DNA Sequence Research Articles

Спорадическая медуллярная карцинома щитовидной железы в детском возрасте: клиническое наблюдение

Medullary thyroid carcinoma (MTC) is one of the rarest tumors of the neuroendocrine system occurring in childhood. MTC represents approximately 4% to 8% of all thyroid malignancies in children with an incidence of 0.03 per 100,000 pediatric population per annum. As a rule, MCT in childhood is presented as part of hereditary syndromes (MEN2A, MEN2B) whereas the prevalence of the sporadic form has not been sufficiently studied as well as its molecular and genetic features. Authors represent the Russia’s first clinical case of sporadic MTC in a 16 years old child. The girl at the age of 14 y/o was examined by an endocrinologist at the place of residence due to the absence of menarche. According to the results of a comprehensive examination, a mass measuring of up to 27 mm was detected in the left lobe of the thyroid gland. Cytological examination revealed a picture suspicious for C-cell carcinoma. The basal calcitonin level was 2160 pg/ml (with 0 to 4.8 pg/ml as a norm). The patient had then underwent thyroidectomy with central lymphadenectomy as a result of histological and immunohistochemical studies of medullary thyroid carcinoma pT2N0 MxLV0Pn0. According to the results of molecular genetic study of peripheral blood, neither germinal pathogenic nor opportunistic mutations in RET gene were detected. Full-exome sequencing of DNA isolated from tumour tissue revealed as pathogenic/conditional pathogenic mutations RET p.M918T, CHEK2 p. R29X, VRK1 p.H119R and ARSE p. G422R. After 3.5 years of follow-up, the patient had a complete structural and biochemical remission of the disease.

Tandem repeat disorders: from diagnosis to emerging therapeutic strategies.

Tandem repeat disorders (TRDs) are genetic conditions characterized by the abnormal expansion of repetitive DNA sequences within specific genes. The growing number of identified TRDs highlights their complexity, with varied molecular mechanisms ranging from toxic protein production and repeat-associated non-AUG translation to RNA toxicity and epigenetic modifications. TRDs also exhibit unique clinical features such as reduced penetrance, anticipation, and repeat motif changes. Advances in molecular diagnostics such as long-read sequencing have significantly improved the detection of TRDs, especially for large or complex repeat expansions. Additionally, emerging therapeutic strategies, particularly antisense oligonucleotides (ASOs) and gene editing technologies, are showing great promise. ASOs in particular have demonstrated success through mechanisms like allele-specific knockdown and splice modulation. In this review, we explore the classification of TRDs, advances in diagnostics, molecular mechanisms, clinical features, and innovative therapeutic strategies, highlighting the need for further research to refine treatments and improve outcomes.

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq.

Accurately quantifying the functional consequences of noncoding mosaic variants requires the pairing of DNA sequences with both accessible and closed chromatin architectures along individual DNA molecules-a pairing that cannot be achieved using traditional fragmentation-based chromatin assays. We demonstrate that targeted single-molecule chromatin fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic, and epigenomic profiling across targeted >100 kb loci with ∼10-fold enrichment over untargeted sequencing. Targeted Fiber-seq reveals that pathogenic expansions of the DMPK CTG repeat that underlie Myotonic Dystrophy 1 are characterized by somatic instability and disruption of multiple nearby regulatory elements, both of which are repeat length-dependent. Furthermore, we reveal that therapeutic adenine base editing of the segmentally duplicated γ-globin (HBG1/HBG2) promoters in primary human hematopoietic cells induced toward an erythroblast lineage increases the accessibility of the HBG1 promoter as well as neighboring regulatory elements. Overall, we find that these non-protein coding mosaic variants can have complex impacts on chromatin architectures, including extending beyond the regulatory element harboring the variant.

Abstract A002: Computational identification for missense mutations of bladder cancer candidate genes using TCGA datasets

