Evolutionary Relationships Research Articles

Germination responses to changing rainfall timing reveal potential climate vulnerability in a clade of wildflowers.

The seasonal timing of life history transitions is often critical to fitness, and many organisms rely upon environmental cues to match life cycle events with favorable conditions. In plants, the timing of seed germination is mediated by seasonal cues such as rainfall and temperature. Variation in cue responses among species can reflect evolutionary processes and adaptation to local climate and can affect vulnerability to changing conditions. Indeed, climate change is altering the timing of precipitation, and germination responses to such change can have consequences for individual fitness, population dynamics, and species distributions. Here, we assessed responses to the seasonal timing of germination-triggering rains for eleven species spanning the Streptanthus/Caulanthus clade (Brassicaceae). To do so, we experimentally manipulated the onset date of rainfall events, measured effects on germination fraction, and evaluated whether responses were constrained by evolutionary relationships across the phylogeny. We then explored the possible consequences of these responses to contemporary shifts in precipitation timing. Germination fractions decreased with later onset of rains and cooler temperatures for all but three Caulanthus species. Species' germination responses to the timing of rainfall and seasonal temperatures were phylogenetically constrained, with Caulanthus species appearing less responsive. Further, four species are likely already experiencing significant decreases in germination fractions with observed climate change, which has shifted the timing of rainfall towards the cooler, winter months in California. Overall, our findings emphasize the sensitivity of germination to seasonal conditions, underscore the importance of interacting environmental cues, and highlight vulnerability to shifting precipitation patterns with climate change, particularly in more northern, mesic species.

Complete mitochondrial genome assembly of Juglans regia unveiled its molecular characteristics, genome evolution, and phylogenetic implications

BackgroundThe Persian walnut (Juglans regia), an economically vital species within the Juglandaceae family, has seen its mitochondrial genome sequenced and assembled in the current study using advanced Illumina and Nanopore sequencing technology.ResultsThe 1,007,576 bp mitogenome of J. regia consisted of three circular chromosomes with a 44.52% GC content encoding 39 PCGs, 47 tRNA, and five rRNA genes. Extensive repetitive sequences, including 320 SSRs, 512 interspersed, and 83 tandem repeats, were identified, contributing to genomic complexity. The protein-coding sequences (PCGs) favored A/T-ending codons, and the codon usage bias was primarily shaped by selective pressure. Intracellular gene transfer occurred among the mitogenome, chloroplast, and nuclear genomes. Comparative genomic analysis unveiled abundant structure and sequence variation among J. regia and related species. The results of selective pressure analysis indicated that most PCGs underwent purifying selection, whereas the atp4 and ccmB genes had experienced positive selection between many species pairs. In addition, the phylogenetic examination, grounded in mitochondrial genome data, precisely delineated the evolutionary and taxonomic relationships of J. regia and its relatives. We identified a total of 539 RNA editing sites, among which 288 were corroborated by transcriptome sequencing data. Furthermore, expression profiling under temperature stress highlighted the complex regulation pattern of 28 differently expressed PCGs, wherein NADH dehydrogenase and ATP synthase genes might be critical in the mitochondria response to cold stress.ConclusionsOur results provided valuable molecular resources for understanding the genetic characteristics of J. regia and offered novel perspectives for population genetics and evolutionary studies in Juglans and related woody species.

Limited Variation in Codon Usage across Mitochondrial Genomes of Non-Biting Midges (Diptera: Chironomidae).

The codon usage patterns of mitochondrial genomes offer insights into the evolutionary and phylogenetic studies of species. Codon usage analysis has been conducted in a few Chironomidae species, and the codon usage patterns in other species remain ambiguous. We aim to reveal the codon usage differences in the mitochondrial genomes across this family. We sequenced the first mitochondrial genome of the genus Conchapelopia and the third mitochondrial genome of the subfamily Tanypodinae. Then, we analyzed its relative synonymous codon usage and effective number of codons with registered mitochondrial genomes from 28 other genera. The results indicated that there was limited variation in codon usage across five subfamilies, Chironominae, Orthocladiinae, Diamesinae, Prodiamesinae and Tanypodinae. While Parochlus steinenii from Podonominae presented a weaker codon bias, P. steinenii possessed the most genes experiencing natural selection. Additionally, ND1, ND2 and ND3 were found to be the most frequently selected genes across all species. Our findings contribute to further understanding the evolutionary and phylogenetic relationships of Chironomidae.

