BMC Genomics最新文献

{"title":"Genomic exploration of Iranian almond (Prunus dulcis) germplasm: decoding diversity, population structure, and linkage disequilibrium through genotyping-by-sequencing analysis.","authors":"Soheila Khojand, Mehrshad Zeinalabedini, Reza Azizinezhad, Ali Imani, Mohammad Reza Ghaffari","doi":"10.1186/s12864-024-11044-0","DOIUrl":"10.1186/s12864-024-11044-0","url":null,"abstract":"<p><p>This study focuses on the genetic diversity and population structure of Prunus dulcis (almond tree), a crucial agricultural component with widespread cultivation and commercial importance, particularly in Iran, a region with a longstanding tradition of almond cultivation. The diverse almond collection in Iran encompasses many local varieties, breeding selections, rootstocks, and international cultivars. This diversity necessitates advanced genotyping techniques to gain insights into genetic diversity, population structure, and linkage disequilibrium (LD). In this paper, genotyping-by-sequencing (GBS) was employed to analyze 62 almond germplasm samples, identifying approximately 63,537 high-quality single nucleotide polymorphisms (SNPs) distributed across the eight chromosomes of the almond genome. On average, there were 30,225 SNPs per chromosome. The analysis yielded an average polymorphism information content (PIC) of 0.315 and an expected heterozygosity (He) rate of 0.28, indicating a significant level of genetic diversity within the studied almond germplasm. The LD analysis demonstrated a rapid decline, with an average LD decay spanning approximately 300 kb for an r² value of 0.2. This suggests substantial hybridization among the sampled almond varieties. Principal Component Analysis (PCA) and structure analysis could not differentiate genotypes based on geographical origin, providing further evidence of genetic mixing among the studied almond populations. An Analysis of Molecular Variance (AMOVA) highlighted significant genetic diversity within populations but revealed minimal differences. This comprehensive study of Iran's almond genotypes offers valuable insights for future breeding and conservation efforts, emphasizing this agriculturally significant species abundant genetic diversity and intricate population structure.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1101"},"PeriodicalIF":3.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666837","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":"qGO: a novel method for quantifying the diversity of mitochondrial genome organization.","authors":"Haihe Shi, Shuai Yang, Meicai Wei, Gengyun Niu","doi":"10.1186/s12864-024-11006-6","DOIUrl":"10.1186/s12864-024-11006-6","url":null,"abstract":"<p><p>Quantifying the features of mitochondrial genome structural variation is crucial for understanding its contribution to complexity. Accurate quantification and interpretation of organizational diversity can help uncover biological evolutionary laws and patterns. The current qMGR approach accumulates the changes in two adjacent genes to calculate the rearrangement frequency RF of each single gene and the rearrangement score RS for specific taxa in the mitogenomes of a given taxonomic group. However, it may introduce bias, as it assigns scores to adjacent genes rather than to rearranged genes. To overcome this limitation, we propose a novel statistical method called qGO to quantify the diversity of gene organization. The qGO method, which is based on the homology of gene order, provides a more accurate representation of genome organizational diversity by partitioning gene strings and individually assigning weights to genes spanning different regions. Additionally, a comprehensive approach is employed for distance computation, generating an extensive matrix of rearrangement distances. Through experiments on more than 5500 vertebrate mitochondrial genomes, we demonstrated that the qGO method outperforms existing methods in terms of accuracy and interpretability. This method improves the comparability of genomes and allows a more accurate comparison of the diversity of mitochondrial genome organization across taxa. These findings have significant implications for unraveling genome evolution, exploring genome function, and investigating the process of molecular evolution.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1097"},"PeriodicalIF":3.