Abstract in English:

Abstract Meckel syndrome (MKS) is a lethal autosomal recessive disease with high phenotypic and genetic heterogeneity. Defects in NPHP3 cause MKS type 7. Herein, we report a case of a Chinese family with a newborn male proband presenting with occipital encephalocele and polycystic kidneys. Whole-exome sequencing was performed on genomic DNA extracted from peripheral blood. Potential variants were assessed for pathogenicity. Two compound heterozygous variants of NPHP3 (c. 950T>C, p. Phe317Ser, and c.2694-2_2694-1delAG) were identified, which were inherited from both parents, with c.950T>C representing a novel variant. Two BRCA2 variants (c.5576_5579delTTAA, p. Ile1859Lysfs*3, and c.9357A>C,p. Leu 3119 Phe) were identified, which were inherited from the father. After the proband was diagnosed with MKS7, the couple chose preimplantation genetic testing for monogenic disorders (PGT-M) to simultaneously prevent the transmission of NPHP3 and BRCA2 pathogenic variants, leading to a successful pregnancy. Our study expands the NPHP3 variant spectrum and contributes to the molecular diagnosis and genetic counseling of MKS. This case indicates that PGT-M is a viable option for NPHP3-related MKS and BRCA-positive patients to avoid transmission while maintaining their families. Successful application of PGT-M provides a potential approach for treating other monogenic diseases.

Abstract in English:

Abstract Polyneoptera comprises hemimetabolous insect orders of significant agricultural, ecological, and medical relevance, motivating phylogenetic and molecular research that has nevertheless focused predominantly on canonical mitochondrial markers. Here, we assembled new mitogenomes for Polyneoptera and evaluated the usefulness of genes located in nucleotide-diversity hotspots as markers for species identification and phylogenetic inference. To expand the available mitogenomic resources, raw sequencing data were retrieved from public databases, resulting in the assembly and annotation of 26 complete mitogenomes, all exhibiting the typical insect mitochondrial architecture. These newly assembled genomes were combined with publicly available mitogenomes from Orthoptera, Blattodea, Plecoptera, Mantodea, and Phasmatodea to reconstruct phylogenetic relationships using both complete and reduced datasets comprising nucleotide-diversity hotspot-associated genes. The performance of these hotspot regions was further assessed through barcoding gap analyses and comparisons with the most comprehensive datasets to identify candidate mitochondrial markers for molecular species identification and phylogenetic inference. Across orders, different mitochondrial regions, including the classical markers 16S and COX1, as well as genes from the NADH dehydrogenase complex, emerged as the most informative, although optimal markers varied among lineages. Overall, our findings highlight the value of publicly accessible sequencing data for generating high-quality genomic resources and improving phylogenetic and taxonomic tools.

Abstract in English:

Abstract The cytochrome c oxidase subunit I (COI), widely adopted as a DNA barcode for Metazoa, exhibits distinct variation levels in different regions within the gene. We investigated the efficacy of combining three arthropod-specific primers to enhance the detection of dietary niches, as opposed to relying on a single primer. This study utilized bat guano collected in bat caves from the Amazon and Caatinga biomes in Brazil. The UEA2-UEA3, UEA3-UEA4, and UEA5-UEA6 primer pairs recovered distinct proportions of Arthropoda (10%, 57%, and 42%, respectively) and exhibited considerable levels of unassigned reads (29%, 33%, and 42%, respectively) and non-target sequences (61%, 10%, and 16%, respectively). The UEA2-UEA3 primarily recovered Chiroptera (57%) but demonstrated the highest taxonomic coverage and richness for Arthropoda. On the other hand, UEA3-UEA4 and UEA5-UEA6 showed the highest α-diversity for Arthropoda; however, UEA5-UEA6 predominantly recovered Lepidoptera (40%) with the highest number of unique Arthropoda genera (45%), while UEA3-UEA4 mostly assigned to Lepidoptera and Diptera. Our results suggest the use of more than one primer pair and show that the analysis of only one primer pair can generate biased outputs. The choice primer is a crucial step in eDNA studies, especially for complex samples such as bat guano.

Abstract in English:

Abstract Syringa is a crucial shrub genus in the family Oleaceae, which has significant ornamental, economic, and medicinal value. However, research on the chloroplast genome (CPG) phylogeny and lineage diversification of this genus remains limited. In this study, all 15 Syringa CPGs exhibited a characteristic quadripartite structure, with genome lengths ranging from 154,019-158,020 bp. These CPGs were highly conserved and moderately differentiated, each containing 130-132 genes. Analysis of inverted repeat (IR) boundaries indicated structural conservation, with six genes: rps19, rpl2, ycf1, trnN, ndhF, and trnH present at the IR/single-copy (SC) junctions. The small single copy (SSC) region displayed greater sequence variability than the IR regions. ycf1, ndhH, trnL-rpl32, ndhF-ycf1, and rbcL-accD were identified as potential molecular markers and rps11, ycf2, and ycf4 may have contributed to the adaptive evolution of Syringa. Phylogenetic reconstruction based on whole CPG data supported the monophyly of the 15 species, which were divided into three distinct subclades. Molecular dating estimated that Syringa diverged from its sister genus approximately 58 million years ago, with most Syringa species diversifying further approximately 47.49 million years ago during the Eocene. Our findings will hopefully stimulate further studies on this genus that may enhance biodiversity knowledge.

Abstract in English:

Abstract The analysis of genotoxicity assays has long posed a major challenge for the standardization of analyses in environmental and occupational settings, as well as in assessing health impacts across various diseases. In this context, we present a mobile application designed to facilitate and standardize scoring in micronucleus, comet, chromosomal aberration, and erythrocyte abnormality assays. The app offers a portable and intuitive interface that allows users to save, resume, and share counting sessions efficiently, supporting both laboratory and field settings. By digitizing the workflow, it enhances data organization, traceability, and time management while preserving the rigor of microscopic analysis. Its adoption offers a practical and reliable alternative to manual tallying, contributing to the evolution of genotoxicity testing practices through mobile technology.

Abstract in English:

Abstract The Cichlidae family, especially the South American genus Cichla, is notable for its rapid diversification and ecological impacts following introductions outside its native range. In this study, we first describe the mitogenomes of three Cichla species. The mitogenome of Cichla piquiti was sequenced from a sample collected at Serra da Mesa Lake, located in the state of Goiás, Brazil. Additionally, the mitogenomes of Cichla monoculus and Cichla temensis were assembled using public data. The mitogenomes were assembled using NovoPlasty, and comparative analyses were performed, including those of the Cichla ocellaris mitogenome data. The mitogenomes ranged from 16,526 bp (C. monoculus) to 16,536 bp (C. piquiti), exhibiting a conserved genomic structure with 13 protein-coding genes, 22 tRNAs, and two rRNAs. These mitogenomes were validated by reconstructing phylogenetic relationships within the Cichlinae subfamily. We identified nucleotide composition biases and observed high nucleotide diversity in the D-loop region. Phylogenetic analysis based on complete mitogenome data indicated that Cichla species form a clade with C. ocellaris, a sister clade to Retroculini. This study provides new mitogenomic insights into Cichla, offering valuable genomic resources for species identification and ecological monitoring.