BMC Genomics最新文献

{"title":"Metabolomics, phytohormone and transcriptomics strategies to reveal the mechanism of barley heading date regulation to responds different photoperiod","authors":"Zhuo Ga, Liyun Gao, Xiruo Quzong, Wang Mu, Pubu Zhuoma, Xiongnu Taba, Guocheng Jiao, Dawa Dondup, Lhundrup Namgyal, Zha Sang","doi":"10.1186/s12864-024-10788-z","DOIUrl":"https://doi.org/10.1186/s12864-024-10788-z","url":null,"abstract":"The correlation between heading date and flowering time significantly regulates grain filling and seed formation in barley and other crops, ultimately determining crop productivity. In this study, the transcriptome, hormone content detection, and metabolome analysis were performed systematically to analyze the regulatory mechanism of heading time in highland barley under different light conditions. The heading date of D18 (winter highland barley variety, Dongqing18) was later than that of K13 (vernal highland barley variety) under normal growth conditions or long-day (LD) treatment, while this situation will reverse with short-day (SD) treatment. The circadian rhythm plant, plant hormone signaling transduction, starch and sucrose metabolism, and photosynthesis-related pathways are significantly enriched in barley under SD and LD to influence heading time. In the plant circadian rhythm pathway, the key genes GI (Gigantea), PRR (Pesudoresponseregulator), FKF1 (Flavin-binding kelch pepeat F-Box 1), and FT (Flowering locus T) are identified as highly expressed in D18SD3 and K13SD2, while they are significantly down-regulated in K13SD3. These genes play an important role in regulating the heading date of D18 earlier than that of K13 under SD conditions. In photosynthesis-related pathways, a-b binding protein and RBS were highly expressed in K13LD3, while NADP-dependent malic enzyme, phosphoenolpyruvate carboxylase, fructose-bisphosphate aldolase, and triosephosphate isomerase were significantly expressed in D18SD3. In the starch and sucrose metabolism pathway, 41 DEGs (differentially expressed genes) and related metabolites were identified as highly expressed and accumulated in D18SD3. The DEGs SAUR (Small auxin-up RNA), ARF (Auxin response factor), TIR1 (Transport inhibitor response 1), EIN3 (Ethylene-insensitive 3), ERS1 (Ethylene receptor gene), and JAZ1 (Jasmonate ZIM-domain) in the plant hormone pathway were significantly up-regulated in D18SD3. Compared with D18LD3, the content of N6-isopentenyladenine, indole-3-carboxylic acid, 1-aminocyclopropanecarboxylic acid, trans-zeatin, indole-3-carboxaldehyde, 1-O-indol-3-ylacetylglucose, and salicylic acid in D18SD3 also increased. The expression levels of vernalization genes (HvVRN1, HvVRN2, and HvVRN3), photoperiod genes (PPD), and PPDK (Pyruvate phosphate dikinase) that affect photosynthetic efficiency in barley are also analyzed, which play important regulatory roles in barley heading date. The WGCNA analysis of the metabolome data and circadian regulatory genes identified the key metabolites and candidate genes to regulate the heading time of barley in response to the photoperiod. These studies will provide a reference for the regulation mechanism of flowering and the heading date of highland barley.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269462","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":"Genetic and genomic analysis of reproduction traits in holstein cattle using SNP chip data and imputed sequence level genotypes","authors":"Leopold Schwarz, Ana-Marija Križanac, Helen Schneider, Clemens Falker-Gieske, Johannes Heise, Zengting Liu, Jörn Bennewitz, Georg Thaller, Jens Tetens","doi":"10.1186/s12864-024-10782-5","DOIUrl":"https://doi.org/10.1186/s12864-024-10782-5","url":null,"abstract":"Reproductive performance plays an important role in animal welfare, health and profitability in animal husbandry and breeding. It is well established that there is a negative correlation between performance and reproduction in dairy cattle. This relationship is being increasingly considered in breeding programs. By elucidating the genetic architecture of underlying reproduction traits, it will be possible to make a more detailed contribution to this. Our study followed two approaches to elucidate this area; in a first part, variance components were estimated for 14 different calving and fertility traits, and then genome-wide association studies were performed for 13 reproduction traits on imputed sequence-level genotypes with subsequent enrichment analyses. Variance components analyses showed a low to moderate heritability (h2) for the traits analysed, ranging from 0.014 for endometritis up to 0.271 for stillbirth, indicating