Genomics最新文献

{"title":"The aminophospholipid transporter, ATP8B3, as a potential biomarker and target for enhancing the therapeutic effect of PD-L1 blockade in colon adenocarcinoma","authors":"Weihao Zhang ,&nbsp;Yongjie Xie ,&nbsp;Ziyun Liu ,&nbsp;Jie Zhang ,&nbsp;Bo Ni ,&nbsp;Wei Gao ,&nbsp;Wenge Xing ,&nbsp;Yaoyao Zhou ,&nbsp;Tongguo Si","doi":"10.1016/j.ygeno.2024.110907","DOIUrl":"10.1016/j.ygeno.2024.110907","url":null,"abstract":"<div><h3>Background</h3><p>Colon adenocarcinoma (COAD) is a prevalent malignant tumor globally, contributing significantly to cancer-related mortality. COAD guidelines label MSI (Microsatellite instability) and MSS (Microsatellite stability) subtypes as global classification criteria and treatment strategy selection criteria for COAD. Various combination therapies involving PD-L1 inhibitors and adjuvant therapy to enhance anti-tumor efficacy.</p></div><div><h3>Methods</h3><p>Datasets from single-cell RNA sequencing and bulk RNA sequencing in the TCGA and GEO databases were utilized to identify differentially expressed genes (DEGs). Furthermore, the correlation between ATP8B3 and PD-L1 was validated using siRNA, shRNA, and western blot analysis. Additionally, the association between ATP8B3 and immune checkpoint blockade (ICB) therapy was investigated through immune infiltration analysis and flow cytometry in both in vivo and in vitro assays.</p></div><div><h3>Results</h3><p>In the COAD patient group, ATP8B3 significantly contributed to the establishment of an immunosuppressive microenvironment. Inhibiting ATP8B3 led to a reduction in PD-L1 expression in colon cancer cell lines. Additionally, ATP8B3 expression levels could serve as a potential guide for PD-L1 treatment in MSI-H COAD patients, with higher ATP8B3 expression associated with increased sensitivity to PD-L1 therapy. However, due to the lack of immuno-killer cells in the microenvironment of MSS subtypes, elevated ATP8B3 expression couldn't increase the sensitivity of MSS COAD patients to PD-L1 inhibitors.</p></div><div><h3>Conclusion</h3><p>Our research results support that Inhibiting ATP8B3 could enhance TIL (tumor-infiltrating lymphocyte) infiltration by reducing PD-L1 expression in MSI-H COAD, thereby serving as an effective strategy to improve PD-L1 blocker efficacy. The treatment strategy of combining ATP8B3 inhibitors and immunotherapy for MSI/MSS COAD patients will be the best choice.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001289/pdfft?md5=5635c02dfd33eab8800ad87fe4783f19&pid=1-s2.0-S0888754324001289-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792367","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":"miR-10167-3p targets TCF7L1 to inhibit bovine adipocyte differentiation and promote bovine adipocyte proliferation","authors":"Chunli Hu,&nbsp;Mengli Yang,&nbsp;Xue Feng,&nbsp;Shuzhe Wang,&nbsp;Yanfen Ma,&nbsp;Yun Ma","doi":"10.1016/j.ygeno.2024.110903","DOIUrl":"10.1016/j.ygeno.2024.110903","url":null,"abstract":"<div><p>MicroRNAs (miRNAs) are widely involved in various lipogenic processes, including adipocyte proliferation and differentiation, lipid droplet formation, and adipocyte-specific gene activation. The present study aimed to investigate the gene expression profiles of bovine preadipocytes under high miR-10167-3p expression using the RNA-seq technique and to verify the functions of its downstream target genes on the proliferation and differentiation of bovine preadipocytes. First, RNA-seq identified 573 differentially expressed genes (DEGs), of which 243 were downregulated and 330 were upregulated. Then, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 15.19% of the DEGs were enriched in pathways related to lipid metabolism. Meanwhile, dual-luciferase reporter gene assay verified the target-binding relationship between miR-10167-3p and <em>TCF7L1</em>. The function of <em>TCF7L1</em> was assessed using several experiments in adipocytes with high <em>TCF7L1</em> expression and RNA interference. The mRNA and protein expression of proliferation, differentiation, and apoptosis marker genes were detected using qPCR and western blot, respectively; lipid droplet synthesis was detected using oil red O, Nile red, and bodipy staining; adipocyte proliferation was detected by EdU; and apoptosis was detected using flow cytometry. The results revealed that <em>TCF7L1</em> overexpression inhibited bovine preadipocyte differentiation and apoptosis and promoted their proliferation, with opposite results obtained with its RNA interference. These results may provide a reference for the subsequent investigation of the molecular mechanism of bovine fat deposition.