Mahanarva fimbriolata (Distant 1909) (Hemiptera: Cercopidae) is a major pest that reduces forage production in Brazil, yet few viable control alternatives exist. The RNA interference (RNAi) gene silencing method is a specific and efficient approach that may aid the development of a sustainable management strategy for this pest. It is known that some genes involved in the RNAi machinery are lacking in certain Hemiptera species; therefore, verifying their presence in each target species is necessary. Here, transcriptome assembly of Mahanarva fimbriolata at different developmental stages (egg, nymph and adult stages) was performed, differentially expressed genes were identified, RNAi-related genes described in the literature were annotated in the transcriptome, and coexpression network modeling for the identification of potential RNAi targets was performed. The analysis revealed that the most significant differences in gene expression were between samples in the egg stage and samples in the other development stages. Enriched Gene Ontology terms related to insect growth (e.g., cell division, metamorphosis and flight) and corresponding pathways (e.g., DNA replication and glycolysis/gluconeogenesis) were identified. Coexpression networks demonstrated the importance of biosynthetic hormone processes within specific modules and revealed potential silencing targets, including hub genes such as RPB7 and Talin-2. Transcript annotation and analysis revealed more than 20 genes related to five major RNAi-related processes and factors (dsRNA cleavage, endonucleases, dsRNA binding, dsRNA transport and uptake, and auxiliary RISC-associated or regulatory factors). This work provides a comprehensive molecular overview of metamorphosis in M. fimbriolata, confirms the presence of active RNAi machinery, and reveals potential targets for future gene silencing approaches.

Effective high-throughput phenotyping is crucial for modern plant breeding, yet the optimal image acquisition parameters for UAV-based systems in forage crops remain poorly defined. We optimized UAV-based phenotyping methods for a Megathyrsus maximus biparental population, examining how ground sampling distance (GSD), environment, and harvest date affect the accuracy of RGB-derived digital traits in predicting yield and canopy height. Machine learning algorithms and mixed model analyses were applied to evaluate predictive power and heritability. Pixel count and Haralick's entropy showed strong correlations with conventional yield measurements, particularly in Environment 2, while most vegetative indices were poor predictors. Integrating machine learning substantially enhanced predictive power for green and dry matter yield (r > 0.80). For canopy height, machine learning models achieved correlations of 0.71 with ground truth measurements despite weak pairwise correlations. Mixed model analysis revealed high broad-sense heritability (0.7 < H 2 < 0.87) for yield traits, pixel count, and entropy, while vegetative indices and canopy height showed greater environmental susceptibility. Moderate GSD resolutions (0.5-1.0 cm) consistently outperformed both very high (0.27 cm) and very low (1.5 cm) resolutions. Coincidence index analysis demonstrated 80% correspondence between top genotypes ranked by pixel count and conventionally measured dry matter yield. This study provides an optimized framework for UAV-based phenotyping in M. maximus, demonstrating that combining advanced digital traits with machine learning accurately predicts key agronomic traits and significantly enhances genotype selection efficiency in forage breeding programs.

Hevea brasiliensis (rubber tree) is the main source of natural rubber worldwide. In commercial plantations, high-yield rubber tree clones are propagated by grafting onto seedling rootstocks. In this study, the transcriptomes of the RRIM 600 clone grafted on different rootstocks in southeastern Brazil were evaluated. Exclusively expressed genes (EEGs) and differentially expressed genes linked to quantitative trait loci and coexpression networks were identified. The combination of an RRIM 600 scion (clone) with a non-clonal PB 235 rootstock resulted in the highest mean yield (76.03 g/tree dry rubber), followed by non-clonal IAN 873 rootstock (64.30 g/tree dry rubber). In the non-clonal IAN 873 rootstock combination, we identified the RPD3b gene, an EEG associated with the jasmonate pathway, which increases latex production. This effect was not detected in the non-clonal RRIM 600 and nonselected seed (NSS) rootstock combination, which resulted in decreased latex production. Distinct coexpression patterns were observed, with scion condition (RRIM 600): PB 235 showing stronger gene aggregation, indicating more synergistic interactions among the rubber-related genes Hevea rubber transferase, rubber elongation factor, and small rubber particle protein. In contrast, the NSS rootstocks presented a more dispersed pattern and low latex yield. Our findings highlight the importance of initiating rootstock-breeding programs to improve the production of rubber trees and provide valuable insights into the complex interactions between scions and rootstocks and their impact on latex yield in rubber trees.

