Pub Date : 2025-01-01DOI: 10.1016/j.ygeno.2024.110972
Victoria Kelson , Jennifer Kiser , Kimberly Davenport , Emaly Suarez , Brenda Murdoch , Holly Neibergs
This study aimed to identify loci (p < 1 × 10−5) and gene sets (normalized enrichment score (NES) ≥ 3.0) associated with the number of times a heifer is bred to attain a successful pregnancy (TBRD) for Holstein heifers bred by artificial insemination (AI, n = 2754) or that were embryo transfer (ET, n = 1566) recipients. Eight loci were associated (p < 1 × 10−5) with TBRD in AI bred heifers and four loci were associated with TBRD in ET recipients. The gene set enrichment analysis with SNP data identified one gene set enriched (NES ≥ 3.0) with TBRD in AI bred heifers and two gene sets that were enriched with TBRD in ET recipients. The estimated pseudo-heritability for times bred to AI was 0.063 and 0.043 for ET. The identification of loci associated with embryonic loss aids in the selection of Holstein heifers with higher reproductive efficiencies that are AI bred or that are ET recipients.
本研究旨在确定人工授精（AI, n = 2754）或胚胎移植（ET, n = 1566）受体荷斯坦小母牛成功妊娠次数（TBRD）相关的基因座（p -5）和基因集（归一化富集评分（NES） ≥ 3.0）。8个基因座与人工授精母牛的TBRD相关（p -5），4个基因座与ET受体的TBRD相关。利用SNP数据对基因集进行富集分析，发现人工智能犊牛中有1个基因集富集TBRD (NES ≥ 3.0)，ET受体中有2个基因集富集TBRD。人工授精和体外授精的拟遗传率分别为0.063和0.043。鉴定与胚胎丢失相关的基因位点有助于选择人工授精或体外授精的繁殖效率更高的荷斯坦小母牛。
{"title":"Genomic regions associated with Holstein heifer times bred to artificial insemination and embryo transfer services","authors":"Victoria Kelson , Jennifer Kiser , Kimberly Davenport , Emaly Suarez , Brenda Murdoch , Holly Neibergs","doi":"10.1016/j.ygeno.2024.110972","DOIUrl":"10.1016/j.ygeno.2024.110972","url":null,"abstract":"<div><div>This study aimed to identify loci (<em>p</em> < 1 × 10<sup>−5</sup>) and gene sets (normalized enrichment score (NES) ≥ 3.0) associated with the number of times a heifer is bred to attain a successful pregnancy (TBRD) for Holstein heifers bred by artificial insemination (AI, <em>n</em> = 2754) or that were embryo transfer (ET, <em>n</em> = 1566) recipients. Eight loci were associated (p < 1 × 10<sup>−5</sup>) with TBRD in AI bred heifers and four loci were associated with TBRD in ET recipients. The gene set enrichment analysis with SNP data identified one gene set enriched (NES ≥ 3.0) with TBRD in AI bred heifers and two gene sets that were enriched with TBRD in ET recipients. The estimated pseudo-heritability for times bred to AI was 0.063 and 0.043 for ET. The identification of loci associated with embryonic loss aids in the selection of Holstein heifers with higher reproductive efficiencies that are AI bred or that are ET recipients.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110972"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779876","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}
With the increasing demand for donkey production, there has been a growing focus on the breeding of donkeys. However, our current understanding of the mechanisms underlying spermatogenesis and maturation in donkeys during reproduction remains limited.
Objectives
This study is to provide a comprehensive single-cell landscape analysis of spermatogenesis and maturation in donkeys.
Methods
In this study, we employed single-cell RNA sequencing to investigate cell composition, gene expression patterns, and regulatory roles during spermatogenesis and maturation in donkeys.
Results
The expression patterns of CDK1, CETN3, and UBE2J1 were found to be indicative of specific germ cells during donkey spermatogenesis. Additionally, the DEFB121, ELSPBP1, and NPC2 genes were specifically identified in the principal cells of the donkey epididymis.
Conclusions
We performed single-cell RNA sequencing to analyze the cellular composition and spatial distribution of donkey testis and epididymis, thereby generating comprehensive transcriptional atlases at the single-cell resolution.
