Rafael Francisco Rivera-Bustamante

The lined sole, Achirus lineatus , is a widely distributed species in the Gulf of Mexico. This basin is constantly exposed to hydrocarbon contamination due to natural oil seeps, oil extraction and oil spills. Previous studies suggest the line sole A. lineatus as a possible sentinel species for oil spills; but the overall landscape of xenobiotic metabolism in this species remains poorly understood. Access to high-quality reference genomes will improve this situation. Here, we report the first whole-genome sequence, assembly, and annotation of the lined sole A. lineatus . We generated 132 Gb of PacBio High-Fidelity (HiFi) reads, which were filtered to retain 93 Gb of ultra-high-quality data. The assembly resulted in a mitogenome of 16,579 bp and a nuclear genome of 486.3 Mb distributed across 199 contigs, with a contig N50 of 9.87 Mb. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis based on the actinopterygii _odb10 database (3,640 orthologs) identified 3,611 (99.2%) complete BUSCOs. Genome annotation strategy resulted in the identification of 22,412 protein-coding genes with a high percentage (95.94%) of functional annotation. The genome of A. lineatus revealed 693 expanded and 3349 contracted gene families. We also identified 123 genes involved in the xenobiotics biodegradation and metabolism pathways, as well as neuroplasticity-related genes that may be associated with responses to environmental toxicants, providing baseline genomic information that suggests an integrated adaptive strategy involving both metabolic and nervous system processes. This assembly represents a valuable genomic resource for future toxicological and ecological studies of this species.

Background: Mitochondrial genomes provide valuable information on evolutionary relationships among organisms and on the selective pressures acting on energy metabolism, increasing their relevance in ecological and environmental genomics studies. Haemulon plumierii is a reef-associated fish distributed throughout the Gulf of Mexico and Caribbean Sea and has been proposed as a bioindicator species within the Mesoamerican Reef System. Methods: In this study, we present a high-quality mitochondrial genome of H. plumierii from the southeastern coast of Mexico generated using PacBio HiFi long-read sequencing. Results: The circular mitogenome is 16,823 bp long and contains the complete set of 37 canonical mitochondrial genes, including 13 protein-coding genes, 22 tRNAs, two rRNAs, and one control region (D-loop). The gene order, strand orientation, and tRNA secondary structures were consistent with the conserved vertebrate mitochondrial architecture. Comparative analyses with closely related haemulid species revealed conserved nucleotide composition patterns, negative GC skew values, strong AT enrichment within the D-loop, and highly conserved mitochondrial synteny. Phylogenetic reconstruction based on complete mitochondrial genomes placed H. plumierii firmly within the Haemulon clade. Selective pressure analyses revealed pervasive purifying selection acting on mitochondrial protein-coding genes, supported by low dN/dS ratios, high amino acid identity, constrained nucleotide diversity in cytochrome oxidase genes, and conserved codon usage patterns shaped primarily by AT-driven mutational bias. Pairwise genetic distance analyses further supported moderate interspecific divergence within Caribbean Haemulon species. Conclusions: Overall, the mitogenomic resource generated here provides an important evolutionary and functional framework for future phylogenetic, ecological, and environmental genomics studies in Caribbean reef fishes.

Chili pepper (Capsicum annuum L.) is an economically important crop in Mexico, with a production that is limited by viral diseases caused by Begomovirus infections such as PHYVV and PepGMV, both transmitted by Bemisia tabaci. These viruses affect both domesticated cultivars and wild populations. The use of resistant genotypes is the most effective strategy to reduce Begomovirus incidence. Since no commercial cultivars with resistance are currently available, in this study, 15 Capsicum annuum accessions with different levels of domestication were inoculated separately with infectious PepGMV and PHYVV dimers by bioballistics, in order to identify sources of genetic resistance or tolerance to these viruses. Symptom progression (severity), incidence, the area under the disease progress curve (AUDPC), and molecular detection of viral DNA by PCR were recorded in asymptomatic plants. PCR results with oligonucleotides targeting PepGMV and PHYVV showed that 96% of asymptomatic plants were positive, confirming that viral replication occurred without the development of visible symptoms. Significant differences were observed among accessions, with wild and semidomesticated accessions showing very low values of severity, incidence, and AUDPC. Notably, the wild accession Acc-106 exhibited resistance to PepGMV and tolerance to PHYVV, with minimum values of severity (0 and 0.13) and incidence (0% and 13%) at 35 days postinoculation.

