Comprehensive Genome-wide Analysis Research Articles

A comprehensive genome-wide cross-trait analysis of sexual factors and uterine leiomyoma.

Age at first sexual intercourse (AFS) and lifetime number of sexual partners (NSP) may influence the pathogenesis of uterine leiomyoma (UL) through their associations with hormonal concentrations and uterine infections. Leveraging summary statistics from large-scale genome-wide association studies conducted in European ancestry for each trait (NAFS = 214,547; NNSP = 370,711; NUL = 302,979), we observed a significant negative genomic correlation for UL with AFS (rg = -0.11, P = 7.83×10-4), but not with NSP (rg = 0.01, P = 0.62). Four specific genomic regions were identified as contributing significant local genetic correlations to AFS and UL, including one genomic region further identified for NSP and UL. Partitioning SNP-heritability with cell-type-specific annotations, a close clustering of UL with both AFS and NSP was identified in immune and blood-related components. Cross-trait meta-analysis revealed 15 loci shared between AFS/NSP and UL, including 7 novel SNPs. Univariable two-sample Mendelian randomization (MR) analysis suggested no evidence for a causal association between genetically predicted AFS/NSP and risk of UL, nor vice versa. Multivariable MR adjusting for age at menarche or/and age at natural menopause revealed a significant causal effect of genetically predicted higher AFS on a lower risk of UL. Such effect attenuated to null when age at first birth was further included. Utilizing participant-level data from the UK Biobank, one-sample MR based on genetic risk scores yielded consistent null findings among both pre-menopausal and post-menopausal females. From a genetic perspective, our study demonstrates an intrinsic link underlying sexual factors (AFS and NSP) and UL, highlighting shared biological mechanisms rather than direct causal effects. Future studies are needed to elucidate the specific mechanisms involved in the shared genetic influences and their potential impact on UL development.

In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis.

Numerous studies have been conducted to investigate the genomic characterization of bZIP genes and their involvement in the cellular response to endoplasmic reticulum (ER) stress. These studies have provided valuable insights into the coordinated cellular response to ER stress, which is mediated by bZIP transcription factors (TFs). However, a comprehensive and systematic investigations regarding the role of bZIP genes and their involvement in ER stress response in pak choi is currently lacking in the existing literature. To address this knowledge gap, the current study was initiated to elucidate the genomic characteristics of bZIP genes, gain insight into their expression patterns during ER stress in pak choi, and investigate the protein-to-protein interaction of bZIP genes with the ER chaperone BiP. In total, 112 members of the BcbZIP genes were identified through a comprehensive genome-wide analysis. Based on an analysis of sequence similarity, gene structure, conserved domains, and responsive motifs, the identified BcbZIP genes were categorized into 10 distinct subfamilies through phylogenetic analysis. Chromosomal location and duplication events provided insight into their genomic context and evolutionary history. Divergence analysis estimated their evolutionary history with a predicted divergence time ranging from 0.73 to 80.71 million years ago (MYA). Promoter regions of the BcbZIP genes were discovered to exhibit a wide variety of cis-elements, including light, hormone, and stress-responsive elements. GO enrichment analysis further confirmed their roles in the ER unfolded protein response (UPR), while co-expression network analysis showed a strong relationship of BcbZIP genes with ER-stress-responsive genes. Moreover, gene expression profiles and protein-protein interaction with ER chaperone BiP further confirmed their roles and capacity to respond to ER stress in pak choi.

Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae.

Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.