This chapter explores the power of phosphorylation reactions in the biological context of nutrient sensing and utilization. Fungal cells adjust their energy status, perceive, and respond to complex external nutrients in their environment by modulating phosphorus reactions. Here, we discuss the related pathways and mechanisms and investigate divergences in phosphorylation at the phylum level in Fungi, providing examples of a rapid, phosphorylation-driven response to important metabolic adaptations, including challenging food sources. The actual research on the topic revealed how a broad, substrate-specific “phospho-switch” orchestrates a critical biological transition, serving as a master regulator that ensures energetic efficiency, sensing, and coordination of the attack on a complex nutrient source. By modulating phosphorylation at specific amino acids, fungi can alter protein properties, conferring different biochemical characteristics or initiating signaling cascades that can modify the expression of multiple genes. By examining these fungal mechanisms, we can distill universal eukaryotic principles of signal transduction that resonate across the tree of life as an efficient and silent language for decoding the environment.

Berry and cluster size are pivotal determinants of grapevine productivity and consumer preferences and remain major targets in grapevine breeding. However, given their complexity as quantitative traits under polygenic control, a deeper understanding of their genetic determinants is needed. The gene pool of the Brazilian grapevine has made a significant contribution to enhancing grapevine performance in tropical and subtropical regions. In this study, we conducted a genome-wide association study (GWAS) using a diverse panel of 288 Vitis spp. accessions from the Instituto Agronômico Germplasm Bank, Brazil. This panel was phenotyped for six cluster architecture traits over 12 years and genotyped using the Vitis18kSNP array. Using two different algorithms, the GWAS identified 56 significant SNPs distributed across 17 chromosomes, validating previously identified quantitative trait loci (QTLs) and revealing novel associations. Four closely spaced markers on Chr1 suggest the presence of a QTL influencing five traits simultaneously. A strong association signal, with phenotypic variance explained (PVE) values of approximately 29-35%, indicated a major QTL for berry length (BL) and width (BWi) on Chr14. Additionally, major-effect SNP loci were identified for cluster weight (CW) on Chr1, cluster length (CL) on Chr7 and 14, cluster width (CWi) on Chr6 and 18, and berry weight (BW) on Chr4, with PVE values ranging from 18-27%. Furthermore, 80 genes associated with berry traits and 52 genes associated with cluster traits were identified as putative candidate genes in the genomic regions associated with significant SNPs. These candidate genes are involved in the regulation of growth and development, hormone regulation, protein synthesis, stress response, and other physiological processes essential for cell health and functionality. Our results provide valuable insights into the genetic determinants of grape berry size and cluster architecture, offering critical data to support future functional studies and enhance the efficiency of related breeding programs.

Fungi represent one of Earth’s most diverse and ecologically vital kingdoms, with an estimated 2.2–3.8 million species, yet only a small part formally described. Their remarkable metabolic versatility enables them to thrive in extreme environments, decompose complex organic compounds, and form symbiotic relationships critical for ecosystem functioning. This chapter explores fungal diversity through the lens of fungi possibilities, highlighting key species and the genetic mechanisms that confer fungi interesting characteristics. We examine fungal adaptability mechanisms—from heat-shock proteins in thermophiles to ligninolytic enzymes in white-rots—and their biotechnological applications in bioremediation, biofuels, and biopharmacos. Nowadays, the bioeconomy based on fungi products and subproducts evolved into cutting-edge engineered bioplatforms for sustainable bioprocesses and carbon-negative technologies. Further, we discuss how advances in genomic data analysis through cloud-based next-generation sequencing pipelines, linked to the growing computational processing capacity, are bringing even more possibilities to fungi discoveries and accelerating the transition to fungal-based technologies. Despite all potential, climate change and biodiversity loss threaten undiscovered species with potential industrial value and pose risks to agriculture and health. Thus, integrating multi-omics, synthetic biology, and conservation strategies will be crucial to harnessing fungi’s full potential in addressing global challenges.