Genomes of Alphanucleorhabdovirus Physostegiae Isolates from Two Different Cultivar Groups of Solanum melongena

Plant rhabdoviruses cause considerable economic losses and are a threat to the agriculture of Solanaceae plants. Two novel virus isolates belonging to the family Rhabdoviridae are identified by high-throughput sequencing (HTS) in Russian eggplant cultivars grown in the Volga river delta region for the first time. The phylogenetic inference of L protein (polymerase) shows that these virus isolates belong to Alphanucleorhabdovirus physostegia (Physostegia chlorotic mottle virus—PhCMoV), and their minus-sense RNA genomes have the typical gene order 3′-nucleocapsid (N)—X protein (X)—phosphoprotein (P)—Y protein (Y)—matrix protein (M)—glycoprotein (G)—polymerase (L)-5′ observed in some plant-infecting alphanucleorhabdoviruses. One of the PhCMoV isolates from the eggplant cultivar Almaz is genetically very similar to the Russian PhCMoV isolate from tomato and grouped in a subclade together with four isolates from Belgium, Germany, the Netherlands, and France. However, another eggplant-infecting isolate from the Russian cultivar Boggart is the most divergent compared with the other 45 virus genomes of European PhCMoV isolates. Thus, our comparative analysis reveals that two virus isolates from Russia may either share a close evolutionary relationship with European isolates or significantly diverge from all known virus isolates. The potential to use the protein sequence comparative analysis of accessory polypeptides, along with the early developed strategy of the nucleotide sequence comparison of the RNA genomes, is shown.

Characterization, Evolution, Expression and Functional Divergence of the DMP Gene Family in Plants.

The DMP (DOMAIN OF UNKNOWN FUNCTION 679 membrane protein) domain, containing a family of membrane proteins specific to green plants, is involved in numerous biological functions including physiological processes, reproductive development and senescence in Arabidopsis, but their evolutionary relationship and biological function in most crops remains unknown. In this study, we scrutinized phylogenetic relationships, gene structure, conserved domains and motifs, promoter regions, gene loss/duplication events and expression patterns. Overall, 240 DMPs were identified and analyzed in 24 plant species selected from lower plants to angiosperms. Comprehensive evolutionary analysis revealed that these DMPs underwent purifying selection and could be divided into five groups (I-V). DMP gene structure showed that it may have undergone an intron loss event during evolution. The five DMP groups had the same domains, which were distinct from each other in terms of the number of DMPs; group III was the largest, closely followed by group V. The DMP promotor region with various cis-regulatory elements was predicted to have a potential role in development, hormone induction and abiotic stresses. Based on transcriptomic data, expression profiling revealed that DMPs were primarily expressed in reproductive organs and were moderately expressed in other tissues. Evolutionary analysis suggested that gene loss events occurred more frequently than gene duplication events among all groups. Overall, this genome-wide study elucidates the potential function of the DMP gene family in selected plant species, but further research is needed in many crops to validate their biological roles.

Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.

Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of "viral dark matter," the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.

