BMC Genomics最新文献

{"title":"Respiratory Chain Complex I Deficiency in Leber Hereditary Optic Neuropathy: Insights from Ophthalmologic and Molecular Investigations in Tunisia.","authors":"Latifa Chkioua, Yessine Amri, Chayma Sahli, Tawfik Nasri, Mohamed Omar Miladi, Taieb Massoud, Sandrine Laradi, Mohamed Ghorbel, Hassen Ben Abdennebi","doi":"10.1186/s12864-024-11060-0","DOIUrl":"https://doi.org/10.1186/s12864-024-11060-0","url":null,"abstract":"<p><strong>Background: </strong>Leber hereditary optic neuropathy (LHON) is a mitochondrial DNA (mtDNA) rare disease due to the pathogenic variant of the NADH dehydrogenase enzyme. LHON is characterized by a sudden central vision loss due to focal degeneration of the retinal ganglion cell layer and optic nerve. Symptoms usually appear between the age of 18 and 35 years. Some individuals present the mtDNA mutations but not presented the LHON clinical features. The heteroplasmic or homoplasmic character of the mutations among patients explains why they develop the disease or not even though they carry the pathogenic variant.</p><p><strong>Methods: </strong>This study was performed in collaboration with the department of ophthalmology of Farhat Hached Hospital, Sousse, Tunisia. Screening for the common mutations in Mt-ND1 gene (m.3460G > A), Mt-ND4 gene (m.11778G > A) and Mt-ND6 gene (m.14484T > C) was performed in five Tunisian families by standard RFLP PCR, followed by direct sequencing of the entire of these genes. Indeed, bioinformatics tools were used to predict the potential functional impact of the identified mutations on the Human mitochondrial respiratory complex I protein.</p><p><strong>Results: </strong>one novel p.L601M (m.1413 C > A) and four previously reported mutations were identified in this study including: rs199476112G > A (m.11778G > A); rs202227543G > A (m.14258G > A); rs1603224763 (m.14510 dup) and NC_012920.1: m.3244G > C. In this present report, only one patient was found carrying the primary point mutation (m. 11778G > A). The ophthalmologic findings showing major fundus changes included hyperemic optic discs; disc pseudo-oedema and microangiopathy leading to optic disc atrophy. The analyses of the stability of protein upon identified mutations using DynaMut tool server demonstrated that these variations induce a rigidification in the region where they are located.</p><p><strong>Conclusion: </strong>This is the first Tunisian report of mtDNA mutations identified in Tunisia causing the LHON. The main factors involved in the pathophysiological mechanisms of this disease are genetic, epigenetic, hormonal and environmental influences.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1133"},"PeriodicalIF":3.5,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome sequencing-based characterization and determination of quinolone resistance among methicillin-resistant and methicillin-susceptible S. Aureus isolates from patients attending regional referral hospitals in Tanzania.","authors":"Masoud A Juma, Happiness Kumburu, Boaz Wadugu, Davis Kuchaka, Mariana Shayo, Patrick Kimu, Livin E Kanje, Melkiory Beti, Marco van Zwetselaar, Blandina Mmbaga, Tolbert Sonda","doi":"10.1186/s12864-024-11045-z","DOIUrl":"https://doi.org/10.1186/s12864-024-11045-z","url":null,"abstract":"<p><strong>Background: </strong>The emergence of multidrug-resistant termed Methicillin-resistant Staphylococcus aureus (MRSA) strain, driven by the acquisition of resistance gene mecA imposes a substantial challenge in the treatment and control of their related infections. Although quinolones have historically been effective against both MRSA and methicillin-susceptible S. aureus (MSSA) strains, the rising resistance to quinolones among S. aureus isolates, particularly in MRSA, has severely curtailed their potency and further narrowed down the therapeutic options. This study aimed to determine the burden of MRSA among isolates, as well as their resistance profile, genotypic characterization, and molecular relatedness through the construction of a phylogenetic tree.</p><p><strong>Materials and methods: </strong>Archived clinical S. aureus isolates from a descriptive, cross-sectional study involving six regional referral hospitals in Dodoma, Songea, Kigoma, Kitete, and Morogoro in the mainland Tanzania and Mnazi Mmoja in Zanzibar were analyzed. Bacterial identification was performed using both classical microbiology and whole genome sequencing on Illumina Nextseq 550 Sequencer. Species identification was done using KmerFinder 3.2, Multilocus Sequence Typing using MLST 2.0, SCCmec typing using SCCmecFinder 1.2, resistance genes using ResFinder 4.1, and phylogenetic relatedness using CSI Phylogeny 1.4.