Chilli pepper (Capsicum annuum L.) is an economically important crop in Mex-21 ico, whose production is limited by viral diseases caused by Begomovirus infections such 22 as PHYVV and PepGMV, both transmitted by Bemisia tabaci. These viruses affect both do-23 mesticated cultivars and wild populations. The use of resistant genotypes is the most ef-24 fective strategy to reduce Begomovirus incidence. Since no commercial cultivars with re-25 sistance are currently available, in this study 15 Capsicum annuum accessions with differ-26 ent levels of domestication were inoculated separately with infectious PepGMV and 27 PHYVV dimers by bioballistics, in order to identify sources of genetic resistance or toler-28 ance to these viruses. Symptom progression (severity), incidence, the area under the dis-29 ease progress curve (AUDPC), and molecular detection of viral DNA by PCR were rec-30 orded in asymptomatic plants. PCR results with oligonucleotides targeting PepGMV and 31 PHYVV showed that 96% of asymptomatic plants were positive, confirming that viral 32 replication occurred without the development of visible symptoms. Significant differ-33 ences were observed among accessions, with wild and semidomesticated accessions 34 showing very low values of severity, incidence, and AUDPC. Notably, the wild accession 35 Acc-106 exhibited resistance to PepGMV and tolerance to PHYVV, with minimum values 36 of severity (0 and 0.13) and incidence (0% and 13%) at 35 days postinoculation.

Viral diseases are a frequent problem in the agricultural sector, causing significant economic losses, so their management is a constant challenge for producers and researchers. One of the factors that often complicates the control of viral diseases in plants is mixed infections, which occur when two or more viruses are present in a plant, generating a complex expression of symptoms. During a mixed infection, the following types of interactions basically occur: complementation and interference, the effect of which produces synergism, antagonism, or no effect. However, there are also subcategories of effects. This makes early detection difficult, and this infection can also give a competitive advantage to the pathogens involved. This review presents updated information on mixed viral infections in plants, the interaction categories, the severity of symptoms, and the impact on plants and vectors. The intention is to share information to better understand the etiology of the diseases.

Geminiviruses are important plant pathogens that affect crops around the world. In some geminivirus–host interactions, infected plants show recovery, a phenomenon characterized by symptom disappearance in newly emerging leaves. In pepper–Pepper golden mosaic virus (PepGMV) interaction, the host recovery process involves a silencing mechanism that includes both post-transcriptional (PTGS) and transcriptional (TGS) gene silencing pathways. Under field conditions, PepGMV is frequently found in mixed infections with Pepper huasteco yellow vein virus (PHYVV), another bipartite begomovirus. Mixed infected plants generally show a synergetic phenomenon and do not present recovery. Little is known about the molecular mechanism of this interaction. In the present study, we explored the effect of superinfection by PHYVV on a PepGMV-infected pepper plant showing recovery. Superinfection with PHYVV led to (a) the appearance of severe symptoms, (b) an increase of the levels of PepGMV DNA accumulation, (c) a decrease of the relative methylation levels of PepGMV DNA, and (d) an increase of chromatin activation marks present in viral minichromosomes. Finally, using heterologous expression and silencing suppression reporter systems, we found that PHYVV REn presents TGS silencing suppressor activity, whereas similar experiments suggest that Rep might be involved in suppressing PTGS.

Viroids are unencapsidated, single-stranded, covalently-closed circular, highly structured, noncoding RNAs of 239–401 nucleotides that cause disease in several economically important crop plants. In tomato (Solanum lycopersicum cv. Rutgers), symptoms of pospiviroid infection include stunting, reduced vigor, flower abortion, and reduced size and number of fruits, resulting in significant crop losses. Dramatic alterations in plant development triggered by viroid infection are the result of differential gene expression; in our study, we focused on the effect of tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) infection on gene networks associated with the regulation of flower and fruit development. The expression of several of the genes were previously reported to be affected by viroid infection, but two genes not previously studied were included. Changes in gene expression of SlBIGPETAL1 (bHLH transcription factor) and SlOVA6 (proline-like tRNA synthetase) are involved in petal morphology and fertility, respectively. Expression of SlOVA6 was down-regulated in flowers of TPMVd- and MPVd-infected plants, while expression of SlBIGPETAL1 was up-regulated in flowers. Up-regulation of SlBIGPETAL1 and down-regulation of SlOVA6 were positively correlated with symptoms such as reduced petal size and flower abortion. Expression analysis of additional tomato genes and a prediction of a global network association of genes involved in flower and fruit development and impacted by viroid infection may further elucidate the pathways underlying viroid pathogenicity.