Insights into the culturable fungal endophytes of Dioscorea bulbifera L. in terms of their diversity, antidiabetic and antioxidant activity

The research on endophytes is focused on understanding the complex microbiome compositions, their interactions with host plants and their bioactive potential. Our study provided an overview of the diversity, distribution and bioactivities of culturable endophytic fungi associated with fungal endophytes of Dioscorea bulbifera L. The phylogenetic analysis depicted the evolutionary relationship among taxa of endophytic fungal isolates. The isolated fungal endophytes belonged to twenty-five genera and thirty-eight species. Further, diversity indices demonstrated significant diversity of fungal endophytes in the different tissues: stem, leaf, tuber and bulbil. A higher consistency of endophytic fungal isolates in the bulbils was found using Shannon index. Furthermore, Simpson's index revealed that the leaf tissue harboured highly diverse fungal endophytes. Likewise, Margalef's index depicted high taxonomic richness in bulbils. The isolates such as Acrocalymma medicaginis, Curvularia lycoperscii, Talaromyces macrospora, Fusarium laceratum, Paecilomyces formosus and Microascus cirrosus isolated in this study have been reported as endophytes for the first time from any plant. In-vitro antioxidant and antidiabetic activities of the ethyl acetate extracts revealed that Nigrospora oryzae (Z2) effectively inhibited α-glucosidase activity with IC50 value of 0.6 µg/ml whereas IC50 value of the acarbose, the positive control was reported to be 0.040 µg/ml. The results of antioxidant activity demonstrated that H15A (Acrocalymma medicaginis) and BD5 (Phomopsis longicolla) could be used as potential sources of antioxidant agents. Moreover, H15A (Acrocalymma medicaginis) was reported to produce 687.1 ± 0.17 µg GAE/mg of TPC and 78.55 ± 0.29 µg QE/mg of TFC quantitatively. These findings suggest that the potential endophytes could be explored using systematic bio-guided investigations to further discover novel natural products. Our study provides an important resource for a deeper understanding of endophyte-plant interactions at molecular and genetic levels.

Antifungal resistance profile and genetic relatedness of moulds from rural groundwater sources

Antifungal resistance remains a significant public health threat, yet poorly investigated. This study for the first time investigated the antifungal profile of moulds isolated from groundwaters in a rural community of Osun State, Southwest Nigeria. Groundwater samples were collected during dry and rainy seasons, and processed for mould isolation using standard methods. The isolates were presumptively identified and screened for in vitro susceptibility using 4 antifungals conventionally employed in clinical cases. Multiple antifungal resistance phenotypes and indices were equally evaluated. Representative of each putatively identified species were confirmed using molecular techniques. A total of 29 and 27 moulds were obtained during the dry and rainy seasons, respectively. Genus Aspergillus was the most prevalent (30.4%). Of the 56 isolates subjected to antifungal susceptibility testing, 55(98%) were resistant to fluconazole, followed by flucytosine 49(88%), ketoconazole 45(80%) and amphotericin B 31(55%). Exactly 46 isolates were multidrug-resistant, 23(50%) each, to 3 and 4 drugs, respectively. The multiple antifungal resistance index (MARI) evaluated was 1 in all the samples A-Q, except C (0.75), transcending the threshold limit of 0.2, indicating the isolates to be of high antifungal usage origin. The molecularly identified species had 99–100% similarity with reference strains from GenBank and evolutionary relationship of taxa revealed 10 distinct clades. The outcome of this study reveals a rise in the frequency of antifungal resistance in moulds towards standard drugs, thus, advocating for adequate investigations targeted at monitoring antifungal resistance in groundwater milieus.

Unusual BA222-like strains of Rotavirus A (Sedoreoviridae: Rotavirus: Rotavirus A): molecular and genetic analysis based on all genome segments.

