the assessment of aquatic ecosystems using fish eDNA or ichthyoplankton, challenges have hampered its broader application in the Neotropical freshwaters. Using five mock communities composed of fish species from two Neotropical River basins, we evaluated the influence of DNA concentration and choice of mitochondrial 12S molecular markers (MiFish, NeoFish, and Teleo) on species detection and relative read abundance (RRA) using DNA metabarcoding. Of the three 12S markers analyzed, only MiFish detected all species from all mock communities. The performance of a taxonomy‐free approach using ASV/MOTUs was not as precise as assigning DNA reads to species using a curated 12S library that includes approximately 100 fish species since more than one ASV/MOTU was observed for the same specimen. Thus, here we showcase the importance of a custom reference database to allow precise assignment of Neotropical fish species in metabarcoding studies and that the RRA is dependent on community composition, marker, and DNA concentration. We highlight the importance of controlled experiments using known species communities before large investments are made in assessing biodiversity using non‐invasive methods that apply DNA metabarcoding.

The enrichment analysis is a standard procedure to interpret ‘omics’ experiments that generate large gene lists as outputs, such as transcriptomics and protemics. However, despite the huge success of enrichment analysis in these classes of experiments, there is a surprising lack of application of this methodology to survey other categories of large-scale biological data available. Here, we report Kegg Orthology enrichMent-Online DetectiOn (KOMODO), a web tool to systematically investigate groups of monophyletic genomes in order to detect significantly enriched groups of homologous genes in one taxon when compared with another. The results are displayed in their proper biochemical roles in a visual, explorative way, allowing users to easily formulate and investigate biological hypotheses regarding the taxonomical distribution of genomic elements. We validated KOMODO by analyzing portions of central carbon metabolism in two taxa extensively studied regarding their carbon metabolism profile (Enterobacteriaceae family and Lactobacillales order). Most enzymatic activities significantly biased were related to known key metabolic traits in these taxa, such as the distinct fates of pyruvate (the known tendency of lactate production in Lactobacillales and its complete oxidation in Enterobacteriaceae), demonstrating that KOMODO could detect biologically meaningful differences in the frequencies of shared genomic elements among taxa. KOMODO is freely available at http://komodotool.org.