Genome-wide identification of polyamine metabolism and ethylene synthesis genes in Chenopodium quinoa Willd. and their responses to low-temperature stress

BackgroundQuinoa (Chenopodium quinoa Willd.) is valued for its nutritional richness. However, pre-harvest sprouting poses a significant threat to yield and grain quality. This study aims to enhance our understanding of pre-harvest sprouting mitigation strategies, specifically through delayed sowing and avoiding rainy seasons during quinoa maturation. The overarching goal is to identify cold-resistant varieties and unravel the molecular mechanisms behind the low-temperature response of quinoa. We employed bioinformatics and genomics tools for a comprehensive genome-wide analysis of polyamines (PAs) and ethylene synthesis gene families in quinoa under low-temperature stress.ResultsThis involved the identification of 37 PA biosynthesis and 30 PA catabolism genes, alongside 227 ethylene synthesis. Structural and phylogenetic analyses showcased conserved patterns, and subcellular localization predictions indicated diverse cellular distributions. The results indicate that the PA metabolism of quinoa is closely linked to ethylene synthesis, with multiple genes showing an upregulation in response to cold stress. However, differential expression within gene families suggests a nuanced regulatory network.ConclusionsOverall, this study contributes valuable insights for the functional characterization of the PA metabolism and ethylene synthesis of quinoa, which emphasize their roles in plant low-temperature tolerance and providing a foundation for future research in this domain.

Cullin-3 proteins be a novel biomarkers and therapeutic targets for hyperchloremia induced by oral poisoning

Oral poisoning can trigger diverse physiological reactions, determined by the toxic substance involved. One such consequence is hyperchloremia, characterized by an elevated level of chloride in the blood and leads to kidney damage and impairing chloride ion regulation. Here, we conducted a comprehensive genome-wide analysis to investigate genes or proteins linked to hyperchloremia. Our analysis included functional enrichment, protein–protein interactions, gene expression, exploration of molecular pathways, and the identification of potential shared genetic factors contributing to the development of hyperchloremia. Functional enrichment analysis revealed that oral poisoning owing hyperchloremia is associated with 4 proteins e.g. Kelch-like protein 3, Serine/threonine-protein kinase WNK4, Serine/threonine-protein kinase WNK1 and Cullin-3. The protein–protein interaction network revealed Cullin-3 as an exceptional protein, displaying a maximum connection of 18 nodes. Insufficient data from transcriptomic analysis indicates that there are lack of information having direct associations between these proteins and human-related functions to oral poisoning, hyperchloremia, or metabolic acidosis. The metabolic pathway of Cullin-3 protein revealed that the derivative is Sulfonamide which play role in, increasing urine output, and metabolic acidosis resulted in hypertension. Based on molecular docking results analysis it found that Cullin-3 proteins has the lowest binding energies score and being suitable proteins. Moreover, no major variations were observed in unbound Cullin-3 and all three peptide bound complexes shows that all systems remain compact during 50 ns simulations. The results of our study revealed Cullin-3 proteins be a strong foundation for the development of potential drug targets or biomarker for future studies.

Genome-wide identification of the CNGC gene family and negative regulation of drought tolerance by HvCNGC3 and HvCNGC16 in transgenic Arabidopsis thaliana

Cyclic nucleotide-gated ion channels (CNGCs), as non-selective cation channels, play essential roles in plant growth and stress responses. However, they have not been identified in Qingke (Hordeum vulgareL.). Here, we performed a comprehensive genome-wide identification and function analysis of the HvCNGC gene family to determine its role in drought tolerance. Phylogenetic analysis showed that 27 HvCNGC genes were divided into four groups and unevenly located on seven chromosomes. Transcription analysis revealed that two closely related members of HvCNGC3 and HvCNGC16 were highly induced and the expression of both genes were distinctly different in two extremely drought-tolerant materials. Transient expression revealed that the HvCNGC3 and HvCNGC16 proteins both localized to the plasma membrane and karyotheca. Overexpression of HvCNGC3 and HvCNGC16 in Arabidopsis thaliana led to impaired seed germination and seedling drought tolerance, which was accompanied by higher hydrogen peroxide (H2O2), malondialdehyde (MDA), proline accumulation and increased cell damage. In addition, HvCNGC3 and HvCNGC16-overexpression lines reduced ABA sensitivity, as well as lower expression levels of some ABA biosynthesis and stress-related gene in transgenic lines. Furthermore, Yeast two hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that HvCNGC3 and HvCNGC16 interacted with calmodulin/calmodulin-like proteins (CaM/CML), which, as calcium sensors, participate in the perception and decoding of intracellular calcium signaling. Thus, this study provides information on the CNGC gene family and provides insight into the function and potential regulatory mechanism of HvCNGC3 and HvCNGC16 in drought tolerance in Qingke.