Rotavirus infection is the major cause of severe dehydrating diarrhea requiring hospitalization in young children worldwide. Due to their segmented genome, rotaviruses are capable of gene reassortment, which makes the emergence and spread of genetically novel strains possible. The purpose of this study was to search for unusual rotaviruses circulating in Nizhny Novgorod in 2021‒2023 and their molecular genetic characterization based on all genome segments. Rotavirus-positive stool samples of children were examined by PCR genotyping and electrophoresis in PAAG. cDNA fragments of each of the 11 genes (VP1‒VP4, VP6, VP7, NSP1‒NSP5), 570 to 850 nucleotide pairs in length were sequenced for the selected strains. The phylogenetic analysis was performed in the MEGA X program. In the study period 2021‒2023, 11 G[P] combinations with a predominance of G3P[8] (59.5%) were identified. Six atypical Rotavirus А (RVA) strains were identified: 2 strains of the G2P[4] genotype (G2-P[4]-I2-R2-C2-M2-A3-N2-T3-E2-H3, G2-P[4]-I2-R2-C2-M2-A3-N2-T3-E3-H2) and 4 G3P[9] strains (all strains had the genotype G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3). Phylogenetic analysis based on all genes showed an evolutionary relationship between rotaviruses similar to rotaviruses of cats and dogs (BA222-like) and unusual strains of the G2P[4] genotype, for which a mixed combination of genotypes was identified and characterized for the first time. The results obtained expand the understanding of the diversity of reassortant RVAs, as well as complement the data on the genotypic structure of the rotavirus population in Nizhny Novgorod. The wide genetic diversity of reassortant RVA can help rotaviruses overcome the immunological pressure provided by natural and vaccine-induced immunity. In this regard, to control the emergence of new variants and assess changes in the virulence of rotaviruses after reassortment processes, continuous molecular monitoring for circulating RVA is necessary.

Sturnidae sensu lato Mitogenomics: Novel Insights into Codon Aversion, Selection, and Phylogeny.

The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes-including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes-and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato.

Genome-Wide Identification of the bHLH Gene Family in Rhododendron delavayi and Its Expression Analysis in Different Floral Tissues.

The bHLH genes play a crucial role in plant growth, development, and stress responses. However, there is currently limited research on bHLH genes in the important horticultural plant Rhododendron delavayi Franch. In this study, we conducted a comprehensive genome-wide identification and in-depth analysis of the bHLH gene family in R. delavayi using bioinformatics approaches. A total of 145 bHLH family members were identified, encoding proteins ranging from 98 to 3300 amino acids in length, with molecular weights ranging from 11.44 to 370.51 kDa and isoelectric points ranging from 4.22 to 10.80. These 145 bHLH genes were unevenly distributed across 13 chromosomes, with three bHLH genes located on contig 52. Chromosome 8 contained the highest number of bHLH family members with 19 genes, while chromosomes 9 and 13 had the lowest, with 7 genes each. Phylogenetic analysis revealed a close evolutionary relationship between bHLH genes in R. delavayi and Arabidopsis thaliana. Subcellular localization analysis indicated that most bHLH genes were located in the nucleus. Promoter analysis of R. delavayi bHLH genes revealed the presence of various cis-regulatory elements associated with light responses, methyl jasmonate responses, low-temperature responses, and coenzyme responses, suggesting that bHLH genes are involved in multiple biological processes in R. delavayi. Through transcriptome analysis, we identified three key functional genes-Rhdel02G0041700, Rhdel03G0013600, and Rhdel03G0341200-that may regulate flower color in R. delavayi. In conclusion, our study comprehensively identified and analyzed the bHLH gene family in R. delavayi and identified three bHLH genes related to flower color, providing a foundation for molecular biology research and breeding in R. delavayi.

Phylogenetic exploration, codon usage bias, and genomic divergence in Hydrocotyle: a comparative plastome study across different geographical locations.

Hydrocotyle himalaica from Bhutan, a perennial herb that thrives from 1500 to 2600m, possesses both ecological importance and medicinal properties. The plastome analysis revealed a length of 153,383bp, showing variation from conspecific taxa in China. Its standard structure comprises two IR regions (18,336bp IRa and 18,336bp IRb), an LSC region of 97,944bp, and an SSC region of 18,767bp, with a GC content of 37.63%. Non-coding regions showed higher mutation susceptibility, with Pi values from 0.006 to 0.107. An AT-rich codon bias was consistent across all 18 Hydrocotyle species. Nucleotide composition and GC% in coding sequences differed among the species. The codon preference in Hydrocotyle is shaped by multiple factors, with natural selection being the primary influence, as indicated by the ENC-plot, PR2-plot, and Neutrality-plot. Codon usage patterns varied, with RSCU values from 0 to 2.23. Codons ending in A or U had RSCU > 1, while those ending in C or G had RSCU < 1. GC2 content surpassed GC3 and GC1 in most genes. The phylogenetic analysis placed H. himalaica, sourced from Kanglung, Bhutan, within the monophyly of the Hydrocotyloideae subfamily. However, the species showed weaker bootstrap support (BS < 50) with H. javanica and H. hookeri subsp., a deviation from a prior report on the same species from Jiangkou, Guizhou, China. This analysis highlighted the genomic characteristics and evolutionary relationships of H. himalaica from Bhutan, underscoring the need for a comprehensive phylogenetic, ecological, and botanical characterization to confirm intra-specific variation within Hydrocotyle species.