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11571882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666975","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":"Correction: ProbC: joint modeling of epigenome and transcriptome effects in 3D genome.","authors":"Emre Sefer","doi":"10.1186/s12864-024-10947-2","DOIUrl":"10.1186/s12864-024-10947-2","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1099"},"PeriodicalIF":3.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11572405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666813","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":"Gene loss in Antarctic icefish: evolutionary adaptations mimicking Fanconi Anemia?","authors":"Seung Chul Shin, Sanghee Kim, Han-Woo Kim, Jun Hyuck Lee, Jin-Hyoung Kim","doi":"10.1186/s12864-024-11028-0","DOIUrl":"10.1186/s12864-024-11028-0","url":null,"abstract":"<p><strong>Background: </strong>The white-blooded Antarctic icefishes is a representative organism that survive under the stenothermal conditions of the Southern Ocean without the hemoglobin genes. To compensate for inefficient oxygen transport, distinct features such as increased heart size, greater blood volume, and reduced hematocrit density enhance the amount of dissolved oxygen and the velocity of blood flow.</p><p><strong>Results: </strong>Here, we investigated these unique characteristics by comparing high-quality genomic data between white-blooded and red-blooded fishes and identified the loss of FAAP20, which is implicated in anemia. Although the gene region containing FAAP20 is conserved in notothenioids as shown through collinear analysis, only remnants of FAAP20 persist in several icefish species. Additionally, we observed the loss of SOAT1, which plays a pivotal role in cholesterol metabolism, providing a clue for further investigations into the unique mitochondrial form of the icefish.</p><p><strong>Conclusions: </strong>The loss of FAAP20, which is known to reduce erythrocyte counts under stress conditions in mice and humans, may provide a clue to understanding the genomic characteristics related to oxygen supply, such as low hematocrit, in Antarctic icefishes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1102"},"PeriodicalIF":3.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666816","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":"Pituitary whole transcriptome analysis reveals key genes regulating reproduction in Hy-Line Brown hens and the construction of their ceRNA molecular regulatory network.","authors":"Yijie Li, Bin Zhai, Haijie Song, Xin Zhang, Yixiang Tian, Donghua Li, Yujie Gong, Yujie Guo, Ruirui Jiang, Ruili Han, Juan Zhang, Yanhua Zhang, Yadong Tian","doi":"10.1186/s12864-024-11035-1","DOIUrl":"10.1186/s12864-024-11035-1","url":null,"abstract":"<p><strong>Background: </strong>The development and egg-laying performance of hens are precisely regulated by hormones secreted by the pituitary. In this study, we performed comprehensive transcriptome sequencing of pituitary from Hy-Line Brown hens at 15, 20, 30 and 68 W of age. Through association analysis, we identified key genes and ceRNA regulatory networks related to pituitary development and egg production.</p><p><strong>Results: </strong>Based on the comprehensive transcriptome data, we identified 470 differentially expressed lncRNAs (DE-lncRNAs), 38 differentially expressed miRNAs (DE-miRNAs), and 2,449 differentially expressed mRNAs (DE-mRNAs). Time-series analysis pinpointed genes and signaling pathways that significantly influence pituitary hormone secretion at various stages. At 15 W, the high expression of GHRHR, NPY1R, and TSHR in the pituitary supports growth. At 20 and 30 W, elevated GNRHR expression sustains continuous egg production. In the late laying period, the expression of PRL may lead to a decline in egg production. Additionally, association analysis enabled the construction of a ceRNA regulatory network involving non-coding RNAs that regulate the development and reproduction of hens.</p><p><strong>Conclusion: </strong>This study elucidated the comprehensive transcriptome expression profiles of the pituitary gland during the development and egg-laying processes in Hy-Line Brown hens and constructed the associated molecular regulatory networks. These findings lay the foundation for investigating the mechanisms by which non-coding RNAs regulate pituitary hormone secretion.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1100"},"PeriodicalIF":3.