Abstract Bladder cancer is the fourth most common cancer in men. According to the American Cancer Society, there were roughly over 80,000 cases in the United States in 2023, and nine out of ten people with this cancer are over the age of 55. The Cancer Genome Atlas (TCGA) project has made it possible for researchers to study mutations and other types of genetic signatures for multiple cancers including Bladder Urothelial Carcinoma (BLCA). A missense mutation is where a single nucleotide change in the DNA sequence results in the substitution of one amino acid for another in the protein. This could lead to a protein with an altered function. The impact of a missense mutation could be benign or harmful. In our previous study, 54 significant clusters for 15 cancer types were identified in The Cancer Genome Atlas (TCGA) network. In this study, we further investigated genes in two significant clusters reported for BLCA. We initially aim to identify genes that have missense mutations that have functional impact. To achieve this goal, we plugged the two clusters of genes (199) into the cBioPortal website and identified eight genes that had missense mutations or met three criteria (Firstly, numbers of mutations in sample must be greater than or equal to 5; secondly, functional impact must meet the following both: SIFT impact is deleterious and Polyphen-2 impact is possibly damaging or probably damaging): AKT3, PARP1, PRKN, APC, GNA11, KMT2A, NEGR1, and FYN. Further analysis showed what specific amino acid had been substituted at what specific position on the sequence. For example, for gene AKT3, at position 286, amino acid K had been substituted into amino acid N. Similarly, for gene PARP1, at position 913, amino acid G had been substituted into amino acid A. We then identified every amino acid missense substitution for all eight genes. By examining the mutation pattern, we hope to identify key genes as biomarkers so that therapeutic efficacy can be optimized. Citation Format: Kai He, Lucas Wang, Yongsheng Bai. Computational identification for missense mutations of bladder cancer candidate genes using TCGA datasets. [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Optimizing Therapeutic Efficacy and Tolerability through Cancer Chemistry; 2024 Dec 9-11; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(12_Suppl):Abstract nr A002

Phylogeny and Genetic Population Structure of Dominant Copepods in Two Ponds with Contrasting Salinities in the Solar Saltern of Sfax (Tunisia) Based on Mitochondrial (COI and Cytb) and Nuclear (18S) DNA Sequences

Due to the complexity of taxonomic classification based on the classical morphological characters of copepods, phylogenies have been ambiguous. In this study, we investigate the phylogeny of copepods, including four species from three orders, in the saltern of Sfax using the small subunit of nuclear ribosomal RNA genes (18S). In the studied area, copepods seemed to be a polyphyletic group, and the genetic structure of these crustaceans is complex and problematic. We have also used two mitochondrial markers, the cytochrome c oxidase subunit I (mtCOI) gene and the cytochrome b (Cytb) sequence data, in order to investigate the genetic diversity and differentiation in a total of 96 individuals from two sets of Paracartia grani, sampled from two ponds with different salinities (42 PSU and 61 PSU). All of the results presented here suggest a low genetic diversity among P. grani species and a weak genetic structure between the sets. The nucleotide and haplotype diversity of P. grani were extremely low, indicating the homogeneity of the two sets, which could be combined into one set living in different ranges of salinity. This small genetic diversity is possibly due to the confined natural distribution range and strong selective pressure in a saltern environment. These data also suggest that gene flow is the main factor shaping the genetic structure of the studied sets.

Effects of Storm Runoff on Bacterial Community Structure and Metabolic Activity and Water Quality in a Drinking Water Reservoir

To explore the influence of storm runoff on bacterial metabolic activity and water quality in Jinpen Reservoir, three-dimensional fluorescence spectroscopy parallel factor analysis, high-throughput DNA sequencing technology, and Biolog technology were used to analyze variations in the components of dissolved organic matter, bacterial community composition, and microbial metabolic activity during three periods （before, during, and one month after runoff）. The results showed that after storm runoff into the reservoir, the water temperature decreased, and dissolved oxygen in the middle of the water column increased significantly. Finally, the aerobic and low-temperature state in the middle water and anaerobic and low-temperature state in the bottom water was formed. Simultaneously, the concentration of total nitrogen, total phosphorus, organic matter, and turbidity increased significantly. After one month of runoff, the concentration of pollutant decreased, however, was still higher than that before runoff. Further, during the runoff period, the proportion of Proteobacteria and Bacteroidetes increased significantly and the sum of their relative abundance accounted for 63.6% of the bacterial community. The bacterial metabolic activity was also higher than that before. One month after runoff, the bacterial population structure did not recover and the bacterial metabolic activity still remained at a high level.