variable degrees of variation within the reproduction traits. For genome-wide association studies, we were able to detect genome-wide significant association signals for nine out of 13 analysed traits after Bonferroni correction on chromosome 6, 18 and the X chromosome. In total, we detected over 2700 associated SNPs encircling more than 90 different genes using the imputed whole-genome sequence data. Functional associations were reviewed so far known and potential candidate regions in the proximity of reproduction events were hypothesised. Our results confirm previous findings of other authors in a comprehensive cohort including 13 different traits at the same time. Additionally, we identified new candidate genes involved in dairy cattle reproduction and made initial suggestions regarding their potential impact, with special regard to the X chromosome as a putative information source for further research. This work can make a contribution to reveal the genetic architecture of reproduction traits in context of trait specific interactions.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264404","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: Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies","authors":"Qussai Abbas, Mathias Wilhelm, Bernhard Kuster, Brigitte Poppenberger, Dmitrij Frishman","doi":"10.1186/s12864-024-10796-z","DOIUrl":"https://doi.org/10.1186/s12864-024-10796-z","url":null,"abstract":"<p><b>Correction: BMC Genomics 25, 619 (2024)</b></p><p>https://doi.org/10.1186/s12864-024-10521-w</p><p>Following publication of the original article, it was noticed that the sensitivity and specificity values of GALBA were reported incorrectly, leading to an error in Fig. 4, and 4b. The incorrect and correct versions of Fig. 4a and b. are given in this correction article.</p><p><b>Incorrect figure panels</b>:</p><figure><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12864-024-10796-z/MediaObjects/12864_2024_10796_Fig1_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure 1\" aria-describedby=\"Fig1\" height=\"801\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12864-024-10796-z/MediaObjects/12864_2024_10796_Fig1_HTML.png\" width=\"685\"/></picture></figure><p><b>Correct Fig. 4a and b</b>:</p><figure><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12864-024-10796-z/MediaObjects/12864_2024_10796_Fig2_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure 2\" aria-describedby=\"Fig2\" height=\"282\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12864-024-10796-z/MediaObjects/12864_2024_10796_Fig2_HTML.png\" width=\"685\"/></picture></figure><p>The following text in the ‘Benchmarking gene prediction tools’ relating to Fig. 4 has been corrected as a result of this correction.</p><p><b>Original text</b>:</p><p>The benchmarking of the selected gene prediction tools was conducted against the well-curated reference annotations of the <i>Arabidopsis thaliana</i> and <i>Medicago truncatula</i> model plant genomes. These tools do not rely on species-specific transcriptomics or proteomics data. Comparative analysis revealed that BRAKER2, GALBA and Helixer exhibited superior performance in terms of sensitivity and specificity compared to the other tools assessed (Fig. 4a and b).</p><p><b>Corrected text</b>:</p><p>The benchmarking of the selected gene prediction tools was conducted against the well-curated reference annotations of the Arabidopsis thaliana and Medicago truncatula model plant genomes. These tools do not rely on species-specific transcriptomics or proteomics data. Comparative analysis revealed that BRAKER2, GALBA and Helixer exhibited superior performance in terms of sensitivity and specificity compared to the other tools assessed (Fig. 4a and b). While GALBA was specifically designed to work well with genomes that present challenges for BRAKER2—such as large genomes with abundant repeats and high GC content—it will not be included in this study and will be evaluated in future research.</p><p>The original article has been updated.