CircRNAs as prognostic markers in pediatric acute myeloid leukemia

Circular RNAs (circRNAs) arise from precursor mRNA processing through back-splicing and have been increasingly recognized for their functions in various cancers including acute myeloid leukemia (AML). However, the prognostic implications of circRNA in AML remain unclear. We conducted a comprehensive genome-wide analysis of circRNAs using RNA-seq data in pediatric AML. We revealed a group of circRNAs associated with inferior outcomes, exerting effects on cancer-related pathways. Several of these circRNAs were transcribed directly from genes with established functions in AML, such as circRUNX1, circWHSC1, and circFLT3. Further investigations indicated the increased number of circRNAs and linear RNAs splicing were significantly correlated with inferior clinical outcomes, highlighting the pivotal role of splicing dysregulation. Subsequent analysis identified a group of upregulated RNA binding proteins in AMLs associated with high number of circRNAs, with TROVE2 being a prominent candidate, suggesting their involvement in circRNA associated prognosis. Through the integration of drug sensitivity data, we pinpointed 25 drugs that could target high-risk AMLs characterized by aberrant circRNA transcription. These findings underscore prognostic significance of circRNAs in pediatric AML and offer an alternative perspective for treating high-risk cases in this malignancy.

Comprehensive Genome-Wide Natural Variation and Expression Analysis of Tubby-like Proteins Gene Family in Brachypodium distachyon.

The Tubby-like proteins (TLPs) gene family is a group of transcription factors found in both animals and plants. In this study, we identified twelve B. distachyon TLPs, divided into six groups based on conserved domains and evolutionary relationships. We predicted cis-regulatory elements involved in light, hormone, and biotic and abiotic stresses. The expression patterns in response to light and hormones revealed that BdTLP3, 4, 7, and 14 are involved in light responses, and BdTLP1 is involved in ABA responses. Furthermore, BdTLP2, 7, 9, and 13 are expressed throughout vegetative and reproductive stages, whereas BdTLP1, 3, 5, and 14 are expressed at germinating grains and early vegetative development, and BdTLP4, 6, 8, and 10 are expressed at the early reproduction stage. The natural variation in the eleven most diverged B. distachyon lines revealed high conservation levels of BdTLP1-6 to high variation in BdTLP7-14 proteins. Based on diversifying selection, we identified amino acids in BdTLP1, 3, 8, and 13, potentially substantially affecting protein functions. This analysis provided valuable information for further functional studies to understand the regulation, pathways involved, and mechanism of BdTLPs.

Analysis of sugar components and identification of SPS genes in citrus fruit development.

Sugar is a primary determinant of citrus fruit flavour, but undergoes varied accumulation processes across different citrus varieties owing to high genetic variability. Sucrose phosphate synthase (SPS), a key enzyme in glucose metabolism, plays a crucial role in this context. Despite its significance, there is limited research on sugar component quality and the expression and regulatory prediction of SPS genes during citrus fruit development. Therefore, we analysed the sugar quality formation process in 'Kiyomi' and 'Succosa', two citrus varieties, and performed a comprehensive genome-wide analysis of citrus CsSPSs. We observed that the accumulation of sugar components significantly differs between the two varieties, with the identification of four CsSPSs in citrus. CsSPS sequences were highly conserved, featuring typical SPS protein domains. Expression analysis revealed a positive correlation between CsSPS expression and sugar accumulation in citrus fruits. However, CsSPS expression displays specificity to different citrus tissues and varieties. Transcriptome co-expression network analysis suggests the involvement of multiple transcription factors in shaping citrus fruit sugar quality through the regulation of CsSPSs. Notably, the expression levels of four CsWRKYs (CsWRKY2, CsWRKY20, CsWRKY28, CsWRKY32), were significantly positively correlated with CsSPSs and CsWRKY20 might can activate sugar accumulation in citrus fruit through CsSPS2. Collectively, we further emphasize the potential importance of CsWRKYs in citrus sugar metabolism, our findings serve as a reference for understanding sugar component formation and predicting CsSPS expression and regulation during citrus fruit development.