</p><p><strong>Results: </strong>Out of the 140 isolates analyzed, 69 (49.3%) were identified as MRSA, with 57 (82.6%) exhibiting quinolone resistance. Conversely, 71 isolates were identified as MSSA, and none of them exhibited resistance to quinolones. Spa-typing revealed six spa types, with t355, t1476, and t498 being the most common. Moreover, all (69) MRSA were found to carry SCCmec type IV. The isolates exhibited 14 different sequence types (STs). Notably, ST152 was prevalent among MSSA (50 isolates, 70%), while ST8 was the predominant sequence type among MRSA (58 isolates, 84%). The antimicrobial resistance profile revealed at least three horizontally acquired resistance genes, with blaZ, dfrG, tet(K), and aac (6')-aph (2'') genes being highly prevalent.</p><p><strong>Conclusion: </strong>There is a high genetic diversity among the S. aureus isolates existing in Tanzania regional hospitals, with a concerning burden of quinolone resistance among MRSA isolates. The diversity in resistance genes among MRSA lineages emphasizes the necessity for the development of sustainable antimicrobial stewardship and surveillance to support evidence-based guidelines for managing and controlling MRSA infections in both community and hospital settings.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1130"},"PeriodicalIF":3.5,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A dual typing system establishment and global diversity analysis for sapoviruses.","authors":"Wei Zhao, Zhiyong Gao, Chiyu Guo, Yuyue Zhang, Yu Zhang, Quanyi Wang, Jiemei Yu","doi":"10.1186/s12864-024-11048-w","DOIUrl":"https://doi.org/10.1186/s12864-024-11048-w","url":null,"abstract":"<p><strong>Background: </strong>The genus Sapovirus in the family Caliciviridae comprises of a genetically diverse group of viruses that are responsible for causing acute gastroenteritis in both human and animals globally. As the number of sequences continues to grow and more recombinant sequences are identified, the classification criteria of genogroups and genotypes of sapovirus need to be further refined. In this study, we aimed to optimize the classification of sapoviruses.</p><p><strong>Results: </strong>Through evolutionary clustering and genetic distance analysis, we have updated the classification criteria for VP1 genogroup and genotypes. We adjusted the original mean values ± 3 standard deviations (SD) of genetic distances to mean values ± 2.5SD, resulting the corresponding cutoff values for the same genotype and genogroup set at <0.161 and <0.503, respectively. Additionally, we established classification criteria for RdRp types and groups, referred to as P-types and P-groups,, with mean values ± 2SD and cutoff values of <0.266 and <0.531 for the same type and group, respectively. This refinement has expanded the VP1 genogroups to thirty-four and identified twenty-four P-groups. For human sapoviruses, the new criteria have resulted in the addition of one genotype, GV.PNA1. Moreover, the new criteria defined three P-groups and 21 P-types for human sapoviruses. Spatial-temporal analysis revealed no specific distribution pattern for human sapoviruses.</p><p><strong>Conclusions: </strong>We established a dual typing system on classification based on VP1 and RdRp nucleotide sequences for sapoviruses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1131"},"PeriodicalIF":3.5,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA-seq analysis reveals genes associated with Macrophomina phaseolina-induced host senescence in soybean.","authors":"Afsana Noor, Christopher R Little","doi":"10.1186/s12864-024-11023-5","DOIUrl":"https://doi.org/10.1186/s12864-024-11023-5","url":null,"abstract":"<p><strong>Background: </strong>Charcoal rot of soybean is caused by the hemibiotrophic fungus Macrophomina phaseolina, a global crop destroyer and an important pathogen in the midwestern USA. The quantitative nature of host resistance and the complexity of the soybean-M. phaseolina interaction at the molecular level have hampered resistance breeding. A previous study showed that L-ascorbic acid (LAA) pre-treatment before M. phaseolina inoculation reduced charcoal rot lesion length in excised soybean stems. This study aimed to elucidate the genetic underpinnings of M. phaseolina-induced senescence and the mitigating effects of ascorbic acid on this physiological process within the same pathosystem.