{"title":"Single-cell RNA sequencing unveils dynamic transcriptional profiles during the process of donkey spermatogenesis and maturation","authors":"Yadan Jin, Fangdi Zhang, Ruixue Ma, Jingya Xing, Min Wang, Yujiang Sun, Guoliang Zhang","doi":"10.1016/j.ygeno.2024.110974","DOIUrl":"10.1016/j.ygeno.2024.110974","url":null,"abstract":"<div><h3>Introduction</h3><div>With the increasing demand for donkey production, there has been a growing focus on the breeding of donkeys. However, our current understanding of the mechanisms underlying spermatogenesis and maturation in donkeys during reproduction remains limited.</div></div><div><h3>Objectives</h3><div>This study is to provide a comprehensive single-cell landscape analysis of spermatogenesis and maturation in donkeys.</div></div><div><h3>Methods</h3><div>In this study, we employed single-cell RNA sequencing to investigate cell composition, gene expression patterns, and regulatory roles during spermatogenesis and maturation in donkeys.</div></div><div><h3>Results</h3><div>The expression patterns of CDK1, CETN3, and UBE2J1 were found to be indicative of specific germ cells during donkey spermatogenesis. Additionally, the DEFB121, ELSPBP1, and NPC2 genes were specifically identified in the principal cells of the donkey epididymis.</div></div><div><h3>Conclusions</h3><div>We performed single-cell RNA sequencing to analyze the cellular composition and spatial distribution of donkey testis and epididymis, thereby generating comprehensive transcriptional atlases at the single-cell resolution.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110974"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853480","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}
Pub Date : 2025-01-01DOI: 10.1016/j.ygeno.2024.110968
Zuwei Yang , Chengliang Zhou , Li Jin , Jiexue Pan
Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder, yet its mechanisms remain elusive. This study employed transcriptome sequencing on granulosa cells from 5 PCOS women and 5 controls, followed by bioinformatic analyses. We identified 684 mRNAs and 167 lncRNAs with significant differential expression. Gene Ontology and KEGG analyses highlighted enrichment in immune and inflammatory responses among these genes. Through CytoHubba plug-in and three machine learning algorithms, CCR7 was identified as the hub gene of PCOS, further validated through analysis of GSE65746, GSE34526 and a cohort of eighty subjects (40 PCOS and 40 controls). Furthermore, a competing endogenous RNA network targeting CCR7 was constructed. Immune infiltration analysis unveiled a significant decrease in monocyte infiltration in PCOS women, with CCR7 expression positively correlated to naïve B cells. Our findings suggest CCR7 and related molecules play a crucial role in the pathogenesis of PCOS, potentially serving as biomarkers for the disorder.
{"title":"Identification of CCR7 as a potential biomarker in polycystic ovary syndrome through transcriptome sequencing and integrated bioinformatics","authors":"Zuwei Yang , Chengliang Zhou , Li Jin , Jiexue Pan","doi":"10.1016/j.ygeno.2024.110968","DOIUrl":"10.1016/j.ygeno.2024.110968","url":null,"abstract":"<div><div>Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder, yet its mechanisms remain elusive. This study employed transcriptome sequencing on granulosa cells from 5 PCOS women and 5 controls, followed by bioinformatic analyses. We identified 684 mRNAs and 167 lncRNAs with significant differential expression. Gene Ontology and KEGG analyses highlighted enrichment in immune and inflammatory responses among these genes. Through CytoHubba plug-in and three machine learning algorithms, CCR7 was identified as the hub gene of PCOS, further validated through analysis of GSE65746, GSE34526 and a cohort of eighty subjects (40 PCOS and 40 controls). Furthermore, a competing endogenous RNA network targeting CCR7 was constructed. Immune infiltration analysis unveiled a significant decrease in monocyte infiltration in PCOS women, with CCR7 expression positively correlated to naïve B cells. Our findings suggest CCR7 and related molecules play a crucial role in the pathogenesis of PCOS, potentially serving as biomarkers for the disorder.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110968"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750457","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}