Genome wide characterization and expression analysis of CrRLK1L gene family in wheat unravels their roles in development and stress-specific responses.

Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) genes encode a subfamily of receptor-like kinases (RLK) that regulate diverse processes during plant growth, development, and stress responses. The first CrRLK1L was identified from the Catharanthus roseus, commonly known as Madagascar periwinkle. Subsequently, CrRLK1L gene families have been characterized in many plants. The genome of T. aestivum encodes 15 CrRLK1L genes with 43 paralogous copies, with three homeologs each, except for -2-D and -7-A, which are absent. Chromosomal localization analysis revealed a markedly uneven distribution of CrRLK1L genes across seven different chromosomes, with chromosome 4 housing the highest number of genes, while chromosome 6 lacked any CrRLK1L genes. Tissue-specific gene expression analysis revealed distinct expression patterns among the gene family members, with certain members exhibiting increased expression in reproductive tissues. Gene expression analysis in response to various abiotic and biotic stress conditions unveiled differential regulation of gene family members. Cold stress induces CrRLK1Ls -4-B and -15-A while downregulating -3-A and -7B. Drought stress upregulates -9D, contrasting with the downregulation of -7D. CrRLK1L-15-B and -15-D were highly induced in response to 1 hr of heat, and combined drought and heat stress, whereas -10-B is downregulated. Similarly, in response to NaCl stress, only CrRLK1L1 homeologs were induced. Fusarium graminearum and Claviceps purpurea inoculation induces homeologs of CrRLK1L-6 and -7. The analysis of cis-acting elements in the promoter regions identified elements crucial for plant growth and developmental processes. This comprehensive genome-wide analysis and expression study provides valuable insights into the essential functions of CrRLK1L members in wheat.

Genome-wide analysis of NPR1-like genes in citrus species and expression analysis in response to citrus canker (Xanthomonas axonopodis pv. citri).

Citrus fruits, revered for their nutritional value, face significant threats from diseases like citrus canker, particularly impacting global citrus cultivation, notably in Pakistan. This study delves into the critical role of NPR1-like genes, the true receptors for salicylic acid (SA), in the defense mechanisms of citrus against Xanthomonas axonopodis pv. citri (Xcc). By conducting a comprehensive genome-wide analysis and phylogenetic study, the evolutionary dynamics of Citrus limon genes across diverse citrus cultivars are elucidated. Structural predictions unveil conserved domains, such as the BTB domain and ankyrin repeat domains, crucial for the defense mechanism. Motif analysis reveals essential conserved patterns, while cis-regulatory elements indicate their involvement in transcription, growth, response to phytohormones, and stress. The predominantly cytoplasmic and nuclear localization of NPR1-like genes underscores their pivotal role in conferring resistance to various citrus species. Analysis of the Ks/Ka ratio indicates a purifying selection of NPR1-like genes, emphasizing their importance in different species. Synteny and chromosomal mapping provide insights into duplication events and orthologous links among citrus species. Notably, Xac infection stimulates the expression of NPR1-like genes, revealing their responsiveness to pathogenic challenges. Interestingly, qRT-PCR profiling post-Xac infection reveals cultivar-specific alterations in expression within susceptible and resistant citrus varieties. Beyond genetic factors, physiological parameters like peroxidase, total soluble protein, and secondary metabolites respond to SA-dependent PR genes, influencing plant characteristics. Examining the impact of defense genes (NPR1) and plant characteristics on disease resistance in citrus, this study marks the inaugural investigation into the correlation between NPR1-associated genes and various plant traits in both susceptible and resistant citrus varieties to citrus bacterial canker.