</p><h3>Authors and Affiliations</h3><ol><li><p>Chair of Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany</p><p>Qussai Abbas & Dmitrij Frishman</p></li><li><p>Computational Mass Spectrometry, TUM Sch","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264405","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":"Screening of mtr-miR156a from exosomes of dairy cow blood to milk and its regulatory effect on milk protein synthesis in BMECs","authors":"Li Shaojin, Jia Jingying, Liu Baobao, Li Yahui, Duan Hongjuan, Yun Ma, Cai Xiaoyan","doi":"10.1186/s12864-024-10761-w","DOIUrl":"https://doi.org/10.1186/s12864-024-10761-w","url":null,"abstract":"MicroRNA (miRNA) is a type of endogenous non-coding small RNA, which is abundant in living organisms. miRNAs play an important role in regulating gene expression and myriad cellular processes by binding to target messenger RNAs through complementary base pairing, and cross-species regulation mammalian cells by plant-derived xeno-miRNAs has been described. Here, we examined the miRNA species in two alfalfa (Medicago sativa, lucerne) cultivars commonly grown in Ningxia, China: cv. Zhongmu 1 and cv. Xinyan 52. Both cultivars have good salt and drought resistance. We found that the miRNA profiles were similar between the cultivars, with a slightly higher number of miRNAs present in the newer cv. Xinyan 52, which may contribute to its improved salt and drought tolerance. miRNAs were stable during drying, and some miRNAs were increased in dry versus fresh alfalfa, suggesting some miRNAs may be upregulated during drying. Alfalfa-derived miRNAs could be detected in exosomes from serum and whey collected from dairy cows, confirming the ability of the exogenous miRNAs (xeno-miRNAs) to enter the circulation and reach the mammary epithelium. In vitro studies confirmed that overexpression of mtr-miR156a could downregulate expression of Phosphatase 2 Regulatory Subunit B'gamma ( PPP2R5D) and Phosphoinositide-3-kinase Regulatory Subunit 2 (PIK3R2). Overexpression of mtr-miR156a also modulated PI3K–AKT–mTOR signaling as well as the casein content of milk produced by bovine mammary epithelial cells. Based on the known roles of PPP2R5D and PIK3R2 in regulating the PI3K–AKT–mTOR pathway as well as the effect of PI3K–AKT–mTOR on milk protein content, our findings implicate alfalfa-derived miR156a as a new cross-species regulator of milk quality in dairy cows.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264403","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":"Deconvolution from bulk gene expression by leveraging sample-wise and gene-wise similarities and single-cell RNA-Seq data","authors":"Chenqi Wang, Yifan Lin, Shuchao Li, Jinting Guan","doi":"10.1186/s12864-024-10728-x","DOIUrl":"https://doi.org/10.1186/s12864-024-10728-x","url":null,"abstract":"The widely adopted bulk RNA-seq measures the gene expression average of cells, masking cell type heterogeneity, which confounds downstream analyses. Therefore, identifying the cellular composition and cell type-specific gene expression profiles (GEPs) facilitates the study of the underlying mechanisms of various biological processes. Although single-cell RNA-seq focuses on cell type heterogeneity in gene expression, it requires specialized and expensive resources and currently is not practical for a large number of samples or a routine clinical setting. Recently, computational deconvolution methodologies have been developed, while many of them only estimate cell type composition or cell type-specific GEPs by requiring the other as input. The development of more accurate deconvolution methods to infer cell type abundance and cell type-specific GEPs is still essential. We propose a new deconvolution algorithm, DSSC, which infers cell type-specific gene expression and cell type proportions of heterogeneous samples simultaneously by leveraging gene-gene and sample-sample similarities in bulk expression and single-cell RNA-seq data. Through comparisons with the other existing methods, we demonstrate that DSSC is effective in inferring both cell type proportions and cell type-specific GEPs across simulated pseudo-bulk data (including intra-dataset and inter-dataset simulations) and experimental bulk data (including mixture data and real experimental data). DSSC shows robustness to the change of marker gene number and sample size and also has cost and time efficiencies. DSSC provides a practical and promising alternative to the experimental techniques to characterize cellular composition and heterogeneity in the gene expression of heterogeneous samples.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264456","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":"Development and validation of a 5K low-density SNP chip for Hainan cattle","authors":"Huan Wang, Hui Wu, Wencan Zhang, Junming Jiang, Hejie Qian, Churiga Man, Hongyan Gao, Qiaoling Chen, Li Du, Si Chen, Fengyang Wang","doi":"10.1186/s12864-024-10753-w","DOIUrl":"https://doi.org/10.1186/s12864-024-10753-w","url":null,"abstract":"This study aimed to design and develop a 5K low-density liquid chip for Hainan cattle utilizing targeted capture sequencing technology. The chip incorporates a substantial number of functional single nucleotide polymorphism (SNP) loci derived from public literature, including