Pub Date : 2025-01-01DOI: 10.1016/j.ygeno.2024.110979
Na Zhang , Puguang Zhao , Wenda Zhang , Huiying Wang , Kaixuan Wang , Xiangyu Wang , Zhanjiang Zhang , Ninghua Tan , Lingyun Chen
Lobelia seguinii is a plant with great ecological and medicinal value and belongs to Campanulaceae. Lobelia contains lobeline, a well-known compound used to treat respiratory diseases. Nevertheless, lobeline biosynthesis needs further exploration. Moreover, whole-genome duplication (WGD) and karyotype evolution within Campanulaceae still need to be better understood. In this study, we obtained a chromosome-level genome of L. seguinii with a size of 1.4 Gb and 38253 protein-coding genes. Analyses revealed two WGDs within Campanulaceae, one at the most recent common ancestor (MRCA) of Campanula and Adenophora, and another at the MRCA of Lobelioideae. Analyses further revealed that the karyotype of Platycodon grandiflorus represents the ancient type within Asterales. We proposed eight enzymes involved in the lobeline biosynthesis pathway of L. seguinii. Molecular cloning and heterologous expression of phenylalanine ammonia-lyase (PAL), a candidate enzyme involved in the first step of lobeline biosynthesis, verified its function to catalyze the deamination of phenylalanine to cinnamic acid. This study sheds light on the evolution of Campanulaceae and lobeline biosynthesis.
{"title":"A chromosome-level genome of Lobelia seguinii provides insights into the evolution of Campanulaceae and the lobeline biosynthesis","authors":"Na Zhang , Puguang Zhao , Wenda Zhang , Huiying Wang , Kaixuan Wang , Xiangyu Wang , Zhanjiang Zhang , Ninghua Tan , Lingyun Chen","doi":"10.1016/j.ygeno.2024.110979","DOIUrl":"10.1016/j.ygeno.2024.110979","url":null,"abstract":"<div><div><em>Lobelia seguinii</em> is a plant with great ecological and medicinal value and belongs to Campanulaceae. <em>Lobelia</em> contains lobeline, a well-known compound used to treat respiratory diseases. Nevertheless, lobeline biosynthesis needs further exploration. Moreover, whole-genome duplication (WGD) and karyotype evolution within Campanulaceae still need to be better understood. In this study, we obtained a chromosome-level genome of <em>L</em>. <em>seguinii</em> with a size of 1.4 Gb and 38253 protein-coding genes. Analyses revealed two WGDs within Campanulaceae, one at the most recent common ancestor (MRCA) of <em>Campanula</em> and <em>Adenophora</em>, and another at the MRCA of Lobelioideae. Analyses further revealed that the karyotype of <em>Platycodon grandiflorus</em> represents the ancient type within Asterales. We proposed eight enzymes involved in the lobeline biosynthesis pathway of <em>L</em>. <em>seguinii</em>. Molecular cloning and heterologous expression of phenylalanine ammonia-lyase (PAL), a candidate enzyme involved in the first step of lobeline biosynthesis, verified its function to catalyze the deamination of phenylalanine to cinnamic acid. This study sheds light on the evolution of Campanulaceae and lobeline biosynthesis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110979"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828056","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}
This study investigated the preventive and protective effects of Portulaca oleracea polysaccharides (PP) on Acute liver injury (ALI) in mice and its regulatory effects on intestinal microorganisms, and explored the underlying protective mechanisms. Initially, PP was administered, and then CCl4 was used to induce the mouse ALI model. Serum and liver markers were measured by ELISA. The fecal microbiota was analyzed by 16S rRNA sequencing. The results showed that PP significantly decreased the expression levels of ALT and AST in the serum of mice. The expression levels of MDA, TNF-α, and IL-6 in liver tissue were found to be reduced, while the levels of GSH and SOD increased. At the same time, PP increased the number of Bacteroides, reduced the number of Proteobacteria, activated the GAG degradation pathway, protected the integrity of the intestinal barrier, inhibited oxidative stress and reduced inflammation, thereby assisting the prevention and protection of ALI.