Abstract 5106: Pharmacological targeting of LSD1 prolongs animal survival times in patient derived orthotopic xenograft models of posterior fossa ependymoma in combination with fractionated radiation

Abstract Background: Posterior Fossa Group A Ependymoma (PFA EPN) constitute one of the most aggressive and highly recurrent molecular subtypes of childhood Ependymomas. We recently performed a comprehensive genome-wide DNA methylation analysis in recurrent pediatric EPN tumors from patients that were followed up for over 13 years. Integrative analysis between tumor DNA methylation and histone modification identified LSD1 as a druggable driver of PFA EPN recurrence. In this study, we examined the therapeutic efficacy of our newly developed LSD1 inhibitor SYC-836 in PDOX models of recurrent PFA EPN. Methodology: To determine the in vitro anti-tumor activities of SYC-836, paired PFA EPN xenograft cell cultures (monolayer and 3D neurospheres) were treated with SYC-836 at 8 concentrations (0.02-25 µM) and examined for changes of cell proliferation every 3-4 days through day 14. To validate the drug’s in vivo efficacy, two established posterior fossa EPN PDOX models, ICb-4423EPN and ICb-2002EPN, were utilized. Forty 8-week old SCID mice of both genders received intra-cerebellar tumor cell implantation and were divided into 4 treatment groups (n=10 per group): 1) control, 2) radiation (2 Gy/day x 5 days), 3) SYC-836 (15 mg/kg, daily intra-peritoneal injection for 28 days), and 4) combination (radiation + SYC-836). Animal survival times were analyzed using log-rank analysis. Changes in LSD1 protein expression and histone lysine methylation were examined through western hybridization. Results: SYC-836 strongly suppressed PFA EPN cell growth in vitro, in both, a time- and dose-dependent manner. While there was no survival benefit with either SYC-836 only (P=0.186) or XRT only (P=0.205); combining SYC-836 with XRT significantly (P=0.04) prolonged the median survival time of ICb-4423EPN, from 46 days in the untreated group to 59 days; and in ICb-2002EPN, even more prominent, from 136 days to 180 days (P=0.007). SYC-836 was well tolerated in mice with no loss of body weight or other toxicities. Changes in LSD1 protein expression and H3K4me2 were detected through western hybridization during and after SYC-836 treatment. Conclusion: Our data support LSD1 as a druggable driver of PFA recurrence and highlights strong anti-tumor activities of SYC-836 in combination with radiation, a standard therapy of pediatric EPN. SYC-836 may have a role in the clinical setting by either reducing radiation dosages or be an adjuvant agent to other chemotherapy drugs in our treatment approach for ependymoma. Citation Format: Milagros M. Suarez Palacios, Sibo Zhao, Huiyuan Zhang, Lin Qi, Holly Lindsay, Mari Kogiso, Frank Braun, Adekunle M. Adesina, Yuchen Du, Yongcheng Song, Xiao-Nan Li. Pharmacological targeting of LSD1 prolongs animal survival times in patient derived orthotopic xenograft models of posterior fossa ependymoma in combination with fractionated radiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5106.

Genome-wide systematic survey and analysis of the RNA helicase gene family and their response to abiotic stress in sweetpotato.