SNP loci significantly associated with immunity, heat stress, meat quality, reproduction, and other traits. Additionally, SNPs located in the coding regions of immune-related genes from the Bovine Genome Variation Database (BGVD) and Hainan cattle-specific SNP loci were included. A total of 5,293 SNPs were selected, resulting in 9,837 DNA probes with a coverage rate of 85.69%, thereby creating a Hainan cattle-specific 5K Genotyping by Target Sequencing (GBTS) liquid chip. Evaluation with 152 cattle samples demonstrated excellent clustering performance and a detection rate ranging from 96.60 to 99.07%, with 94.5% of SNP sites exhibiting polymorphism. The chip achieved 100% gender coverage and displayed a heterozygosity rate between 14.20% and 29.65%, with a repeatability rate of 99.65–99.85%. Analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed the potential regulatory roles of exonic SNPs in immune response pathways. The development and validation of the 5K GBTS liquid chip for Hainan cattle represent a valuable tool for genome analysis and genetic diversity assessment. Furthermore, it facilitates breed identification, gender determination, and kinship analysis, providing a foundation for the efficient utilization and development of local cattle genetic resources.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264455","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":"Transcriptomic analysis reveals molecular insights into lactation dynamics in Jakhrana goat mammary gland","authors":"Mahesh Shivanand Dige, Ankita Gurao, Lalit Pratap Singh, Meenakshi Chitkara, Manoj Kumar Singh, Gopal Dass, Arun Kumar Verma, Rakesh Kumar Pundir, Ranjit Singh Kataria","doi":"10.1186/s12864-024-10744-x","DOIUrl":"https://doi.org/10.1186/s12864-024-10744-x","url":null,"abstract":"Goat milk is gaining popularity as a superior alternative to bovine milk due to its closer resemblance to human milk. Understanding the molecular processes underlying lactation is crucial for improving milk quality and production in goats. However, the genetic mechanisms governing lactation in goats, particularly in indigenous breeds like the Jakhrana, remain largely unexplored. In this study, we performed a comprehensive transcriptomic analysis of Jakhrana goat mammary glands during early and late lactation stages. We isolated milk somatic cells and conducted RNA sequencing, followed by transcript quantification and mapping against the ARS1.2 Capra hircus reference assembly. Our analysis identified differentially expressed genes (DEGs) and commonly expressed genes (CEGs) across the lactation phases. Early lactation showed enrichment of genes encoding antimicrobial peptides and lubrication proteins, while late lactation exhibited heightened expression of genes encoding major milk proteins. Additionally, DEG analysis revealed upregulation of pivotal genes, such as the ABC transporter gene MRP4, implicated in modulating milk composition and quality. Our findings provide insights into the genetic mechanisms underlying lactation dynamics in the Jakhrana goat. Understanding these mechanisms could help in improving milk production and quality in goats, benefiting both the dairy industry and consumers.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264464","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":"Genome-wide identification and expressional analysis of carotenoid cleavage oxygenase (CCO) gene family in Betula platyphylla under abiotic stress","authors":"Jiajie Yu, Yiran Wang, Heming Bai, Xiang Zhang, Ruiqi Wang","doi":"10.1186/s12864-024-10777-2","DOIUrl":"https://doi.org/10.1186/s12864-024-10777-2","url":null,"abstract":"Carotenoid cleavage oxygenases (CCOs) are a group of enzymes that catalyze the oxidative cleavage of carotenoid molecules. These enzymes widely exist in plants, fungi, and certain bacteria, and are involved in various biological processes. It would be of great importance and necessity to identify CCO members in birch and characterize their responses upon abiotic stresses. A total of 16 BpCCOs, including 8 BpCCDs and 8 BpNCEDs were identified in birch, and phylogenetic tree analysis showed that they could be classified into six subgroups. Collinearity analysis revealed that BpCCOs have the largest number of homologous genes in Gossypium hirsutum and also have more homologous genes in other dicotyledons. In addition, promoter analysis revealed that the promoter regions of BpCCOs contained many abiotic stress-related and hormone-responsive elements. The results of qRT-PCR showed that most of the BpCCOs were able to respond significantly to ABA, PEG, salt and cold stresses. Finally, the prediction of the interacting proteins of BpCCOs by STRING revealed several proteins that may interact with BpCCOs and be involved in plant growth and development/abiotic stress processes, such as HEC1 (bHLH), ATABA1, ATVAMP714, etc. In this study, the CCO members were identified in birch in a genome-wide scale. These results indicate that BpCCO genes may play important roles in the abiotic stress responses of birch plants.