In filamentous fungi, light plays a key role in regulating physiological processes such as growth, conidiation, secondary metabolism, and the expression of hydrolytic enzymes. The processes that depend on light are controlled by photoreceptors, including BLR1, BLR2, and ENV1, as well as by signaling pathways involving heterotrimeric G-proteins and cyclic adenosine monophosphate (cAMP). Trichoderma harzianum is a promising candidate for biotechnological use and is able to promote hydrolytic reactions under biomass degradation conditions. However, the genetic mechanisms underlying its response to light remain poorly understood, especially under degradative conditions. This study aimed to assess the expression of carbohydrate-active enzymes (CAZymes), transcription factors (TFs), and signaling pathway proteins under different light conditions and carbon sources. The results revealed distinct patterns of relative gene expression influenced by these environmental factors, highlighting the complex regulatory mechanisms at play in T. harzianum . Moreover, our results suggested that env1 , cre1 , and blr2 are critical for adjusting to different light conditions and carbon sources. This highlights the importance of both factors in regulating gene expression and supporting metabolic adaptation in T. harzianum . To our knowledge, such findings have not been previously reported in the context of cellulose degradation for this species. Overall, these results offer valuable insights into how T. harzianum responds to environmental changes, revealing a complex regulatory network that is not only crucial for optimizing fungal growth in industrial applications but also deepens our understanding of its biology and ecological interactions. Highlights ![Figure][1] ### Competing Interest Statement The authors have declared no competing interest. Fundação de Amparo à Pesquisa do Estado de São Paulo, 2015/09202-0, 2018/19660-4, 2020/13420-1, 2024/01728-2 Conselho Nacional de Desenvolvimento Científico e Tecnológico, 312777/2018-3 Coordenação de Aperfeicoamento de Pessoal de Nível Superior, 88882.160095/2013-01 [1]: pending:yes

Sugarcane holds significant economic importance in sugar and biofuel production. Despite extensive research, understanding highly quantitative traits remains challenging due to its complex genomic landscape. We conducted a multiomic investigation to elucidate the genetic architecture and molecular mechanisms governing sugarcane sucrose accumulation. Using a biparental cross and a genetically diverse collection of sugarcane genotypes, we evaluated the soluble solids (Brix) and sucrose content (POL) across various years. Both populations were genotyped using a genotyping-by-sequencing approach. Genotype‒phenotype associations were established using a combination of traditional linear mixed-effect models and machine learning algorithms. Furthermore, we conducted an RNA sequencing experiment on genotypes exhibiting distinct Brix and POL profiles across different developmental stages. Differentially expressed genes (DEGs) potentially associated with variations in sucrose accumulation were identified. All findings were integrated through gene coexpression network analyses. Strong correlations among the evaluated characteristics were observed, with estimates of modest to high heritabilities. By leveraging a broad set of single-nucleotide polymorphisms (SNPs) identified for both populations, we identified several SNPs potentially linked to phenotypic variance. Our examination of genes close to these markers facilitated the association of such SNPs with DEGs for contrasting sucrose levels. Through the integration of these results with a gene coexpression network, we delineated a set of genes potentially involved in the regulatory mechanisms of sucrose accumulation. Our findings constitute a significant resource for biotechnology and plant breeding initiatives. Furthermore, our genotype‒phenotype association models hold promise for application in genomic selection, offering valuable insights into the molecular underpinnings governing sucrose accumulation in sugarcane. Our multiomic investigation of sugarcane reveals significant genetic markers and regulatory genes linked to sucrose accumulation, providing valuable resources for biotechnology and plant breeding to enhance sugar production.