</p><p><strong>Results: </strong>RNA was sequenced from M. phaseolina-resistant and -susceptible soybean genotypes following M. phaseolina inoculation, LAA, and hydrogen peroxide (H₂O₂)-an oxidative stress inducer-application followed by inoculation. More genes were down-regulated in the resistant and susceptible genotypes than up-regulated when the M. phaseolina-inoculated treatments were compared to mock-inoculated control treatments. Gene ontology (GO) term and KEGG pathways analysis detected M. phaseolina-induced up-regulation of receptor-like kinase genes. In contrast, many genes related to antioxidants, defense, and hormonal pathways were down-regulated in both genotypes. LAA pre-treatment induced genes related to photosynthesis and reactive oxygen species responses in both genotypes. H₂O₂ pre-treatment following inoculation up-regulated many stress-response genes, while hormone signal transduction and photosynthesis-related genes were down-regulated in both genotypes.</p><p><strong>Conclusions: </strong>Results revealed transcriptional variation and genes associated with M. phaseolina-induced senescence in soybean. Ascorbic acid induced many photosynthetic genes, suggesting a complex regulation of defense and immunity in the plant against the hemibiotroph. Soybean plants also exhibited enhanced stress responsiveness when treated with H₂O₂ followed by inoculation with M. phaseolina. This study will broaden more research avenues related to transcriptional regulation during the M. phaseolina-soybean interaction and the potential role of receptor-like kinases, oxidative stress-responsive genes, ethylene-mediated signaling and enhanced photosynthetic gene expression when mounting host resistance to this important soybean pathogen.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1129"},"PeriodicalIF":3.5,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics analysis of the Microsporidia sp. MB genome: a malaria transmission-blocking symbiont of the Anopheles arabiensis mosquito.","authors":"Lilian Mbaisi Ang'ang'o, Jeremy Keith Herren, Özlem Tastan Bishop","doi":"10.1186/s12864-024-11046-y","DOIUrl":"https://doi.org/10.1186/s12864-024-11046-y","url":null,"abstract":"<p><strong>Background: </strong>The use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mosquitoes, can be transmitted both vertically and horizontally with minimal effects on its mosquito host. Its genome, recently sequenced from An. arabiensis, comprises a compact 5.9 Mbp.</p><p><strong>Results: </strong>Here, we analyze the Microsporidia sp. MB genome, highlighting its major genomic features, gene content, and protein function. The genome contains 2247 genes, predominantly encoding enzymes. Unlike other members of the Enterocytozoonida group, Microsporidia sp. MB has retained most of the genes in the glycolytic pathway. Genes involved in RNA interference (RNAi) were also identified, suggesting a mechanism for host immune suppression. Importantly, meiosis-related genes (MRG) were detected, indicating potential for sexual reproduction in this organism. Comparative analyses revealed similarities with its closest relative, Vittaforma corneae, despite key differences in host interactions.</p><p><strong>Conclusion: </strong>This study provides an in-depth analysis of the newly sequenced Microsporidia sp. MB genome, uncovering its unique adaptations for intracellular parasitism, including retention of essential metabolic pathways and RNAi machinery. The identification of MRGs suggests the possibility of sexual reproduction, offering insights into the symbiont's evolutionary strategies. Establishing a reference genome for Microsporidia sp. MB sets the foundation for future studies on its role in malaria transmission dynamics and host-parasite interactions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1132"},"PeriodicalIF":3.5,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Capturing resilience from phenotypic deviations: a case study using feed consumption and whole genome data in pigs.","authors":"Enrico Mancin, Christian Maltecca, Jicaj Jiang, Yi Jian Huang, Francesco Tiezzi","doi":"10.1186/s12864-024-11052-0","DOIUrl":"10.1186/s12864-024-11052-0","url":null,"abstract":"<p><strong>Background: </strong>In recent years, interest has grown in quantifying resilience in livestock by examining deviations in target phenotypes. This method is based on the idea that variability in these phenotypes reflects an animal's ability to adapt to external factors. By utilizing routinely collected time-series feed intake data in pigs, researchers can obtain a broad measure of resilience. This measure extends beyond specific conditions, capturing the impact of various unknown external factors that influence phenotype variations. Importantly, this method