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666853","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":"Genomic Single Nucleotide Polymorphism (SNP) markers and mitochondrial haplotypes illuminate the origins of Crown-of-Thorns Starfish (Acanthaster solaris) outbreaks in the South China Sea.","authors":"Peng Tian, Wei Wang, Site Luo, Xiao Du, Yinghui Zhong, Fucheng Sun, Ziqing Xu, Jiaguang Xiao, Shuangen Yu, Wentao Niu","doi":"10.1186/s12864-024-11011-9","DOIUrl":"10.1186/s12864-024-11011-9","url":null,"abstract":"<p><strong>Background: </strong>Outbreaks of the coral predator Crown-of-Thorns Starfish (CoTS) pose a severe threat to coral reefs in the Indo-Pacific Ocean. In 2018, the South China Sea (SCS) experienced significant CoTS outbreaks, leading to extensive coral mortality across the Xisha, Zhongsha, Dongsha, and Nansha Islands, severely impacting the coral reef ecosystem.</p><p><strong>Results: </strong>To explore the origins of these outbreaks, we conducted a comprehensive genomic analysis using data from genomic single nucleotide polymorphism sites (SNPs) and mitochondrial haplotypes. Our analysis reveals that CoTS populations in the SCS, which exhibit moderate genetic diversity and may have undergone positive selection or population expansion. There was limited genetic differentiation among CoTS populations from XS, ZS, and NS groups. Especially between the XS and ZS groups, there was almost no genetic differentiation. The populations from XS, ZS, and NS groups have strong genetic connections with populations in Vietnam and the Philippines. There was high gene flow from Vietnam to the Xisha Islands and from the Philippines to the Nansha Islands, suggesting that the CoTS populations in these regions primarily originate from these neighboring countries.</p><p><strong>Conclusion: </strong>The comprehensive analyses of SNP and mitochondrial genomes have provided valuable insights into the population genetics of CoTS. This research has generated significant genomic resources and facilitated important studies on the genetics of the CoTS species. By identifying potential source populations and understanding the genetic basis of their spread, managers can develop more effective conservation strategies to protect vulnerable coral reef ecosystems in the SCS.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1094"},"PeriodicalIF":3.5,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643622","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":"Metabolic status is a key factor influencing proteomic changes in ewe granulosa cells induced by chronic BPS exposure.","authors":"Marie-Emilie Lebachelier de la Riviere, Ophélie Téteau, Coline Mahé, Olivier Lasserre, Alice Desmarchais, Svetlana Uzbekova, Pascal Papillier, Daniel Tomas, Valérie Labas, Virginie Maillard, Marie Saint-Dizier, Aurélien Binet, Sebastien Elis","doi":"10.1186/s12864-024-11034-2","DOIUrl":"10.1186/s12864-024-11034-2","url":null,"abstract":"<p><strong>Background: </strong>Bisphenol S (BPS) is the main substitute for bisphenol A (BPA), a well-known plasticiser and endocrine disruptor. BPS disrupts ovarian function in several species. Moreover, a few studies have reported that the effects of BPS might be modulated by the metabolic status, and none have characterised the granulosa cell (GC) proteome after chronic BPS exposure.</p><p><strong>Objectives: </strong>This study aimed to decipher the mechanisms of action of chronic BPS exposure on the proteome of ewe GCs while considering the interaction between a deliberate contrasted metabolism and reproductive function.</p><p><strong>Methods: </strong>Forty ewes were split into two groups with contrasted diets: restricted (R, n = 20) and well-fed (WF, n = 20). The R and WF ewes were subdivided according to the dose of BPS administered through the diet (0-50 µg/kg/day), forming four groups: R0, R50, WF0 and WF50. After 3-month BPS daily exposure, GCs were recovered during the pre-ovulatory stage and proteins were analysed by nano-liquid chromatography coupled with tandem mass spectrometry.</p><p><strong>Results: </strong>Chronic exposure to BPS affected the GC proteome differently according to the ewe metabolic status. Fifty-nine out of 958 quantified proteins were differentially abundant between groups and are mainly involved in carbohydrate and lipid pathways. Unsupervised hierarchical clustering of differentially abundant proteins (DAPs) identified four clusters of 34, 6, 5 and 14 proteins according to the BPS exposure and diet interaction. Pairwise comparisons between groups also revealed a strong effect of BPS exposure and diet interaction. Functional analysis of DAPs highlighted that BPS upregulated β-glucuronidase (GUSB; p = 0.002), a protein especially able to deconjugate bisphenol glucuronides (BP-g). Moreover, among unexposed ewes, GUSB was detected only in well-fed ewes.