North American Vitis species serve as a vital reservoir of genetic variation, offering valuable resources for molecular breeding programs focused on developing cultivars with enhanced resistance, adaptability, and quality traits for sustainable viticulture. The effective conservation and utilization of collections involving these species require a thorough understanding of their genetic diversity, population structure, and gene flow. In this study, 323 North American Vitis accessions categorized into six species groups were genotyped using 29 polymorphic microsatellite (SSR) markers. The objectives were to assess the genetic diversity and population structure, as well as to establish a representative core collection. Additionally, SSR markers associated with 15 resistance loci (R-loci) were analyzed to identify potential resistance to downy mildew, powdery mildew, black rot, Pierce's disease, and phylloxera. The analysis revealed high genetic diversity, with 643 alleles identified, an expected heterozygosity (HE) of 0.86, and an observed heterozygosity (HO) of 0.74. Nine genetic groups were identified, with clear evidence of a substructure within some species. A core collection comprising 95 accessions capable of retaining all SSR alleles detected in the entire collection was established. Characterization of the R-loci revealed that 123 wild genotypes carried a single R-locus, 36 carried two R-loci, and 10 harbored three R-loci associated with pathogen resistance. The richness evident in the studied genetic pool represents an extensive reservoir of underexplored genetic diversity and crossbreeding potential. These findings have the potential to bolster the sustainable management, conservation, and subsequent molecular breeding applications of wild Vitis resources amidst emerging challenges in viticulture.

Pinus taeda (loblolly pine) is one of the most economically significant forest trees worldwide. Among growth traits, stem volume is the most widely considered trait in tree improvement programs. However, deciphering the genetic markers associated with growth trait variations in conifers is challenging due to the intricate complexity of Pinus genomes. In this study, we present a comprehensive genetic analysis of loblolly pine, focusing on single-nucleotide polymorphisms (SNPs) associated with stem volume variation to elucidate the molecular mechanisms governing high-performance phenotypes. We used 1,692 individuals phenotyped for stem volume and genotyped using sequence capture probes. To determine genome-wide associations, we utilized both genome-wide association study (GWAS) analysis and machine learning (ML). The SNPs identified in association with stem volume best linear unbiased estimates (BLUEs) were linked with assembled genes from three distinct transcriptomes, which were employed to construct gene coexpression networks. Through topological evaluations, we identified key genes with potential regulatory roles within stem volume variation. From 31,589 SNPs, we defined 7 GWAS-associated SNPs and 128 ML-associated SNPs, affecting genes involved in diverse molecular mechanisms. Key genes directly implicated in the regulation of growth and response to stress were identified. Gene coexpression network analysis revealed functional relationships between genes near SNPs associated with stem volume BLUEs, highlighting potential key regulators. These findings significantly advance our understanding of the genetics influencing growth traits, reveal candidate genes for functional studies, and contribute to the understanding of the genetic architecture underlying volume traits in loblolly pine.

Lignocellulosic biomass is a complex carbon source with recalcitrant properties whose degradation via industrial enzymatic hydrolysis is challenging, directly affecting the cost of reliable energy production. In nature, filamentous fungi, including Trichoderma species, degrade lignocellulose via an arsenal of hydrolytic and oxidative enzymes that act synergistically to process it into soluble sugar monomers. This work explored the genomic content of Trichoderma atroviride and Trichoderma harzianum strains with hydrolytic abilities by identifying regions possessing degradative enzyme-encoding genes, namely, hydrolytic clusters. We employed bacterial artificial chromosome (BAC) methodology to target specific genomic regions and explore their genetic organization, proximal gene context, and gene expression under degradative conditions. With this tool, it was possible to inspect the linear structure and expression profile of target hydrolytic-rich genomic regions. The present work offers a perspective on the organization of genome regions related to carbohydrate metabolism. This study revealed novel genes and genome regions that are positively regulated during cellulose degradation, contributing to elucidating differences in gene organization that potentially impact hydrolysis among Trichoderma species.