does not require additional phenotyping investments. Despite growing interest, the relationship between resilience indicators-calculated as deviations from longitudinally recorded target traits-and the mean of those traits remains largely unexplored. This gap raises the risk of inadvertently selecting for the mean rather than accurately capturing true resilience. Additionally, distinguishing between random phenotype fluctuations (white noise) and structural variations linked to resilience poses a challenge. With the aim of developing general resilience indicators applicable to commercial swine populations, we devised four resilience indicators utilizing daily feed consumption as the target trait. These include a canonical resilience indicator (BALnVar) and three novel ones (BAMaxArea, SPLnVar, and SPMaxArea), designed to minimize noise and ensure independence from daily feed consumption. We subsequently integrated these indicators with Whole Genome Sequencing using SLEMM algorithm, data from 1,250 animals to assess their efficacy in capturing resilience and their independence from the mean of daily feed consumption.</p><p><strong>Results: </strong>Our findings revealed that conventional resilience indicators failed to differentiate from the mean of daily feed consumption, underscoring potential limitations in accurately capturing true resilience. Notably, significant associations involving conventional resilience indicators were identified on chromosome 1, which is commonly linked to body weight.</p><p><strong>Conclusion: </strong>We observed that deviations in feed consumption can effectively serve as indicators for selecting resilience in commercial pig farming, as confirmed by the identification of genes such as PKN1 and GYPC. However, the identification of other genes, such as RNF152, related to growth, suggests that common resilience quantification methods may be more closely related to the mean of daily feed consumption rather than capturing true resilience.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1128"},"PeriodicalIF":3.5,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction.","authors":"Tomàs Montserrat-Ayuso, Anna Esteve-Codina","doi":"10.1186/s12864-024-11015-5","DOIUrl":"https://doi.org/10.1186/s12864-024-11015-5","url":null,"abstract":"<p><p>The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we will show that prominent initiatives such as the Human Cell Atlas [1], the Tabula Sapiens [2] and the Tabula Muris [3] contain a significant amount of contamination products (frequently affecting the whole organ) in their data portals due to suboptimal quality filtering. Our work addresses a critical gap by advocating for more stringent quality filtering, highlighting the imperative for a shift from existing standards, which currently lean towards greater permissiveness. We will show the importance of incorporating cell intronic fraction in quality control -or MALAT1 expression otherwise- showcasing its informative nature and potential to elevate cell atlas data reliability. In summary, here, we unveil the hidden intronic landscape of every tissue and highlight the importance of more rigorous single-cell RNA-sequencing quality assessment in cell atlases to enhance their applicability in diverse downstream analyses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1124"},"PeriodicalIF":3.5,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species.","authors":"Li-Fang Li, Min Yang, Ying Qi, Peng-Hua Gao, Shao-Wu Yang, Yong-Teng Zhao, Jian-Wei Guo, Huan-Yu Wei, Jia-Ni Liu, Jian-Rong Zhao, Fei-Yan Huang, Lei Yu","doi":"10.1186/s12864-024-11053-z","DOIUrl":"10.1186/s12864-024-11053-z","url":null,"abstract":"<p><strong>Background: </strong>The genus Amorphophallus (Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of Amorphophallus is limited. In this study, four chloroplast genomes of Amorphophallus were sequenced and assembled. For the first time, comparative analyses of chloroplast genomes were conducted on the 13 Amorphophallus species in conjunction with nine published sequences.