Time-calibrated phylogeny of neotropical freshwater fishes

Neotropical Freshwater Fish (NFF) fauna exhibits the greatest phenotypic disparity and species richness among all continental aquatic vertebrate faunas, with more than 6,345 species distributed across the mostly tropical regions of Central and South America. The last two decades have seen a proliferation of molecular phylogenies, often at the species level, covering almost all 875 valid NFF genera. This study presents the most comprehensive genome-wide, time-calibrated phylogenetic hypothesis of NFF species to date, based on DNA sequences generated over decades through the collaborative efforts of the multinational ichthyological research community. Our purpose is to build and curate an extensive molecular dataset allowing researchers to evaluate macroevolutionary hypotheses in the NFF while facilitating continuous refinement and expansion. Using thousands of DNA sequences from dozens of studies, we compiled a supermatrix of 51 markers for 5,984 taxa, representing 3,167 NFF species. Based on this dataset, we built the most species-rich time-calibrated phylogeny of the NFF taxa to date, summarizing the collective efforts of the ichthyological research community since the midpoint of the last century. We provide a summary review of this remarkable evolutionary history and hope this dataset provides a framework for forthcoming studies of the NFF fauna, documenting compelling, emergent patterns in the world’s most diverse continental vertebrate fauna.

Phylogeny and Taxonomy of the Naematelia aurantialba Complex in Southwestern China

Naematelia aurantialba and its allies are important edible and medicinal mushrooms in China. They are usually called Jiner (金耳) and have been cultivated on a commercial scale. However, due to the lack of DNA sequences from the holotype of Naematelia aurantialba, the taxonomic issues of the species complex are unresolved. In this study, the authors successfully generated DNA sequences from the holotype of N. aurantialba by a genome skimming approach and additional allied species by Sanger sequencing. Based on morphological characteristics, molecular phylogenetic data, and geographic distribution patterns, four species, including three new ones, in the complex in southwestern China were uncovered. Naematelia aurantialba occurs at high altitudes (over 3000 m above sea level), with subalpine dead plants as its substrates, and has larger basidiospores, while the commonly cultivated species, described as N. sinensis in this work, is distributed in subtropical areas at altitudes between 1800 m and 2600 m on the dead wood of subtropical plants and has smaller basidiospores. The third species, namely N. nodulosa, has habitats similar to those of N. sinensis but differs from the latter in its basidiomata with an uneven nodulose surface, a loose context with small internal cavities, and numerous conidia. The fourth species, N. pedicellata, is easily distinguished from the others by its basidia, with long basal stalks and broadly ellipsoid basidiospores measuring 10.5–12.5 × 8.0–10.0 μm. All these species are parasitic on Stereum species. This study provides a solid basis for future guidance for the selection of new strains and cultivation practices of these valuable fungi.

Morphological, Molecular, and Pathogenic Characterization of Rhizoctonia solani Isolates Associated with Bean Drying in Northern Sinaloa, Mexico.

Objective: The objective of this study was to characterize, using morphology, DNA sequence analysis, and pathogenicity, R. solani isolates associated with bean plants with root rot symptoms in commercial plots in northern Sinaloa. Design/methodology/approach: During the 2020-2021 cycle, diseased plants infected by Rhizoctonia were collected in the municipalities of Ahome, El Fuerte, and Guasave. Pure fungal isolates were obtained in specific media; which were morphologically characterized in PDA medium and preserved. Subsequently, the pathogenicity of the isolates was evaluated and they were molecularly identified. Genomic DNA was extracted from the isolates, part of the RPB2 gene was amplified by PCR, and the amplified products were sequenced. Results: Phylogenetic analysis with RPB2 sequence data confirmed the identification of 63 isolates as R. solani and allowed them to be assigned to the anastomosis group (AG): AG-4. Of the total isolates analyzed, 86% correspond to the AG-4 HGI anastomosis subgroup and 14% to the AG-4 HGIII subgroup. In pathogenicity, the percentage of germination and severity of the isolates were evaluated, showing different levels of pathogenicity. Limitations of the study/implications: None. Findings/conclusions: Rhizoctonia solani AG-4 anastomosis subgroups HGI and HGIII are associated with bean drying in northern Sinaloa. Therefore, this study will serve as a basis for other studies that generate control strategies for this pathogen.

Characterization of Nodulation-Compatible Strains of Native Soil Rhizobia from the Rhizosphere of Soya Bean (Glycine max L.) Fields in South Africa