{"title":"Purslane (Portulaca oleracea L.) polysaccharide attenuates carbon tetrachloride-induced acute liver injury by modulating the gut microbiota in mice","authors":"Jiahui Li, Yuyang Chen, Shuang Zhang, Yuehan Zhao, Demeng Gao, Jiaying Xing, YuYan Cao, Guangyu Xu","doi":"10.1016/j.ygeno.2024.110983","DOIUrl":"10.1016/j.ygeno.2024.110983","url":null,"abstract":"<div><div>This study investigated the preventive and protective effects of <em>Portulaca oleracea</em> polysaccharides (PP) on Acute liver injury (ALI) in mice and its regulatory effects on intestinal microorganisms, and explored the underlying protective mechanisms. Initially, PP was administered, and then CCl4 was used to induce the mouse ALI model. Serum and liver markers were measured by ELISA. The fecal microbiota was analyzed by 16S rRNA sequencing. The results showed that PP significantly decreased the expression levels of ALT and AST in the serum of mice. The expression levels of MDA, TNF-α, and IL-6 in liver tissue were found to be reduced, while the levels of GSH and SOD increased. At the same time, PP increased the number of <em>Bacteroides</em>, reduced the number of <em>Proteobacteria</em>, activated the GAG degradation pathway, protected the integrity of the intestinal barrier, inhibited oxidative stress and reduced inflammation, thereby assisting the prevention and protection of ALI.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110983"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142902875","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}
Pub Date : 2025-01-01DOI: 10.1016/j.ygeno.2024.110977
Shuqiang Huang , Cuiyu Tan , Wanru Chen , Tongtong Zhang , Liying Xu , Zhihong Li , Miaoqi Chen , Xiaojun Yuan , Cairong Chen , Qiuxia Yan
Background
Abnormal programmed cell death (PCD) plays a central role in spermatogenic dysfunction. However, the molecular mechanisms and biomarkers of PCD in patients with nonobstructive azoospermia (NOA) remain unclear.
Methods
The genetic conditions of NOA patients were analysed using bulk transcriptomic, single-cell transcriptomic, single nucleotide polymorphism (SNP), and clinical data from multiple centres. A total of 675 machine learning methods were applied to construct models from 12 different PCDs and to screen for distinctive genes. A new PCDscore system was created to measure the degree of PCD in patients. Using the NOA mouse model, TUNEL, qRT–PCR, Western blotting, and immunohistochemistry (IHC) were utilized to validate the PCD status in NOA testes and the expression levels of hub PCD-related genes (PCDRGs). Mouse testicular samples were used for sequencing of the whole transcriptome. The sequencing results were used to evaluate the correlation between PCD scores and expression of hub genes.
Results
A PCDscore system was built using 12 characteristic PCDRGs chosen by machine learning. PCD scores correlated with gene interaction and immune activity changes. Leydig, Sertoli, and T cells were prominent in cell interactions with PCDscore changes. PCDscore in the NOA mouse testis was increased. Among the 12 PCDRGs, BCL2L14, GGA1, GPX4, PHKG2, and SLC39A8 were strongly linked to spermatogenesis. BCL2L14, GGA1, GPX4, and PHKG2 strongly correlated with PCD statuses. The changes in the expression of these genes may be due to the effects of SNPs, which may lead to the male reproductive system disorders.
Conclusions
Our study provides new insights into PCD-related mechanisms in NOA patients via multiomics and proposes reliable models for the diagnosis of NOA via the use of PCD biomarkers. A deeper understanding of these mechanisms may aid in the clinical diagnosis and treatment of NOA.