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001241/pdfft?md5=cb5d0b6fde740e95307390a61567622c&pid=1-s2.0-S0888754324001241-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787782","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":"De novo assembly and comprehensive analysis of the mitochondrial genome of Taxus wallichiana reveals different repeats mediate recombination to generate multiple conformations","authors":"Kai Qu ,&nbsp;Dan Liu ,&nbsp;Limin Sun ,&nbsp;Meng Li ,&nbsp;Tiantian Xia ,&nbsp;Weixia Sun ,&nbsp;Yufei Xia","doi":"10.1016/j.ygeno.2024.110900","DOIUrl":"10.1016/j.ygeno.2024.110900","url":null,"abstract":"<div><p><em>Taxus</em> plants are the exclusive source of paclitaxel, an anticancer drug with significant medicinal and economic value. Interspecies hybridization and gene introgression during evolution have obscured distinctions among <em>Taxus</em> species, complicating their phylogenetic classification. While the chloroplast genome of <em>Taxus wallichiana</em>, a widely distributed species in China, has been sequenced, its mitochondrial genome (mitogenome) remains uncharacterized.We sequenced and assembled the <em>T. wallichiana</em> mitogenome using BGI short reads and Nanopore long reads, facilitating comparisons with other gymnosperm mitogenomes. The <em>T. wallichiana</em> mitogenome spanning 469,949 bp, predominantly forms a circular configuration with a GC content of 50.51%, supplemented by 3 minor configurations mediated by one pair of LRs and two pairs of IntRs. It includes 32 protein-coding genes, 7 tRNA genes, and 3 rRNA genes, several of which exist in multiple copies.We detailed the mitogenome's structure, codon usage, RNA editing, and sequence migration between organelles, constructing a phylogenetic tree to elucidate evolutionary relationships. Unlike typical gymnosperm mitochondria, <em>T. wallichiana</em> shows no evidence of mitochondrial-plastid DNA transfer (MTPT), highlighting its unique genomic architecture. Synteny analysis indicated extensive genomic rearrangements in <em>T. wallichiana</em>, likely driven by recombination among abundant repetitive sequences. This study offers a high-quality <em>T. wallichiana</em> mitogenome, enhancing our understanding of gymnosperm mitochondrial evolution and supporting further cultivation and utilization of <em>Taxus</em> species.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001216/pdfft?md5=151a70eb7e8c78a2bfff1f7303b4fa30&pid=1-s2.0-S0888754324001216-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787783","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":"De novo genome assembly and functional insights of the first commercial pink Auricularia cornea","authors":"Lei Ye ,&nbsp;Lingzi Zhang ,&nbsp;Xin Li ,&nbsp;Yu Huang ,&nbsp;Bo Zhang ,&nbsp;Xuezhen Yang ,&nbsp;Wei Tan ,&nbsp;Xiaolin Li ,&nbsp;Xiaoping Zhang","doi":"10.1016/j.ygeno.2024.110902","DOIUrl":"10.1016/j.ygeno.2024.110902","url":null,"abstract":"<div><p>A pioneering pink cultivar of <em>Auricularia cornea</em>, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink <em>A. cornea</em> Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink <em>A. cornea</em> genome and provides a comprehensive insight into its complex functions.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400123X/pdfft?md5=e29e1581ba4c1349c90bca58b752a31d&pid=1-s2.0-S088875432400123X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758137","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 binding of NF-Y in mouse and human cells","authors":"Mirko Ronzio ,&nbsp;Andrea Bernardini ,&nbsp;Valentina Taglietti ,&nbsp;Michele Ceribelli ,&nbsp;Giacomo Donati ,&nbsp;Alberto Gallo ,&nbsp;Giulio Pavesi ,&nbsp;Paolo Dellabona ,&nbsp;Giulia Casorati ,&nbsp;Graziella Messina ,&nbsp;Roberto Mantovani ,&nbsp;Diletta Dolfini","doi":"10.1016/j.ygeno.2024.110895","DOIUrl":"10.1016/j.ygeno.2024.110895","url":null,"abstract":"<div><p>NF-Y is a Transcription Factor that regulates transcription through binding to the CCAAT-box. To understand its strategy, we analyzed 16 ChIP-seq datasets from human and mouse cells. Shared loci, mostly located in promoters of expressed genes of <em>cell cycle</em>, <em>metabolism</em> and <em>gene expression</em> pathways, are associated with histone marks of active chromatin and specific modules of TFs. Other peaks are in enhancers and Transposable Elements -TE- of retroviral origin in human and mouse. We evaluated the relationship with USF1, a common synergistic partner in promoters and MLT1 TEs, upon NF-YB inactivation: USF1 binding decreases in promoters, modestly in MLT1, suggesting a pioneering role of NF-Y in formers, not in the latters. These data define a common set of NF-Y functional targets across different mammalian cell types, suggesting a pioneering role in promoters with respect to TEs.