Prolonged inoculation of soya bean (Glycine max L.) farms with exotic strains of Bradyrhizobium species starting in the 1960s resulted in the establishment of populations of Bradyrhizobium strains in the soils of several soya bean farms in South Africa. With the increasing number of new soya bean genotypes in the country, it is challenging to determine which genotypes are highly compatible with a given rhizobium strain. In this study, we investigated the symbiotic compatibility of native rhizobial isolates and the strains from the South African Rhizobium Culture Collection (SARCC) on ten selected locally available soya bean genotypes. A glasshouse soil trap experiment using soil samples collected from Lothair, Bothaville, and Standerton was performed on five cultivars. The trapped rhizobial strains were further screened in the glasshouse to authenticate their nodulation compatibility with the different soya bean cultivars. The rhizobial strains showed significant nodulation compatibility with the selected cultivars. These strains were also tested for beneficial traits in vitro and characterized using DNA sequencing methods to elucidate their taxonomic identity. Some of the most nodulation-compatible strains characterized as Bradyrhizobium and Sinorhizobium species exhibited significant symbiotic performance in terms of plant biomass, nodule number, and nodule dry weight. The study generated valuable data that provide information on the extent of symbiotic compatibility of some of the existing cultivars used in South Africa with native rhizobia and whether inoculation of soya bean with commercial products is vital on some soya bean farms.

Representing DNA for machine learning algorithms: A primer on one-hot, binary, and integer encodings.

This short paper presents an educational approach to teaching three popular methods for encoding DNA sequences: one-hot encoding, binary encoding, and integer encoding. Aimed at bioinformatics and computational biology students, our learning intervention focuses on developing practical skills in implementing these essential techniques for efficient representation and analysis of genetic data. The primary goal of this study is to enhance students' understanding and practical application of DNA encoding methods, which are crucial for various computational analyses in bioinformatics. Our intervention consists of three key components: (1) a conceptual framework that contextualizes these encoding methods within broader bioinformatics applications, (2) an interactive Jupyter Notebook with Python code examples (https://github.com/yashmgupta/Representing-DNA/tree/main), and (3) a user-friendly Streamlit application for visualizing encoded sequences (https://dnaencoding.streamlit.app/) that also enables students to input their own DNA sequences and visualize the different encoding methods, further enhancing their understanding and practical experience. By combining conceptual overview with practical coding and visualization tools, our approach provides a comprehensive foundation for students to leverage these key DNA sequence encoding methods in their future work. This study contributes to bioinformatics education by offering effective, hands-on learning resources that bridge the gap between theoretical knowledge and practical application in DNA sequence analysis, preparing students for advanced research and data analysis projects in the field.

Prenatal cfDNA Sequencing and Incidental Detection of Maternal Cancer

BackgroundCell-free DNA (cfDNA) sequence analysis to screen for fetal aneuploidy can incidentally detect maternal cancer. Additional data are needed to identify DNA-sequencing patterns and other biomarkers that can identify pregnant persons who are most likely to have cancer and to determine the best approach for follow-up.MethodsIn this ongoing study we performed cancer screening in pregnant or postpartum persons who did not perceive signs or symptoms of cancer but received unusual clinical cfDNA-sequencing results or results that were nonreportable (i.e., the fetal aneuploidy status could not be assessed) from one of 12 different commercial laboratories in North America. We used a uniform cancer-screening protocol including rapid whole-body magnetic resonance imaging (MRI), laboratory tests, and standardized cfDNA sequencing for research purposes with the use of a genomewide platform. The primary outcome was the presence of cancer in participants after the initial cancer-screening evaluation. Secondary analyses included test performance.ResultsCancer was present in 52 of the 107 participants in the initial cohort (48.6%). The sensitivity and specificity of whole-body MRI in detecting occult cancer were 98.0% and 88.5%, respectively. Physical examination and laboratory tests were of limited use in identifying participants with cancer. Research sequencing showed that 49 participants had a combination of copy-number gains and losses across multiple (≥3) chromosomes; cancer was present in 47 of the participants (95.9%) with this sequencing pattern. Sequencing patterns of cfDNA in which there were only chromosomal gains (multiple trisomies) or only chromosomal losses (one or more monosomies) were found in participants with nonmalignant conditions, such as fibroids.ConclusionsIn this study, 48.6% of participants who received unusual or nonreportable clinical cfDNA-sequencing results had an occult cancer. Further study of DNA-sequencing patterns that are suggestive of occult cancer during prenatal screening is warranted. (Funded by the NIH Intramural Research Programs; ClinicalTrials.gov number, NCT04049604.)

Administration of 1-kestose to beluga reduces intestinal Turicibacter andcollagenase gene levels, and blood creatinine levels.