</p><p><strong>Results: </strong>The Amorphophallus chloroplast genomes exhibited typical quadripartite structures with lengths ranging from 164,417 to 177,076 bp. These structures consisted of a large single copy (LSC, 90,705 - 98,561 bp), a small single copy (SSC, 14,172 - 21,575 bp), and a pair of inverted repeats (IRs, 26,225 - 35,204 bp). The genomes contain 108 - 113 unique genes, including 76 - 79 protein-coding genes, 28 - 29 tRNA genes, and 4 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) within Amorphophallus were generally conserved. However, several variations in intron loss and gene expansion on the IR-SSC boundary regions were found among these 13 genomes. Four mutational hotspot regions, including trnM-atpE, atpB, atpB-rbcL and ycf1 were identified. They could identify and phylogeny future species in the genus Amorphophallus. Positive selection was found for rpl36, ccsA, rpl16, rps4, rps8, rps11, rps12, rps14, clpP, rps3, ycf1, rpl20, rps2, rps18, rps19, atpA, atpF, rpl14, rpoA, rpoC1, rpoC2 and rps15 based on the analyses of Ka/Ks ratios. Phylogenetic inferences based on the complete chloroplast genomes revealed a sister relationship between Amorphophallus and Caladieae. All Amorphophallus species formed a monophyletic evolutionary clade and were divided into three groups, including CA-II, SEA, and CA-I. Amorphophallus albus, A. krausei, A. kachinensis and A. konjac were clustered into the CA-II clade, A. paeoniifolius and A. titanum were clustered into the SEA clade, A. muelleri 'zhuyajin1', Amorphophallus sp, A. coaetaneus, A. tonkinensis and A. yunnanensis were clustered into CA- I clade.</p><p><strong>Conclusions: </strong>The genome structure and gene content of Amorphophallus chloroplast genomes are consistent across various species. In this study, the structural variation and comparative genome of chloroplast genomes of Amorphophallus were comprehensively analyzed for the first time. The results provide important genetic information for species classification, identification, molecular breeding, and evolutionary exploration of the genus Amorphophallus.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1122"},"PeriodicalIF":3.5,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11580329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive study of Z-DNA density and its evolutionary implications in birds.","authors":"Yu-Ren Wang, Shao-Ming Chang, Jinn-Jy Lin, Hsiao-Chian Chen, Lo-Tung Lee, Dien-Yu Tsai, Shih-Da Lee, Chung-Yu Lan, Chuang-Rung Chang, Chih-Feng Chen, Chen Siang Ng","doi":"10.1186/s12864-024-11039-x","DOIUrl":"https://doi.org/10.1186/s12864-024-11039-x","url":null,"abstract":"<p><strong>Background: </strong>Z-DNA, a left-handed helical form of DNA, plays a significant role in genomic stability and gene regulation. Its formation, associated with high GC content and repetitive sequences, is linked to genomic instability, potentially leading to large-scale deletions and contributing to phenotypic diversity and evolutionary adaptation.</p><p><strong>Results: </strong>In this study, we analyzed the density of Z-DNA-prone motifs of 154 avian genomes using the non-B DNA Motif Search Tool (nBMST). Our findings indicate a higher prevalence of Z-DNA motifs in promoter regions across all avian species compared to other genomic regions. A negative correlation was observed between Z-DNA density and developmental time in birds, suggesting that species with shorter developmental periods tend to have higher Z-DNA densities. This relationship implies that Z-DNA may influence the timing and regulation of development in avian species. Furthermore, Z-DNA density showed associations with traits such as body mass, egg mass, and genome size, highlighting the complex interactions between genome architecture and phenotypic characteristics. Gene Ontology (GO) analysis revealed that Z-DNA motifs are enriched in genes involved in nucleic acid binding, kinase activity, and translation regulation, suggesting a role in fine-tuning gene expression essential for cellular functions and responses to environmental changes. Additionally, the potential of Z-DNA to drive genomic instability and facilitate adaptive evolution underscores its importance in shaping phenotypic diversity.</p><p><strong>Conclusions: </strong>This study emphasizes the role of Z-DNA as a dynamic genomic element contributing to gene regulation, genomic stability, and phenotypic diversity in avian species. Future research should experimentally validate these associations and explore the molecular mechanisms by which Z-DNA influences avian biology.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1123"},"PeriodicalIF":3.5,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: A survey of the Desulfuromonadia \"cytochromome\" provides a glimpse of the unexplored diversity of multiheme cytochromes in nature.","authors":"Ricardo Soares, Bruno M Fonseca, Benjamin W Nash, Catarina M Paquete, Ricardo O Louro","doi":"10.1186/s12864-024-11050-2","DOIUrl":"https://doi.org/10.1186/s12864-024-11050-2","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1125"},"PeriodicalIF":3.5,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}