BACKGROUND:Sugarcane (Saccharum spp.) is a preeminent sugar and bioenergy crop and has great economic importance in tropical countries. A major disease affecting this crop is yellow leaf disease, caused by sugarcane yellow leaf virus (SCYLV, Polerovirus SCYLV, Solemoviridae). The sugarcane aphid Melanaphis sacchari is considered the main vector of SCYLV, and the closely related sorghum aphid Melanaphis sorghi, which has recently emerged as a pest of great relevance in sorghum, has also been suspected to be a vector. Genetic resistance is an important resource for preventing yield losses caused by SCYLV and its vectors, but knowledge on the underlying molecular mechanisms is lacking. Therefore, the present work aimed to investigate the transcriptomic responses of sugarcane to SCYLV and M. sorghi, which was reported to transmit this virus for the first time herein. RESULTS:Two sugarcane cultivars, one susceptible and one tolerant to SCYLV, were fed upon by aviruliferous and viruliferous aphids. The transcriptome of the plants was assessed via RNA-Seq via differential gene expression analyses and a gene coexpression network. The susceptible cultivar showed an incipient reaction to both M. sorghi and SCYLV, with very few differentially expressed genes (DEGs) identified in comparison with aphid-free plants. The response of the tolerant cultivar to aviruliferous M. sorghi involved pathways typically associated with defense against herbivory, which were also enriched in coexpression network modules in which DEGs were overrepresented. Some of these genes were hubs in their respective modules, indicating that they are potential key regulators of defense responses. However, these responses were diminished when viruliferous aphids were used, and other processes linked to infection with SCYLV were altered. CONCLUSIONS:These results indicated that SCYLV could affect sugarcane defense responses to its vector, similar to other viruses of the same genus. Possible implications for the epidemiology and impact of SCYLV and M. sorghi are discussed.

The characterization of genetic resources is essential to carry out a breeding program. This study aimed to characterize Paspalum genotypes with potential use as soil surface covering to support breeding programs on the development of turf cultivars. Forty-three Paspalum genotypes, comprising 11 species, were evaluated. The embryo-sacs structure was determined by cleared ovaries analysis and eight accessions were classified as sexual, 15 as apomictic, and 20 presenting facultative apomixis. Most of the genotypes have 40 chromosomes, with the exception of one accession of Paspalum vaginatum, two of Paspalum indecorum, one of Paspalum modestum, and two of Paspalum notatum that have 20 and one accession of Paspalum jesuiticum and one of Paspalum mandiocanum that have 60 chromosomes. DNA content was determined by flow cytometry, ranging from 1.35 to 4.00 pg of DNA, with most of the accessions corresponding to tetraploidy, but also diploidy and hexaploidy were found, corroborating chromosome counts. High genetic variability was found among the 43 accessions based on 11 microsatellite markers and their use to estimate Jaccard similarity coefficients and Bayesian analysis, forming six different genetic groups. Considering only the P. notatum accessions, great variability was observed with four distinct groups formed. The results presented in this work reveal the possibility to obtain assertive crosses between compatible parents, aiming to explore the genetic variability between and within species of this genus.

Spittlebugs cause large production losses that affect agribusiness worldwide. Understanding plant-herbivore interactions at the molecular level may be the key to developing resistant cultivars. After a nymph survival experiment, root transcriptomes were assembled from two Paspalum regnellii genotypes (BGP 248 and 344) with different first-line defense strategies, with no infestation and at two times after the initial attack of the spittlebug (Mahanarva spectabilis) nymph, thus integrating differential expression analysis and biological network modeling supplemented by root anatomical analysis. Gene Ontology terms related to different stress responses, such as salicylic acid catabolic process, were enriched in BGP 248, while some specific to spittlebugs, such as response to herbivores, were enriched in BGP 344. Enriched pathways were related to structural differences between genotypes, such as those related to cutin, suberin, and wax biosynthesis. BGP 344 also presented pathways related to induced defense, such as glutathione metabolism. Metabolic networks highlighted kinases, and coexpression networks demonstrated a complex cascade response that included lncRNAs. This study provides the first molecular insights into the defense mechanisms of P. regnellii against M. spectabilis. The genotype with the fastest response to insect attack and highest nymph mortality (BGP 344) presented kinases and an enriched glutathione pathway, in addition to constitutive barriers, such as lignin, which can make it difficult for the insect to colonize the plant.