In recent years, an increased emphasis on enhancing the care and health management of captive marine mammals has been observed. Belugas (White Whale, Delphinapterus leucas), belonging to the family Monodontidae, are of considerable importance and often the centerpiece of aquarium collections worldwide. This study aimed to investigate the effects of the administration of prebiotics on the gut microbiota and overall health of the beluga. Prebiotic 1-kestose, a fructooligosaccharide comprising sucrose and fructose, was administered to three belugas, alongside their regular vitamin supplements for a duration of 8 weeks. 16S rRNA gene amplicon sequencing of intestinal DNA revealed that the relative abundance of the genus Turicibacter, a potentially pathogenic bacteria, significantly reduced after 1-kestose administration when compared to that at baseline (P=0.050). In addition, a quantitative PCR analysis revealed that the levels of collagenase gene, a putative virulence factor gene of Turicibacter, significantly reduced after 1-kestose administration (P=0.050). Blood creatinine levels that were initially above the normal value also reduced after 1-kestose administration (P=0.023). Therefore, this study demonstrated the potential of 1-kestose to improve the health and welfare of aquarium belugas.

Dynamic principles of the microbiome and the bovine vagina: a review

The role of microbes inhabiting various body sites in supporting host physiology and health is substantial, and recent advancements in DNA sequencing technology have facilitated a more in-depth understanding of these microbial contributions. The influence of microbiota within a given organ can be broadly categorized as having two main functions: (1) promoting organ homeostasis and (2) creating conditions that inhibit the growth of pathogenic microorganisms, thereby protecting the host from diseases. In livestock production, numerous phenotypes critical to industry outcomes are affected by the microbiome, which has sparked considerable academic interest in recent years. This review aims to analyze the extensive data available on the microbiomes of humans and other mammalian species, examining microbiome ecology to elucidate principles that may assist in interpreting data on livestock microbiomes. Additionally, the review will discuss techniques available for investigating various microbiome aspects and will examine existing data on the reproductive microbiome, with a particular focus on the bovine vaginal microbiome.

Revealing a cryptic species of mole cricket genus Gryllotalpa Latreille, 1802 (Orthoptera: Gryllotalpidae) in Roi Et Province, Thailand, detected by mitochondrial DNA sequences

Revealing a cryptic species of mole cricket genus Gryllotalpa Latreille, 1802 (Orthoptera: Gryllotalpidae) in Roi Et Province, Thailand, detected by mitochondrial DNA sequences

Linking adults and cystacanths of a new species of Rhadinorhynchus Lühe, 1911 (Acanthocephala: Rhadinorhynchidae) from the Pacific coast of Mexico by using morphological and molecular data

During parasitological surveys of marine fishes and zooplankton in localities of the Northwestern Pacific coast of Mexico, 28 Gafftopsail pompano (Trachinotus rhodopus Gill) and 50 mysid crustaceans (Metamysidopsis frankfiersi Hendrickx & Hernández-Payán) we identified to be infected with adults and cystacanths, respectively of an acanthocephalan morphologically corresponding to the genus Rhadinorhynchus Lühe, 1911. DNA sequences of the small (SSU) and large (LSU) subunits of ribosomal DNA, and cytochrome c oxidase subunit 1 (cox 1) from mitochondrial DNA were obtained. Phylogenetic analyses revealed that the newly sequenced individuals in a clade with Rhadinorhynchus sp. from carangids in other localities of the Pacific coast of Mexico; together, all these individuals formed an independent lineage that is recognized herein as a new species, Rhadinorhynchus trachinotin. sp. The new species is morphologically distinguished from the other 38 congeners by having a long and cylindrical proboscis armed with 12 longitudinal rows bearing 16–18 hooks each. The ecological information gathered from the parasites, together with genetic evidence, confirms that the Gafftopsail pompano is the definitive host of R. trachinotin. sp., while mysid crustaceans serve as the intermediate host. Current records also indicate that R. trachinotin. sp. is distributed along the Pacific coast of Mexico, from Mazatlán, Sinaloa in the north to Puerto Angel, Oaxaca in the south. This distribution aligns with the Mexican Coastal Current, which extends from the Gulf of Tehuantepec in Oaxaca to the entrance of the Gulf of California and southern Baja California.

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.