Molecular analyses of the tubby-like protein gene family and their response to salt and high temperature in the foxtail millet (Setaria italica).

Tubby-like proteins (TLPs) are a group of proteins found in both eukaryotes and prokaryotes. They are significant in various physiological and biochemical processes, especially in plants' response to abiotic stress. However, the role of TLP in foxtail millet (Setaria italica) remains unclear. The millet genome has 16 members of the TLP family with typical Tub domains, which can be sorted into five subgroups based on gene structure, motif, and protein domain distribution. SiTLPs were discovered to be predominantly located in the nucleus and also had extracellular distribution. The interspecific evolutionary analysis indicated that SiTLPs had a closer evolutionary relationship with monocots and were consistent with the morphological classification of foxtail millet. When subjected to salt stress, the abundance of SiTLP was affected, and qRT-PCR results showed that the expression levels of certain SiTLP members were induced by salt stress while others remained unresponsive. Except for SiTLP14, all other SiTLP genes were up-regulated in response to high-temperature stress, implying a potentially crucial role for SiTLP in mitigating high-temperature-induced damage. This study provides valuable insights into understanding the functional significance of the TLP gene family in foxtail millet.

Utilization of Microfluidic Droplet-Based Methods in Diagnosis and Treatment Methods of Hepatocellular Carcinoma: A Review.

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and is associated with high morbidity and mortality. One of the main challenges in the management of HCC is late clinical presentation and thus diagnosis of the disease, which results in poor survival. The pathogenesis of HCC is complex and involves chronic liver injury and genetic alterations. Diagnosis of HCC can be made either by biopsy or imaging; however, conventional tissue-based biopsy methods and serological biomarkers such as AFP have limited clinical applications. While hepatocellular carcinoma is associated with a range of molecular alterations, including the activation of oncogenic signaling pathways, such as Wnt-TGFβ, PI3K-AKT-mTOR, RAS-MAPK, MET, IGF, and Wnt-β-catenin and TP53 and TERT promoter mutations, microfluidic applications have been limited. Early diagnosis is crucial for advancing treatments that would address the heterogeneity of HCC. In this context, microfluidic droplet-based methods are crucial, as they enable comprehensive analysis of the genome and transcriptome of individual cells. Single-cell RNA sequencing (scRNA-seq) allows the examination of individual cell transcriptomes, identifying their heterogeneity and cellular evolutionary relationships. Other microfluidic methods, such as Drop-seq, InDrop, and ATAC-seq, are also employed for single-cell analysis. Here, we examine and compare these microfluidic droplet-based methods, exploring their advantages and limitations in liver cancer research. These technologies provide new opportunities to understand liver cancer biology, diagnosis, treatment, and prognosis, contributing to scientific efforts in combating this challenging disease.

Molecular Sensomics Combined with Random Forest Model Can Reveal the Evolution of Flavor Type of Baijiu Based on Differential Markers.