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001162/pdfft?md5=6850140a6102f7e5bec34cde46b029a4&pid=1-s2.0-S0888754324001162-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723398","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":"Integrated morphological, physiological and transcriptomic analyses reveal the responses of Toona sinensis seedlings to low-nitrogen stress","authors":"Hu Zhao,&nbsp;Miaomiao Ge,&nbsp;Fengzhe Zhang,&nbsp;Didi Du,&nbsp;Zilu Zhao,&nbsp;Cheng Shen,&nbsp;Qingping Hao,&nbsp;Min Xiao,&nbsp;Xiaopu Shi,&nbsp;Juan Wang,&nbsp;Mingqin Fan","doi":"10.1016/j.ygeno.2024.110899","DOIUrl":"10.1016/j.ygeno.2024.110899","url":null,"abstract":"<div><p>Nitrogen is one of the most essential elements for plant growth and development. In this study, the growth, physiology, and transcriptome of <em>Toona sinensis</em> (A. Juss) Roem seedlings were compared between low-nitrogen (LN) and normal-nitrogen (NN) conditions. These results indicate that LN stress adversely influences <em>T. sinensis</em> seedling growth. The activities of key enzymes related to nitrogen assimilation and phytohormone contents were altered by LN stress. A total of 2828 differentially expressed genes (DEGs) in roots and 1547 in leaves were identified between the LN and NN treatments. A differential enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that nitrogen and sugar metabolism, flavonoid biosynthesis, plant hormone signal transduction, and ABC transporters, were strongly affected by LN stress. In summary, this research provides information for further understanding the response of <em>T. sinensis</em> to LN stress.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001204/pdfft?md5=8e7b6b59ffd47e6d24fc5ecafa41a27e&pid=1-s2.0-S0888754324001204-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758140","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 cellular heterogeneity in Spodoptera frugiperda midgut cell line through single cell RNA sequencing","authors":"Surjeet Kumar Arya ,&nbsp;Douglas A. Harrison ,&nbsp;Subba Reddy Palli","doi":"10.1016/j.ygeno.2024.110898","DOIUrl":"10.1016/j.ygeno.2024.110898","url":null,"abstract":"<div><p>Using the 10x Genomics Chromium single-cell RNA sequencing (scRNA-seq) platform, we discovered unexpected heterogeneity in an established cell line developed from the midgut of the Fall armyworm, <em>Spodoptera frugiperda,</em> a major global pest. We analyzed the sequences of 18,794 cells and identified ten unique cellular clusters, including stem cells, enteroblasts, enterocytes and enteroendocrine cells, characterized by the expression of specific marker genes. Additionally, these studies addressed an important knowledge gap by investigating the expression of genes coding for respiratory and midgut membrane insecticide targets classified by the Insecticide Resistance Action Committee. Dual-fluorescence tagging method, fluorescence microscopy and fluorescence-activated cell sorting confirmed the expression of midgut cell type-specific genes. Stem cells were isolated from the heterogeneous population of SfMG-0617 cells. Our results, validated by KEGG and Gene Ontology analyses and supported by Monocle 3.0, advance the fields of midgut cellular biology and establish standards for scRNA-seq studies in non-model organisms.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001198/pdfft?md5=6846659334c462f6e93963047776ea48&pid=1-s2.0-S0888754324001198-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758138","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":"Identification of differentially expressed genes in the medial prefrontal cortex of rats subjected to chronic unpredictable mild stress and treated with electroacupuncture","authors":"Yujiao Zhang ,&nbsp;Haiyan Zhang ,&nbsp;Xinjie Zheng ,&nbsp;Yi Hou ,&nbsp;Xiaoli Chang ,&nbsp;Lili Zhang ,&nbsp;Ying Wang ,&nbsp;Shaozong Chen","doi":"10.1016/j.ygeno.2024.110901","DOIUrl":"10.1016/j.ygeno.2024.110901","url":null,"abstract":"<div><p>Major depressive disorder is a chronic mental health condition that seriously impacts afflicted individuals. Although electroacupuncture has proven to be an effective therapy for depression, its underlying biological mechanism remains largely unknown. In this study, we aimed to investigate the effects of electroacupuncture on depression-like behavior and to identify potential target genes related to those effects. To achieve this, we subjected rats to chronic unpredictable mild stress (CUMS) and used sucrose preference, forced swimming, and open-field tests to determine their depression-like behavior in the absence or after receipt of electroacupuncture treatment. RNA sequencing technology was then used to reveal the differentially expressed genes associated with depression and electroacupuncture