{"title":"Multiomics identification of programmed cell death-related characteristics for nonobstructive azoospermia based on a 675-combination machine learning computational framework","authors":"Shuqiang Huang , Cuiyu Tan , Wanru Chen , Tongtong Zhang , Liying Xu , Zhihong Li , Miaoqi Chen , Xiaojun Yuan , Cairong Chen , Qiuxia Yan","doi":"10.1016/j.ygeno.2024.110977","DOIUrl":"10.1016/j.ygeno.2024.110977","url":null,"abstract":"<div><h3>Background</h3><div>Abnormal programmed cell death (PCD) plays a central role in spermatogenic dysfunction. However, the molecular mechanisms and biomarkers of PCD in patients with nonobstructive azoospermia (NOA) remain unclear.</div></div><div><h3>Methods</h3><div>The genetic conditions of NOA patients were analysed using bulk transcriptomic, single-cell transcriptomic, single nucleotide polymorphism (SNP), and clinical data from multiple centres. A total of 675 machine learning methods were applied to construct models from 12 different PCDs and to screen for distinctive genes. A new PCDscore system was created to measure the degree of PCD in patients. Using the NOA mouse model, TUNEL, qRT–PCR, Western blotting, and immunohistochemistry (IHC) were utilized to validate the PCD status in NOA testes and the expression levels of hub PCD-related genes (PCDRGs). Mouse testicular samples were used for sequencing of the whole transcriptome. The sequencing results were used to evaluate the correlation between PCD scores and expression of hub genes.</div></div><div><h3>Results</h3><div>A PCDscore system was built using 12 characteristic PCDRGs chosen by machine learning. PCD scores correlated with gene interaction and immune activity changes. Leydig, Sertoli, and T cells were prominent in cell interactions with PCDscore changes. PCDscore in the NOA mouse testis was increased. Among the 12 PCDRGs, <em>BCL2L14</em>, <em>GGA1</em>, <em>GPX4</em>, <em>PHKG2</em>, and <em>SLC39A8</em> were strongly linked to spermatogenesis. <em>BCL2L14</em>, <em>GGA1</em>, <em>GPX4</em>, and <em>PHKG2</em> strongly correlated with PCD statuses. The changes in the expression of these genes may be due to the effects of SNPs, which may lead to the male reproductive system disorders.</div></div><div><h3>Conclusions</h3><div>Our study provides new insights into PCD-related mechanisms in NOA patients via multiomics and proposes reliable models for the diagnosis of NOA via the use of PCD biomarkers. A deeper understanding of these mechanisms may aid in the clinical diagnosis and treatment of NOA.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110977"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142812830","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}
Pub Date : 2025-01-01DOI: 10.1016/j.ygeno.2024.110981
Jinlei Han , Yan Dai , Jialiang Zhou , Jingjing Tian , Qi Chen , Xiaobing Kou , Ghulam Raza , Baohong Zhang , Kai Wang
Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.
{"title":"Tissue-specific chromatin accessibility and transcriptional regulation in maize cold stress response","authors":"Jinlei Han , Yan Dai , Jialiang Zhou , Jingjing Tian , Qi Chen , Xiaobing Kou , Ghulam Raza , Baohong Zhang , Kai Wang","doi":"10.1016/j.ygeno.2024.110981","DOIUrl":"10.1016/j.ygeno.2024.110981","url":null,"abstract":"<div><div>Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110981"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863318","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}
Pub Date : 2025-01-01DOI: 10.1016/j.ygeno.2024.110966
Zhijian Yang , Xue Liu , Xiaohui Qin , Zhen Xiao , Qian Luo , Danni Pan , Hong Yang , Sufeng Liao , Xuanyang Chen
Cuscuta gronovii Willd., a member of the Convolvulaceae family, is noted for its potential medicinal and nutritional benefits. In this study, we utilized a combination of Illumina and Oxford Nanopore sequencing technologies to successfully assemble the complete circular mitochondrial genome (mitogenome) of C. gronovii. The mitogenome, spanning 304,467 base pairs, includes 54 genes: 33 protein-coding genes, three ribosomal RNA (rRNA) genes, and 18 transfer RNA (tRNA) genes. Beyond its primary circular structure, we discovered and validated several alternative genomic conformations, driven by five specific repeat sequences. Three inverted repeats were found to initiate rearrangements, resulting in the creation of seven distinct chromosomal structures, while two direct repeats split a larger molecule into two subgenomic entities. We also mapped 421 RNA editing sites across the protein-coding sequences, influencing 33 protein-coding genes with varying distribution, particularly noting high frequencies in the nad4 and ccmB genes. Sixteen of these RNA editing sites were experimentally validated through PCR amplification and Sanger sequencing, confirming their presence with 100 % accuracy. This research not only introduces the first mitochondrial genome of C. gronovii but also highlights its complex conformational variability induced by repeat-mediated recombination, providing a valuable genomic resource for further molecular breeding efforts and phylogenetic evolution within the genus Cuscuta.