Understanding the population dynamics of vectors is crucial for effective control of vector-borne diseases. In the Northeastern Brazilian semi-arid region, Triatoma brasiliensis persists as the most significant Chagas disease vector, frequently displaying recurrent domiciliary infestations. This situation raises relevant public health concerns in the municipality of Currais Novos in the state of Rio Grande do Norte. This area has experienced a high prevalence of peridomiciliary re-infestations by T. brasiliensis, coupled with elevated rates of Trypanosoma cruzi infection. Therefore, we assessed the distribution of genetic variation via mitochondrial Cytochrome b gene (MT-CYB) sequencing (n = 109) and single nucleotide polymorphisms (SNPs, n = 86) to assess the gene flow among distinct populations distributed in varied geographic spots and environments, mainly sylvatic and peridomiciliary. Insects were collected from rural communities at Currais Novos, enclosed within a 16 km radius. Sampling included 13 populations: one intradomiciliary, eight peridomiciliary, and four sylvatic. Furthermore, an external population located 220 km from Currais Novos was also included in the study. The method employed to obtain SNP information relied on ddRAD-seq genotyping-by-sequencing (GBS), enabling a genome-wide analysis to infer genetic variation. Through AMOVA analysis of MT-CYB gene variation, we identified four distinct population groups with statistical significance (FCT= 0.42; p<0.05). We identified a total of 3,013 SNPs through GBS, with 11 loci showing putative signs of being under selection. The variation based on 3,002 neutral loci evidenced low genetic structuration based on low FST values (p>0.05), indicating local panmixia. However, resampling algorithms pointed out that three samples from the external population were assigned (>98 %) in a cluster contrasting from the ones putatively under local panmixia - validating the newly applied genome-wide marker for studies on the population genetics at finer-scale resolution for T. brasiliensis. The presence of population structuring in some of the sampled points, as suggested by the mitochondrial marker, leads us to assume that infestations were probably initiated by small populations of females - demographic event poses a risk for rapid re-infestations. The local panmictic pattern revealed by the GBS marker poses a challenge for vector control measures, as re-infestation foci may be distributed over a wide geographical and ecological range. In such instances, vectors exhibit reduced susceptibility to conventional insecticide spraying operations since sylvatic populations are beyond the reach of these interventions. The pattern of infestation exhibited by T. brasiliensis necessitates integrating innovative strategies into the existing control framework, holding the potential to create a more resilient and adaptive vector control program. In our dataset, the results demonstrated that the genetic signals from both markers were complementary. Therefore, it is essential to consider the nature and inheritance pattern of each marker when inferring the pattern of re-infestations.