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264460","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":"Transcriptomic profiling reveals the complex interaction between a bipartite begomovirus and a cucurbitaceous host plant","authors":"Wen-Ze He, Li Zhao, Kai Sun, Zhen Feng, Gen Zhou, Qiong Rao","doi":"10.1186/s12864-024-10781-6","DOIUrl":"https://doi.org/10.1186/s12864-024-10781-6","url":null,"abstract":"Begomoviruses are major constraint in the production of many crops. Upon infection, begomoviruses may substantially modulate plant biological processes. While how monopartite begomoviruses interact with their plant hosts has been investigated extensively, bipartite begomoviruses-plant interactions are understudied. Moreover, as one of the major groups of hosts, cucurbitaceous plants have been seldom examined in the interaction with begomoviruses. We profiled the zucchini transcriptomic changes induced by a bipartite begomovirus squash leaf curl China virus (SLCCNV). We identified 2275 differentially-expressed genes (DEGs), of which 1310 were upregulated and 965 were downregulated. KEGG enrichment analysis of the DEGs revealed that many pathways related to primary and secondary metabolisms were enriched. qRT-PCR verified the transcriptional changes of twelve selected DEGs induced by SLCCNV infection. Close examination revealed that the expression levels of all the DEGs of the pathway Photosynthesis were downregulated upon SLCCNV infection. Most DEGs in the pathway Plant-pathogen interaction were upregulated, including some positive regulators of plant defenses. Moreover, the majority of DEGs in the MAPK signaling pathway-plant were upregulated. Our findings indicates that SLCCNV actively interact with its cucurbitaceous plant host by suppressing the conversion of light energy to chemical energy and inducing immune responses. Our study not only provides new insights into the interactions between begomoviruses and host plants, but also adds to our knowledge on virus-plant interactions in general.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264409","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-quality chromosome-level genomic insights into molecular adaptation to low-temperature stress in Madhuca longifolia in southern subtropical China","authors":"Shuyu Wang, Haoyou Lin, Shuiyun Ye, Zhengli Jiao, Zhipeng Chen, Yifei Ma, Lu Zhang","doi":"10.1186/s12864-024-10769-2","DOIUrl":"https://doi.org/10.1186/s12864-024-10769-2","url":null,"abstract":"Madhuca longifolia, the energy-producing and medicinal tropical tree originally from southern India, faces difficulties in adapting to the low temperatures of late autumn and early winter in subtropical southern China, impacting its usability. Therefore, understanding the molecular mechanisms controlling the ability of this species to adapt to environmental challenges is essential for optimising horticulture efforts. Accordingly, this study aimed to elucidate the molecular responses of M. longifolia to low-temperature stress through genomic and transcriptomic analyses to inform strategies for its effective cultivation and utilisation in colder climates. Herein, the high-quality reference genome and genomic assembly for M. longifolia are presented for the first time. Using Illumina sequencing, Hi-C technology, and PacBio HiFi sequencing, we assembled a chromosome-level genome approximately 737.92 Mb in size, investigated its genomic features, and conducted an evolutionary analysis of the genus Madhuca. Additionally, using transcriptome sequencing, we identified 17,941 differentially expressed genes related to low-temperature response. Through bioinformatics analysis of the WRKY gene family, 15 genes crucial for M. longifolia low-temperature resistance were identified. This research not only lays the groundwork for the successful ecological adaptation and cultivation of M. longifolia in China’s southern subtropical regions but also offers valuable insights for the genetic enhancement of cold tolerance in tropical species, contributing to their sustainable horticulture and broader industrial, medicinal, and agricultural use.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264408","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}