treatment effects in the medial prefrontal cortex (mPFC). Repeated electroacupuncture treatments at the Baihui (GV20) and Taichong (LR3) acupoints significantly alleviated depression-like behavioral defects in the animals. Genomic RNA sequencing revealed several significant changes in the mPFC transcriptome of rats that received treatment. Through differential gene expression analysis, we found that electroacupuncture reversed the CUMS-induced downregulation of 46 genes and upregulation of 13 genes. Among the differentially expressed genes, <em>Casr</em>, <em>Bdkrb2</em>, <em>Gnb3</em>, and <em>Ccl1</em> were found to be associated with depression and electroacupuncture treatment effects. In conclusion, we verified that electroacupuncture treatment has an effective antidepressant effect, and the underlying mechanism involves multiple systems and targets.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001228/pdfft?md5=2548044293fb3e8dd1813b4216bdb241&pid=1-s2.0-S0888754324001228-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758139","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":"Repetitive element expansions contribute to genome size gigantism in Pamphagidae: A comparative study (Orthoptera, Acridoidea)","authors":"Yimeng Nie,&nbsp;Xuanzeng Liu,&nbsp;Lina Zhao,&nbsp;Yuan Huang","doi":"10.1016/j.ygeno.2024.110896","DOIUrl":"10.1016/j.ygeno.2024.110896","url":null,"abstract":"<div><p>Pamphagidae is a family of Acridoidea that inhabits the desert steppes of Eurasia and Africa. This study employed flow cytometry to estimate the genome size of eight species in the Pamphagidae. The results indicate that the genome size of the eight species ranged from 13.88 pg to 14.66 pg, with an average of 14.26 pg. This is the largest average genome size recorded for the Orthoptera families, as well as for the entire Insecta. Furthermore, the study explored the role of repetitive sequences in the genome, including their evolutionary dynamics and activity, using low-coverage next-generation sequencing data. The genome is composed of 14 different types of repetitive sequences, which collectively make up between 59.9% and 68.17% of the total genome. The Pamphagidae family displays high levels of transposable element (TE) activity, with the number of TEs increasing and accumulating since the family's emergence. The study found that the types of repetitive sequences contributing to the TE outburst events are similar across species. Additionally, the study identified unique repetitive elements for each species. The differences in repetitive sequences among the eight Pamphagidae species correspond to their phylogenetic relationships. The study sheds new light on genome gigantism in the Pamphagidae and provides insight into the correlation between genome size and repetitive sequences within the family.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001174/pdfft?md5=b3d96f38f32a82b26dfe6c684a5ee84b&pid=1-s2.0-S0888754324001174-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723399","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":"Assembly and comparative analysis of the complete mitochondrial genome of Vaccinium carlesii Dunn","authors":"Liwei Chu ,&nbsp;Qianhui Du ,&nbsp;Siyu Zuo ,&nbsp;Guiting Liu ,&nbsp;Hexin Wang ,&nbsp;Guoling Liu ,&nbsp;Lina Zhao ,&nbsp;Guohui Xu","doi":"10.1016/j.ygeno.2024.110897","DOIUrl":"10.1016/j.ygeno.2024.110897","url":null,"abstract":"<div><p><em>Vaccinium</em> L. is an important fruit tree with nutritional, medicinal, and ornamental values. However, the mitochondrial (mt) genome of <em>Vaccinium</em> L. remains largely unexplored. <em>Vaccinium carlesii</em> Dunn is an endemic wild resource in China, which is crucial for blueberry breeding. The <em>V. carlesii</em> mt genomes were sequenced using Illumina and Nanopore, which total length was 636,904 bp with 37 protein coding genes, 20 tRNA genes, and three rRNA genes. We found four pairs of long repeat fragments homologous recombination mediated the generation of substructures in the <em>V. carlesii</em> mt genome. We predicted 383 RNA editing sites, all converting cytosine (C) to uracil (U). According to the phylogenetic analysis, <em>V. carlesii</em> and <em>V. macrocarpon</em> of the Ericaceae exhibited the closest genetic relationship. This study provides a theoretical basis for understanding the evolution of higher plants, species classification and identification, and will also be useful for further utilization of <em>Vaccinium</em> germplasm resources.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001186/pdfft?md5=39eb0d5485e6035017c04f3f09a2a092&pid=1-s2.0-S0888754324001186-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733924","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}