Baijiu is popular with a long history and balanced flavor. Flavor type is the most widely used classification mode for Baijiu. However, the evolutionary relationships of Baijiu flavor types and the differential markers between flavor types are still unclear, significantly impacting the development of the Baijiu industry. In this study, a total of 319 trace components were identified using gas chromatography-olfactometry-mass spectrometry and gas chromatography-mass spectrometry. Among them, 91 trace components with high odor active values or taste active values were recognized as flavor components. Then random forests were conducted to screen differential markers between the derived and basic flavor types, while a principal component analysis assessed their effectiveness in distinguishing the flavor types of Baijiu. Finally, 19 differential markers (including 3-methylbutyric acid, pentanoic acid, 2-butanol, 2,3-butanediol, ethyl pro-panoate, isobutyl acetate, ethyl butanoate, ethyl hexanoate, ethyl heptanoate, ethyl lactate, ethyl 2-hydroxy butanoate, isopentyl hexanoate, ethyl nonanoate, isopropyl myristate, ethyl tetradecanoate, ethyl benzoate, 2,4-di-t-butylphenol, 2-methylbutanal and 3-octanone) were screened and proven to effectively reveal the evolution of Baijiu flavor types; these were further verified as key differential markers using addition tests and a correlation analysis.

Biodiversidade faunistica coletada em 3 locais diferentes com pelo menos 10 espécies de insetos

Taxonomy, Systematics, and Phylogeny are important fields of study in the context of Biological Sciences. Studying biodiversity as well as understanding the evolutionary relationships between taxa is of fundamental importance. The objective of the present work is to demonstrate the presence of several species of insects, particularly mosquitoes, collected in the 2024.1 semester, by students of the mandatory discipline of General Systematics and Phylogênia (TA 464) as a practical part of the discipline's activities mediated by Academic Monitoring. The students of the discipline of General Systematics and Phylogeny (TA 464), due to the practical work carried out throughout the 2024.1 semester, postulate that it is a matter of time for the arrival of oropouche fever in the city of Tauá due to the faunal biodiversity of mosquitoes in the city and the fact that BR 020 serves as a "corridor" for the entry and exit of humans and mosquitoes transported by motor vehicles circulating 24 hours a day. day on BR 020. Stressing that interdisciplinary and transdisciplinary measures must be taken to minimize the impact on the population. As well as new research should be carried out with partnerships between CECITEC and LACEN/Tauá.

Reconstructing tumor clonal heterogeneity and evolutionary relationships based on tumor DNA sequencing data.

The heterogeneity of tumor clones drives the selection and evolution of distinct tumor cell populations, resulting in an intricate and dynamic tumor evolution process. While tumor bulk DNA sequencing helps elucidate intratumor heterogeneity, challenges such as the misidentification of mutation multiplicity due to copy number variations and uncertainties in the reconstruction process hinder the accurate inference of tumor evolution. In this study, we introduce a novel approach, REconstructing Tumor Clonal Heterogeneity and Evolutionary Relationships (RETCHER), which characterizes more realistic cancer cell fractions by accurately identifying mutation multiplicity while considering uncertainty during the reconstruction process and the credibility and reasonableness of subclone clustering. This method comprehensively and accurately infers multiple forms of tumor clonal heterogeneity and phylogenetic relationships. RETCHER outperforms existing methods on simulated data and infers clearer subclone structures and evolutionary relationships in real multisample sequencing data from five tumor types. By precisely analysing the complex clonal heterogeneity within tumors, RETCHER provides a new approach to tumor evolution research and offers scientific evidence for developing precise and personalized treatment strategies. This approach is expected to play a significant role in tumor evolution research, clinical diagnosis, and treatment. RETCHER is available for free at https://github.com/zlsys3/RETCHER.

Bioinformatics Identification and Expression Analysis of Acetyl-CoA Carboxylase Reveal Its Role in Isoflavone Accumulation during Soybean Seed Development.