{"title":"Unveiling the intricate structural variability induced by repeat-mediated recombination in the complete mitochondrial genome of Cuscuta gronovii Willd","authors":"Zhijian Yang , Xue Liu , Xiaohui Qin , Zhen Xiao , Qian Luo , Danni Pan , Hong Yang , Sufeng Liao , Xuanyang Chen","doi":"10.1016/j.ygeno.2024.110966","DOIUrl":"10.1016/j.ygeno.2024.110966","url":null,"abstract":"<div><div><em>Cuscuta gronovii</em> Willd., a member of the Convolvulaceae family, is noted for its potential medicinal and nutritional benefits. In this study, we utilized a combination of Illumina and Oxford Nanopore sequencing technologies to successfully assemble the complete circular mitochondrial genome (mitogenome) of <em>C. gronovii</em>. The mitogenome, spanning 304,467 base pairs, includes 54 genes: 33 protein-coding genes, three ribosomal RNA (rRNA) genes, and 18 transfer RNA (tRNA) genes. Beyond its primary circular structure, we discovered and validated several alternative genomic conformations, driven by five specific repeat sequences. Three inverted repeats were found to initiate rearrangements, resulting in the creation of seven distinct chromosomal structures, while two direct repeats split a larger molecule into two subgenomic entities. We also mapped 421 RNA editing sites across the protein-coding sequences, influencing 33 protein-coding genes with varying distribution, particularly noting high frequencies in the <em>nad</em>4 and <em>ccm</em>B genes. Sixteen of these RNA editing sites were experimentally validated through PCR amplification and Sanger sequencing, confirming their presence with 100 % accuracy. This research not only introduces the first mitochondrial genome of <em>C. gronovii</em> but also highlights its complex conformational variability induced by repeat-mediated recombination, providing a valuable genomic resource for further molecular breeding efforts and phylogenetic evolution within the genus <em>Cuscuta</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110966"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686648","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}
Pub Date : 2025-01-01DOI: 10.1016/j.ygeno.2024.110975
Ling Pan , Lirong Cai , Yang Lu , Junming Zhao , Xuebing Yan , Xiaoshan Wang
Paspalum vaginatum, valued for its salt tolerance, is a vital species in the turfgrass and agricultural industries. Despite its significance, there are still gaps in its genetic composition, particularly in the mitochondrial (mtDNA) and chloroplast (cpDNA) genomes. Our study aimed to fill these knowledge gaps by investigating the evolutionary relationships within the paspalum family and examining the functions of organelle-encoded genes as well as the critical role of reactive oxygen species (ROS) in organelle-nucleus communication. By genome sequencing, assembly, and annotation, we determined 504,515 bp of P. vaginatum mtDNA and 140,483 bp of its cpDNA. Comparative analyses with other Paspalum species and major crops highlight the intricate evolutionary dynamics and varying levels of genetic relatedness observed across different organelle genomes. The complex response of organelle gene expression to salt stress in this study will aid in understanding the molecular mechanisms and evolutionary trajectories of P. vaginatum organelle genomes.
覆盆子（Paspalum vaginatum）因其耐盐性而受到重视，是草坪和农业领域的重要物种。尽管其重要性不言而喻，但其基因组成，尤其是线粒体（mtDNA）和叶绿体（cpDNA）基因组仍然存在空白。我们的研究旨在通过调查覆盆子家族内部的进化关系、研究细胞器编码基因的功能以及活性氧（ROS）在细胞器-细胞核交流中的关键作用来填补这些知识空白。通过基因组测序、组装和注释，我们确定了 504,515 bp 的 P. vaginatum mtDNA 和 140,483 bp 的 cpDNA。与其他覆盆子物种和主要农作物的比较分析凸显了在不同细胞器基因组中观察到的错综复杂的进化动态和不同程度的遗传相关性。本研究中细胞器基因表达对盐胁迫的复杂反应将有助于了解海带细胞器基因组的分子机制和进化轨迹。
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