ABSTRACT Mangroves are coastal ecosystems of great socioenvironmental importance that are highly threatened by human activities. Mangrove trees live under harsh environmental conditions, which makes them sensitive to extreme weather events, particularly freezing events. Such events are unpredictable and have catastrophic consequences for mangrove trees; therefore, understanding and anticipating the impacts of such events are essential for directing future mitigation measures. Freezing cold currently limits the distribution of mangroves to tropical and subtropical latitudes worldwide. Mangrove trees are seriously affected by freezing conditions and suffer severe metabolic fluctuations due to photosystem and cellular structure damage. However, land plants more broadly have developed sophisticated mechanisms of resistance to freezing during their evolution, and the central molecular mechanisms involved in this process are consistent. However, the known information is restricted to models of herbaceous plants, such as Arabidopsis thaliana , that are native to temperate habitats, and there is a research gap regarding tropical trees such as mangroves. This work aimed to improve the understanding of the molecular aspects of the response and tolerance to freezing in mangrove trees using Avicennia schaueriana as a model. This species occurs within the colder range limits of South American mangroves and shows evidence of the existence of two functional groups that are locally adapted to the equatorial (EQ) and subtropical (ST) portions of the Brazilian coast. We investigated the transcriptional profiles of seedlings from both functional groups under freezing shock (−4°C) in a time series. We analyzed transcriptomic data by combining differential expression, coexpression network and protein interaction data. Our results allowed us to describe the profile of the molecular response of A. schaueriana to freezing and the divergence in the behavior of the EQ and ST functional groups. In EQ plants, the response strongly depended on the action of abscisic acid (ABA) and stress signals throughout the experiment. Notably, ABA negatively affects plant growth and promotes the accumulation of carotenoids, anthocyanins and lipids through chlorophyll degradation. On the other hand, in the ST, there were fewer hormones active in the process of primary growth maintenance and metabolic normalization. The accumulation of substances is mainly based on sucrose, anthocyanin and lipid levels, and lipid synthesis is not dependent on chlorophyll degradation. Based on these results, we hypothesize that susceptibility to freezing damage is greater in EQ mangroves than in ST mangroves. Therefore, we recommend that this fact be considered when managing this species, especially at higher latitudes, which are more prone to lower temperatures and extreme freezing events.

The mountains in the Atlantic Forest domain are environments that harbor a high biodiversity, including species adapted to colder climates that were probably influenced by the climatic variations of the Pleistocene. To understand the phylogeographic pattern and assess the taxonomic boundaries between two sister montane species, a genomic study of the butterflies Actinote mantiqueira and A. alalia (Nymphalidae: Acraeini) was conducted. Analyses based on partial sequences of the mitochondrial gene COI (barcode region) failed to recover any phylogenetic or genetic structure discriminating the two species or sampling localities. However, single nucleotide polymorphisms gathered using Genotyping‐by‐Sequencing provided a strong isolation pattern in all analyses (genetic distance, phylogenetic hypothesis, clustering analyses, and FST statistics) which is consistent with morphology, separating all individuals of A. alalia from all populations of A. mantiqueira. The three sampled mountain ranges where A. mantiqueira populations occur—Serra do Mar, Serra da Mantiqueira, and Poços de Caldas Plateau—were identified as three isolated clusters. Paleoclimate simulations indicate that both species' distributions changed according to climatic oscillations in the Pleistocene period, with the two species potentially occurring in areas of lower altitude during glacial periods when compared to the interglacial periods (as the present). Besides, a potential path between their distribution through the Serra do Mar Mountain range was inferred. Therefore, the Pleistocene climatic fluctuation had a significant impact on the speciation process between A. alalia and A. mantiqueira, which was brought on by isolation at different mountain summits during interglacial periods, as shown by the modeled historical distribution and the observed genetic structure.

Unraveling the patterns of genetic structure and demographic history of marine species, as well as the factors that shape their genetic variations, is fundamental for informing conservation strategies for species and their environments. In this work, we investigate the current population structure and historical demographic patterns of the conspicuous seaweed-associated amphipod Hyale niger at a fine spatial scale in the subtropical SW Atlantic coast, in Brazil, by using both genome-wide and mitochondrial DNA markers. We also investigate how geographic distance, current oceanographic conditions, and variations in a key morphological trait contribute to the genetic variability of the amphipod. We observed an evident population genetic structure, even at a fine spatial scale, although genetic differentiation was lower than our expectations for a benthic direct brooder. Demographic history inferences were consistent across populations and showed two major demographic expansions on interglacial periods during the late Pleiostocene, before and after the last glacial maximum. We also demonstrated that isolation-by-environment (IBE) was the main driver of genetic differentiation, although we could not separate it from the effects of isolation-by-distance (IBD). Among environmental factors, nutrient concentrations in seawater were most relevant for explaining genetic structure. In addition, our data suggest that morphological variation in gnathopod 2 structure of males were not genetic-related and were probably plastic as a response to variations in macroalgae frond size. Our study reinforces the importance of using multiple molecular markers and analytical approaches to unveil patterns and processes generating genetic variation in natural populations.