</p><p><strong>Discussion: </strong>Conjugation of glucuronides inhibits the oestrogenic activity of bisphenols. Upregulation of GUSB in ewes dosed with BPS would prolong the oestrogenic effects of BPS by deconjugating BPS-g into free BPS. In addition, literature has reported an up-regulation of GUSB in people suffering from obesity. Therefore, people suffering from obesity could be subjected to prolonged and aggravated exposure to BPS. These data highlighted the deleterious effects of BPS and its interaction with metabolic status.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1095"},"PeriodicalIF":3.5,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643634","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":"HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes.","authors":"Amit Yadav, Srikrishna Subramanian","doi":"10.1186/s12864-024-10950-7","DOIUrl":"10.1186/s12864-024-10950-7","url":null,"abstract":"<p><strong>Background: </strong>Microbes produce diverse bioactive natural products with applications in fields such as medicine and agriculture. In their genomes, these natural products are encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Genome and metagenome sequencing advances have enabled high-throughput identification of BGCs as a promising avenue for natural product discovery. BGC mining from (meta)genomes using in silico tools has allowed access to a vast diversity of potentially novel natural products. However, a fundamental limitation has been the ability to assemble complete BGCs, especially from complex metagenomes. With their fragmented assemblies, short-read technologies struggle to recover complete BGCs, such as the long and repetitive nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS). Recent advances in long-read sequencing, such as the High Fidelity (HiFi) technology from PacBio, have reduced this limitation and can help retrieve both accurate and complete BGCs from metagenomes, warranting improvement in the existing BGC identification approach for better utilization of HiFi data.</p><p><strong>Results: </strong>Here, we present HiFiBGC, a command-line-based workflow to identify BGCs in PacBio HiFi metagenomes. HiFiBGC leverages an ensemble of assemblies from three HiFi-tailored metagenome assemblers and the reads not represented in these assemblies. Based on our analyses of four HiFi metagenomic datasets from four different environments, we show that HiFiBGC identifies, on average, 78% more BGCs than the top-performing single-assembler-based method. This increase is due to HiFiBGC's ensemble assembly approach, which improves recovery by 25%, as well as from the inclusion of mostly fragmented BGCs identified in the unmapped reads.</p><p><strong>Conclusions: </strong>HiFiBGC is a computational workflow for identifying BGCs in long-read HiFi metagenomes, implemented majorly using Python programming language and workflow manager Snakemake. HiFiBGC is available on GitHub at https://github.com/ay-amityadav/HiFiBGC under the MIT license. The code related to the figures and analyses presented in the manuscript is available at https://github.com/ay-amityadav/HiFiBGC_analyses .</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1096"},"PeriodicalIF":3.5,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11569603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643624","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":"Analyses of Xenorhabdus griffiniae genomes reveal two distinct sub-species that display intra-species variation due to prophages.","authors":"Jennifer K Heppert, Ryan Musumba Awori, Mengyi Cao, Grischa Chen, Jemma McLeish, Heidi Goodrich-Blair","doi":"10.1186/s12864-024-10858-2","DOIUrl":"10.1186/s12864-024-10858-2","url":null,"abstract":"<p><strong>Background: </strong>Nematodes of the genus Steinernema and their Xenorhabdus bacterial symbionts are lethal entomopathogens that are useful in the biocontrol of insect pests, as sources of diverse natural products, and as research models for mutualism and parasitism. Xenorhabdus play a central role in all aspects of the Steinernema lifecycle, and a deeper understanding of their genomes therefore has the potential to spur advances in each of these applications.