Sweetpotato (Ipomoea batatas (L.) Lam.) holds a crucial position as one of the staple foods globally, however, its yields are frequently impacted by environmental stresses. In the realm of plant evolution and the response to abiotic stress, the RNA helicase family assumes a significant role. Despite this importance, a comprehensive understanding of the RNA helicase gene family in sweetpotato has been lacking. Therefore, we conducted a comprehensive genome-wide analysis of the sweetpotato RNA helicase family, encompassing aspects such as chromosome distribution, promoter elements, and motif compositions. This study aims to shed light on the intricate mechanisms underlying the stress responses and evolutionary adaptations in sweetpotato, thereby facilitating the development of strategies for enhancing its resilience and productivity. 300 RNA helicase genes were identified in sweetpotato and categorized into three subfamilies, namely IbDEAD, IbDEAH and IbDExDH. The collinearity relationship between the sweetpotato RNA helicase gene and 8 related homologous genes from other species was explored, providing a reliable foundation for further study of the sweetpotato RNA helicase gene family's evolution. Furthermore, through RNA-Seq analysis and qRT-PCR verification, it was observed that the expression of eight RNA helicase genes exhibited significant responsiveness to four abiotic stresses (cold, drought, heat, and salt) across various tissues of ten different sweetpotato varieties. Sweetpotato transgenic lines overexpressing the RNA helicase gene IbDExDH96 were generated using A.rhizogenes-mediated technology. This approach allowed for the preliminary investigation of the role of sweetpotato RNA helicase genes in the response to cold stress. Notably, the promoters of RNA helicase genes contained numerous cis-acting elements associated with temperature, hormone, and light response, highlighting their crucial role in sweetpotato abiotic stress response.

Genome-Wide Exploration of the Ethylene-Responsive Element-Binding Factor Gene Family in Sweet Cherry (Prunus avium L.): Preliminarily Unveiling Insights into Normal Development and Fruit Cracking

The ERF subfamily, a significant part of the APETALA2/ethylene-responsive element-binding factor (AP2/ERF) transcription family, plays a crucial role in plant growth, development, and stress responses. Despite its importance, research on this gene family in sweet cherry (Prunus avium L.) is limited. This study identified and analyzed the sweet cherry ERF subfamily in terms of classification, physicochemical properties, structural characteristics, chromosome distribution, gene replication and collinearity, Cis-acting elements, and potential protein interactions. Preliminary investigations of transcription during fruit cracking and normal development were also conducted. Fifty ERFs (PatiERF1~50) were identified, distributed unevenly across eight chromosomes and classified into ten groups with nineteen conserved motifs. Collinearity analysis with other plant species revealed homology, with the highest number of ERF orthologous genes found in apple (Malus domestica L.). Cis-acting elements, particularly abscisic acid response factor, were abundant in PatiERF promoters. Weighted gene co-expression network analysis (WGCNA) and quantitative real-time PCR (RT-qPCR) analysis indicated the involvement of PatiERFs in sweet cherry fruit development and cracking, and nine and four significant candidates related to these processes were speculated, respectively. Furthermore, four other classes of transcription factors (TFs), namely MYB, GRAS, BHLH, and BZIP, as well as 23 structure genes, were predicted to have co-expression and interaction relationships with PatiERFs during fruit development. This suggests their potential synergistic regulation with ERFs in the cherry fruit development process. Our study represents the first comprehensive genome-wide analysis of the ERF subfamily in sweet cherry, laying a crucial foundation for a deeper understanding of the molecular mechanisms correlated with fruit growth, development, and cracking mediated by ERF genes.

Comprehensive genome-wide analyses of R2R3-MYB transcription factors and tolerance to drought stress in Populus davidiana × Populus bolleana

Comprehensive genome-wide analyses of R2R3-MYB transcription factors and tolerance to drought stress in Populus davidiana × Populus bolleana

Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards.