DNA sequencing of multiple bulk samples from a tumor provides the opportunity to investigate tumor heterogeneity and reconstruct a phylogeny of a patient's cancer. However, since bulk DNA sequencing of tumor tissue measures thousands of cells from a heterogeneous mixture of distinct sub-populations, accurate reconstruction of the tumor phylogeny requires simultaneous deconvolution of cancer clones and inference of ancestral relationships, leading to a challenging computational problem. Many existing methods for phylogenetic reconstruction from bulk sequencing data do not scale to large datasets, such as recent datasets containing upwards of ninety samples with dozens of distinct sub-populations. We develop an approach to reconstruct phylogenetic trees from multi-sample bulk DNA sequencing data by separating the reconstruction problem into two parts: a structured regression problem for a fixed tree [Formula: see text], and an optimization over tree space. We derive an algorithm for the regression sub-problem by exploiting the unique, combinatorial structure of the matrices appearing within the problem. This algorithm has both asymptotic and empirical improvements over linear programming (LP) approaches to the problem. Using our algorithm for this regression sub-problem, we develop fastBE, a simple method for phylogenetic inference from multi-sample bulk DNA sequencing data. We demonstrate on simulated data with hundreds of samples and upwards of a thousand distinct sub-populations that fastBE outperforms existing approaches in terms of reconstruction accuracy, sample efficiency, and runtime. Owing to its scalability, fastBE enables both phylogenetic reconstruction directly from indvidual mutations without requiring the clustering of mutations into clones, as well as a new phylogeny constrained mutation clustering algorithm. On real data from fourteen B-progenitor acute lymphoblastic leukemia patients, fastBE infers mutation phylogenies with fewer violations of a widely used evolutionary constraint and better agreement to the observed mutational frequencies. Using our phylogeny constrained mutation clustering algorithm, we also find mutation clusters with lower distortion compared to state-of-the-art approaches. Finally, we show that on two patient-derived colorectal cancer models, fastBE infers mutation phylogenies with less violation of a widely used evolutionary constraint compared to existing methods.

Genetic diversity analysis and core collection construction of tea plant from the Yunnan Province of China using ddRAD sequencing

Tea plants are economically important woody plants that originated in southwestern China. The Yunnan Province in China is regarded as the central origin of tea plants owing to the abundance and diversity of the tea germplasm present in this region. However, there is a lack of knowledge regarding the genetic diversity and evolutionary relationships among tea plants in this region. Here, a total of 266,397 high-quality single nucleotide polymorphisms were obtained using double digest restriction-site associated DNA sequencing from 468 tea accessions collected from Yunnan. The phylogenetic relationship and population structure of the 468 tea accessions revealed remarkable inter- and intraspecific introgression across different sect. Thea species. We found that Camellia taliensis (W. W. Smith) Melchior is the main genetic donor that greatly contributed to the domestication of C. sinensis (L.) O. Kuntze, as evidenced by the frequent generation of genetic intermediates derived from the hybridization between C. sinensis and C. taliensis in Lincang, Xishuangbanna, and Pu’er. Notable genetic differences were observed across the populations from distinct regions of Yunnan. Additionally, the Lancang River may have attenuated the genetic interflow between Lincang and Pu’er. Finally, a core collection of 50 tea accessions was constructed based on the genetic diversity of the 468 tea accessions. Our results provide novel insights into the evolutionary and domestication history of tea plants in Yunnan Province and can facilitate the development of strategies for the conservation, breeding, and utilization of the core collection.

Characterization of DNA methylation reader proteins of Arabidopsis thaliana.

In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted-or read-differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date preferentially bind to the methylated probes, along with a range of new mC-binding protein candidates. Functional characterization of these mC readers, focused on the MBD and SUVH families, was undertaken by ChIP-seq mapping of genome-wide binding sites, their protein interactors, and the impact of high-order mutations on transcriptomic and epigenomic profiles. Together, these results highlight specific context preferences for these proteins, and in particular the ability of MBD2 to bind predominantly to gbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodeling processes in plants.

Phylogeny of two species of Lactarius subsection Scrobiculati associated with Abies religiosa in Cofre de Perote National Park, Mexico

Species of the genus Lactarius subsection Scrobiculati are distributed in the northern hemisphere and are associated with temperate forests. In Mexico, four species and two varieties of this subsection have been reported; however, their identification is complex due to morphological variability and the lack of DNA sequences and phylogenetic analysis. This study describes and illustrates Lactarius alnicola and L. mexicanus in Abies religiosa forests through morphological and phylogenetic analysis. The ITS sequences were deposited in GenBank (MF040818 and MH820031). The morphology of both species matches the original descriptions, and, phylogenetically, the Mexican sporomes form well-defined clades. L. alnicola is closely related to L. scrobiculatus from Europe, while L. mexicanus is grouped with L. intermedius from Italy. The use of morphological and phylogenetic characters will be key for the accurate identification and understanding of the distribution of Lactarius species in Mexico.