</p><p><strong>Results: </strong>Here, we report a comparative genomics analysis of Xenorhabdus griffiniae, including the symbiont of Steinernema hermaphroditum nematodes, for which genetic and genomic tools are being developed. We sequenced and assembled circularized genomes for three Xenorhabdus strains: HGB2511, ID10 and TH1. We then determined their relationships to other Xenorhabdus and delineated their species via phylogenomic analyses, concluding that HGB2511 and ID10 are Xenorhabdus griffiniae while TH1 is a novel species. These additions to the existing X. griffiniae landscape further allowed for the identification of two subspecies within the clade. Consistent with other Xenorhabdus, the analysed X. griffiniae genomes each encode a wide array of antimicrobials and virulence-related proteins. Comparative genomic analyses, including the creation of a pangenome, revealed that a large amount of the intraspecies variation in X. griffiniae is contained within the mobilome and attributable to prophage loci. In addition, CRISPR arrays, secondary metabolite potential and toxin genes all varied among strains within the X. griffiniae species.</p><p><strong>Conclusions: </strong>Our findings suggest that phage-related genes drive the genomic diversity in closely related Xenorhabdus symbionts, and that these may underlie some of the traits most associated with the lifestyle and survival of entomopathogenic nematodes and their bacteria: virulence and competition. This study establishes a broad knowledge base for further exploration of not only the relationships between X. griffiniae species and their nematode hosts but also the molecular mechanisms that underlie their entomopathogenic lifestyle.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1087"},"PeriodicalIF":3.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638351","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":"Deciphering the anthocyanin metabolism gene network in tea plant (Camellia sinensis) through structural equation modeling.","authors":"Pan Xia, Mei Chen, Linbo Chen, Yijian Yang, Ling Ma, Pinpin Bi, Song Tang, Qiongxian Luo, Jiwei Chen, Hongwei Chen, Hongling Zhang","doi":"10.1186/s12864-024-11012-8","DOIUrl":"10.1186/s12864-024-11012-8","url":null,"abstract":"<p><strong>Background: </strong>Tea is an important cash crop that significantly contributes to rural development, poverty reduction and food security in many developing countries. It provides livelihoods for millions of smallholder producers and aids their economic stability. Anthocyanins in tea leaves provides excellent commercial quality and germplasm exploration potential. These compounds give tea leaves vibrant colors and increase health benefits. The current understanding of the synergistic regulation mechanisms responsible for color changes in purple tea, attributed to anthocyanin degradation, remains unclear.</p><p><strong>Results: </strong>In this study, we have identified 30 gene families within the genome that are associated to with anthocyanin metabolism from tea. These gene families play distinct roles in the biosynthesis of anthocyanin including the formation of the core, structure, modification of the molecular framework, facilitation of transport process, regulation of gene expression, breakdown pathways, sugar transportation and iron ion respectively. Subsequently, we investigated the synergistic mechanisms of anthocyanin metabolism related gene families within tea leaves using structural equation modeling. The results showed that sugar transport positively affects anthocyanin transportation, and promotes anthocyanin degradation during leaf pigmentation, whereas, it inhibits anthocyanin degradation during the fading of leaf color. Further, Iron ions facilitate the degradation of anthocyanins during their deposition and conversely, impede this degradation process during digestion. These finding suggests that tea plants may regulate the synthesis and degradation of anthocyanins through sugar transport and iron ions ensure healthy levels and vibrant colors.</p><p><strong>Conclusions: </strong>Our study contributes valuable information into the dynamic equilibrium anthocyanin mechanism and sheds light on complex regulatory mechanisms that govern the synthesis, transport and degradation of these pigments. These insights could be further used to develop strategies for enhancing anthocyanins content in unique tea germplasm to aid tea industry in producing new tea products with increased health benefits and aesthetic appeals.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1093"},"PeriodicalIF":3.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643618","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}