Mangroves are coastal ecosystems of great socioenvironmental importance that are highly threatened by human activities. Mangrove trees live under harsh environmental conditions, which makes them sensitive to extreme weather events, particularly freezing events. Such events are unpredictable and have catastrophic consequences for mangrove trees; therefore, understanding and anticipating the impacts of such events are essential for directing future mitigation measures. Freezing cold currently limits the distribution of mangroves to tropical and subtropical latitudes worldwide. Mangrove trees are seriously affected by freezing conditions and suffer severe metabolic fluctuations due to photosystem and cellular structure damage. However, land plants more broadly have developed sophisticated mechanisms of resistance to freezing during their evolution, and the central molecular mechanisms involved in this process are consistent. However, the known information is restricted to models of herbaceous plants, such as Arabidopsis thaliana , that are native to temperate habitats, and there is a research gap regarding tropical trees such as mangroves. This work aimed to improve the understanding of the molecular aspects of the response and tolerance to freezing in mangrove trees using Avicennia schaueriana as a model. This species occurs within the colder range limits of South American mangroves and shows evidence of the existence of two functional groups that are locally adapted to the equatorial (EQ) and subtropical (ST) portions of the Brazilian coast. We investigated the transcriptional profiles of seedlings from both functional groups under freezing shock (−4°C) in a time series. We analyzed transcriptomic data by combining differential expression, coexpression network and protein interaction data. Our results allowed us to describe the profile of the molecular response of A. schaueriana to freezing and the divergence in the behavior of the EQ and ST functional groups. In EQ plants, the response strongly depended on the action of abscisic acid (ABA) and stress signals throughout the experiment. Notably, ABA negatively affects plant growth and promotes the accumulation of carotenoids, anthocyanins and lipids through chlorophyll degradation. On the other hand, in the ST, there were fewer hormones active in the process of primary growth maintenance and metabolic normalization. The accumulation of substances is mainly based on sucrose, anthocyanin and lipid levels, and lipid synthesis is not dependent on chlorophyll degradation. Based on these results, we hypothesize that susceptibility to freezing damage is greater in EQ mangroves than in ST mangroves. Therefore, we recommend that this fact be considered when managing this species, especially at higher latitudes, which are more prone to lower temperatures and extreme freezing events. ### Competing Interest Statement The authors have declared no competing interest.

Elucidating the intricacies of the sugarcane genome is essential for breeding superior cultivars. This economically important crop originates from hybridizations of highly polyploid Saccharum species. However, the large size (10 Gb), high polyploidy, and aneuploidy of the sugarcane genome pose significant challenges to complete genome sequencing, assembly, and annotation. One successful strategy for identifying candidate genes linked to agronomic traits, particularly those associated with sugar accumulation, leverages synteny and potential collinearity with related species. In this study, we explored synteny between sorghum and sugarcane. Genes from a sorghum Brix QTL were used to screen bacterial artificial chromosome (BAC) libraries from two Brazilian sugarcane varieties (IACSP93-3046 and SP80-3280). The entire region was successfully recovered, confirming synteny and collinearity between the species. Manual annotation identified 51 genes in the hybrid varieties that were subsequently confirmed to be present in Saccharum spontaneum . To identify candidate genes for sugar accumulation, this study employed a multifaceted approach, including retrieving the genomic region of interest, performing gene-by-gene analysis, analyzing RNA-seq data of internodes from Saccharum officinarum and S. spontaneum accessions, constructing a coexpression network to examine the expression patterns of genes within the studied region and their neighbors, and finally identifying differentially expressed genes (DEGs). This comprehensive approach led to the discovery of three candidate genes potentially involved in sugar accumulation: an ethylene-responsive transcription factor (ERF), an ABA 8’-hydroxylase, and a prolyl oligopeptidase (POP). These findings could be valuable for identifying additional candidate genes for other important agricultural traits and directly targeting candidate genes for further work in molecular breeding.### Competing Interest StatementThe authors have declared no competing interest.