Isoflavones belong to the class of flavonoid compounds, which are important secondary metabolites that play a crucial role in plant development and defense. Acetyl-CoA carboxylase (ACCase) is a biotin-dependent enzyme that catalyzes the conversion of Acetyl-CoA into Malonyl-CoA in plants. It is a key enzyme in fatty acid synthesis and also catalyzes the production of various secondary metabolites. However, information on the ACC gene family in the soybean (Glycine max L. Merr.) genome and the specific members involved in isoflavone biosynthesis is still lacking. In this study, we identified 20 ACC family genes (GmACCs) from the soybean genome and further characterized their evolutionary relationships and expression patterns. Phylogenetic analysis showed that the GmACCs could be divided into five groups, and the gene structures within the same groups were highly conserved, indicating that they had similar functions. The GmACCs were randomly distributed across 12 chromosomes, and collinearity analysis suggested that many GmACCs originated from tandem and segmental duplications, with these genes being under purifying selection. In addition, gene expression pattern analysis indicated that there was functional divergence among GmACCs in different tissues. The GmACCs reached their peak expression levels during the early or middle stages of seed development. Based on the transcriptome and isoflavone content data, a weighted gene co-expression network was constructed, and three candidate genes (Glyma.06G105900, Glyma.13G363500, and Glyma.13G057400) that may positively regulate isoflavone content were identified. These results provide valuable information for the further functional characterization and application of GmACCs in isoflavone biosynthesis in soybean.

Brassica rapa BrICE1 and BrICE2 Positively Regulate the Cold Tolerance via CBF and ROS Pathways, Balancing Growth and Defense in Transgenic Arabidopsis.

Winter rapeseed (Brassica rapa) has a good chilling and freezing tolerance. inducer of CBF expression 1 (ICE1) plays a crucial role in cold signaling in plants; however, its role in Brassica rapa remains unclear. In this study, we identified 41 ICE1 homologous genes from six widely cultivated Brassica species. These genes exhibited high conservation, with evolutionary complexity between diploid and allotetraploid species. Cold stress induced ICE1 homolog expression, with differences between strongly and weakly cold-tolerant varieties. Two novel ICE1 paralogs, BrICE1 and BrICE2, were cloned from Brassica rapa Longyou 6. Subcellular localization assays showed that they localized to the nucleus, and low temperature did not affect their nuclear localization. The overexpression of BrICE1 and BrICE2 increased cold tolerance in transgenic Arabidopsis and enhanced reactive oxygen species' (ROS) scavenging ability. Furthermore, our data demonstrate that overexpression of BrICE1 and BrICE2 inhibited root growth in Arabidopsis, and low temperatures could induce the degradation of BrICE1 and BrICE2 via the 26S-proteasome pathway. In summary, ICE1 homologous genes exhibit complex evolutionary relationships in Brassica species and are involved in the C-repeat/DREB binding factor (CBF) pathway and ROS scavenging mechanism in response to cold stress; these regulating mechanisms might also be responsible for balancing the development and cold defense of Brassica rapa.

Genome-wide identification of the OVATE family proteins and functional analysis of BhiOFP1, BhiOFP5, and BhiOFP18 during fruit development in wax gourd (Benincasa hispida)

OVATE family proteins (OFPs) are transcriptional regulators in plants. They have a common domain called the OVATE domain and control the development of leaves, fruits, and flowers in plants. Although the OFP gene family has been widely explored in the plant kingdom, the identification and characterization of this family have not yet been performed in wax gourd. In this study, we conducted a genome-wide investigation of the OFP gene family and identified 18 OFP (BhiOFP) genes in wax gourd. Next, we discovered their evolutionary relationships, conserved motifs, gene structures, cis-acting elements, and expression patterns. The BhiOFP genes were irregularly distributed on nine chromosomes, with only two BhiOFP genes containing introns. The BhiOFP gene promoters contained cis-acting elements in response to phytohormones and environmental signals. The majority of BhiOFP genes were derived from whole-genome duplication events. Expression analysis demonstrated that the BhiOFP genes showed disparate modes of expression and some of them were highly expressed in fruits. Overexpression of BhiOFP1, BhiOFP5, and BhiOFP18 in Arabidopsis resulted in dwarf plants, small rosette leaves, and shortened siliques, while the BhiOFP1 overexpression plants displayed a more severe phenotype. In summary, our study systematically analyzed the wax gourd OFP gene family, facilitated the functional research of BhiOFP1, BhiOFP5, and BhiOFP18, and offered a theoretical foundation for the improvement of wax gourd varieties with appropriate fruit length.