Understanding the genetic basis for adapting to thermal environments is important due to serious effects of global warming on ectothermic species. Various genes associated with thermal adaptation in lizards have been identified mainly focusing on changes in gene expression or the detection of positively selected genes using coding regions. Only a few comprehensive genome-wide analyses have included noncoding regions. This study aimed to identify evolutionarily conserved and accelerated genomic regions using whole genomes of eight Anolis lizard species that have repeatedly adapted to similar thermal environments in multiple lineages. Evolutionarily conserved genomic regions were extracted as regions with overall sequence conservation (regions with fewer base substitutions) across all lineages compared with the neutral model. Genomic regions that underwent accelerated evolution in the lineage of interest were identified as those with more base substitutions in the target branch than in the entire background branch. Conserved elements across all branches were relatively abundant in "intergenic" genomic regions among noncoding regions. Accelerated regions (ARs) of each lineage contained a significantly greater proportion of noncoding RNA genes than the entire multiple alignment. Common genes containing ARs within 5 kb of their vicinity in lineages with similar thermal habitats were identified. Many genes associated with circadian rhythms and behavior were found in hot-open and cool-shaded habitat lineages. These genes might play a role in contributing to thermal adaptation and assist future studies examining the function of genes involved in thermal adaptation via genome editing.

Characterization of the DUF868 gene family in Nicotiana and functional analysis of NtDUF868-E5 involved in pigment metabolism

Domains of unknown function (DUF) proteins represent a large group of uncharacterized protein families. The DUF868 gene family in Nicotiana has not yet been described. In the present study, we identified 12, 11, and 25 DUF868 family members in the genome of Nicotiana sylvestris, N. tomentosiformis, and N. tabacum, respectively. Based on phylogenetic analysis, these were categorized into five groups (A-E). Within each group, the gene structures, motifs, and tertiary structures showed high similarity. NtDUF868 family expansion during evolution was mainly driven by segmental duplication events. MicroRNA (miRNA) target site prediction identified 12 miRNA members that target 16 NtDUF868 family genes. The promoters of these genes contain cis-regulatory elements responsive to light, phytohormones, and abiotic stresses. Expression profiling revealed their tissue- and stage-specific expression patterns. RNA-sequencing and quantitative reverse transcription PCR revealed that the NtDUF868 family genes are potentially involved in the response to abiotic and biotic stresses, particularly drought and hormone stresses, and in the resistance to black shank and bacterial wilt. We generated transformed plants using NtDUF868-E5 overexpression and gene-editing vectors. NtDUF868-E5 overexpression resulted in enhanced tobacco plant growth and development, leading to increased leaf photosynthetic capacity and higher chlorophyll and carotenoid contents. This study provided a comprehensive genome-wide analysis of the DUF868 gene family, shedding light on their potential roles in plant growth and stress responses.

Integrative Analysis of the DUF668 Gene Family in Nicotiana tabacum to Excavate Their Potential Roles in Abiotic Stress Responses

The domain of the unknown function (DUF) gene families assumes pivotal roles in plant metabolic and stress responses. However, our comprehension of the tobacco DUF668 (NtDUF668) gene family and its specific reactions to heavy metal, drought, and salt stresses remain circumscribed. In the current investigation, a comprehensive genome-wide analysis of the NtDUF668 gene family was undertaken utilizing bioinformatics tools. The results unveiled a total of 20 members in the NtDUF668 gene family, denominated NtDUF668-01 to NtDUF668-20. Phylogenetic analyses indicated a closer genetic relationship of DUF668 genes between Nicotiana tabacum and Ipomoea batatas. The examination of gene structure and conservative motifs revealed a bifurcation into two major Clades, aligning with previous studies on DUF668 gene families from various plant species, emphasizing its highly conserved evolutionary mechanism across plants. The exploration of promoter regions of NtDUF668 genes revealed a plethora of cis-acting elements associated with abiotic and biotic stresses, light signaling, and phytohormones. Gene duplication events and selection pressure analysis disclosed the segmental duplication and strong purifying selection pressure during the evolution of NtDUF668 genes. Syntenic analysis indicated a relatively conserved evolutionary mechanism of DUF668 gene families within dicotyledons. Tissue-specific expression analysis suggested that NtDUF668 family members are potentially involved in root development, floral organ formation, and abscission. The expression patterns and qRT–PCR analysis of NtDUF668 genes implied the potentially functional involvements of NtDUF668s in response to multiple abiotic stresses. Furthermore, the stress-triggered member NtDUF668-08 exhibited specific nuclear localization. In conclusion, this genome-wide analysis illuminates the composition, phylogenetic relationships, and potential roles of the NtDUF668 gene family in abiotic stress responses. The identified candidate genes, particularly NtDUF668-08, warrant further research for functional investigation.

Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean.

Hundred-seed weight (HSW) and reproductive period length (RPL) are two major agronomic traits critical for soybean production and adaptation. However, both traits are quantitatively controlled by multiple genes that have yet to be comprehensively elucidated due to the lack of major genes; thereby, the genetic basis is largely unknown. In the present study, we conducted comprehensive genome-wide association analyses (GWAS) of HSW and RPL with multiple sets of accessions that were phenotyped across different environments. The large-scale analysis led to the identification of sixty-one and seventy-four significant QTLs for HSW and RPL, respectively. An ortholog-based search analysis prioritized the most promising candidate genes for the QTLs, including nine genes (TTG2, BZR1, BRI1, ANT, KLU, EOD1/BB, GPA1, ABA2, and ABI5) for HSW QTLs and nine genes (such as AGL8, AGL9, TOC1, and COL4) and six known soybean flowering time genes (E2, E3, E4, Tof11, Tof12, and FT2b) for RPL QTLs. We also demonstrated that some QTLs were targeted during domestication to drive the artificial selection of both traits towards human-favored traits. Local adaptation likely contributes to the increased genomic diversity of the QTLs underlying RPL. The results provide additional insight into the genetic basis of HSW and RPL and prioritize a valuable resource of candidate genes that merits further investigation to reveal the complex molecular mechanism and facilitate soybean improvement.

Genome-Wide Bioinformatics Analysis of SWEET Gene Family and Expression Verification of Candidate PaSWEET Genes in Potentilla anserina

Sugars act as the main energy sources in many fruit and vegetable crops. The biosynthesis and transportation of sugars are crucial and especially contribute to growth and development. SWEET is an important gene family that plays a vital role in plants’ growth, development, and adaptation to various types of stresses (biotic and abiotic). Although SWEET genes have been identified in numerous plant species, there is no information on SWEETs in Potentilla anserina. In the present study, we performed a comprehensive genome-wide bioinformatics analysis and identified a total of 23 candidate PaSWEETs genes in the Potentilla anserina genome, which were randomly distributed on ten different chromosomes. The phylogenetic analysis, chromosomal location, gene structure, specific cis-elements, protein interaction network, and physiological characteristics of these genes were systematically examined. The identified results of the phylogenetic relationship with Arabidopsis thaliana revealed that these PaSWEET genes were divided into four clades (I, II, III, and IV). Moreover, tissue-specific gene expression through quantitative real-time polymerase chain reaction (qRT-PCR) validation exposed that the identified PaSWEETs were differentially expressed in various tissues (roots, stems, leaves, and flowers). Mainly, the relative fold gene expression in swollen and unswollen tubers effectively revealed that PaSWEETs (7, 9, and 12) were highly expressed (300-, 120-, and 100-fold) in swollen tubers. To further elucidate the function of PaSWEETs (7, 9, and 12), their subcellular location was confirmed by inserting them into tobacco leaves, and it was noted that these genes were present on the cell membrane. On the basis of the overall results, it is suggested that PaSWEETs (7, 9, and 12) are the candidate genes involved in swollen tuber formation in P. anserina. In crux, we speculated that our study provides a valuable theoretical base for further in-depth function analysis of the PaSWEET gene family and their role in tuber development and further enhancing the molecular breeding of Potentilla anserina.