Genome Biology最新文献_第2页

Dissecting the genetic basis of UV-B responsive metabolites in rice 剖析水稻紫外线-B 反应性代谢物的遗传基础

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-08-29 DOI: 10.1186/s13059-024-03372-x

Feng Zhang, Chenkun Yang, Hao Guo, Yufei Li, Shuangqian Shen, Qianqian Zhou, Chun Li, Chao Wang, Ting Zhai, Lianghuan Qu, Cheng Zhang, Xianqing Liu, Jie Luo, Wei Chen, Shouchuang Wang, Jun Yang, Cui Yu, Yanyan Liu

{"title":"Dissecting the genetic basis of UV-B responsive metabolites in rice","authors":"Feng Zhang, Chenkun Yang, Hao Guo, Yufei Li, Shuangqian Shen, Qianqian Zhou, Chun Li, Chao Wang, Ting Zhai, Lianghuan Qu, Cheng Zhang, Xianqing Liu, Jie Luo, Wei Chen, Shouchuang Wang, Jun Yang, Cui Yu, Yanyan Liu","doi":"10.1186/s13059-024-03372-x","DOIUrl":"https://doi.org/10.1186/s13059-024-03372-x","url":null,"abstract":"UV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. However, the molecular mechanisms underlying the response to UV-B stress remain elusive in rice. We perform comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal light conditions using a widely targeted metabolomics approach. Our results reveal substantial differences in metabolite accumulation between the two major rice subspecies indica and japonica, especially after UV-B treatment, implying the possible role and mechanism of metabolome changes in subspecies differentiation and the stress response. We next conduct a transcriptome analysis from four representative rice varieties under UV-B stress, revealing genes from amino acid and flavonoid pathways involved in the UV-B response. We further perform a metabolite-based genome-wide association study (mGWAS), which reveals 3307 distinct loci under UV-B stress. Identification and functional validation of candidate genes show that OsMYB44 regulates tryptamine accumulation to mediate UV-B tolerance, while OsUVR8 interacts with OsMYB110 to promote flavonoid accumulation and UV-B tolerance in a coordinated manner. Additionally, haplotype analysis suggests that natural variation of OsUVR8groupA contributes to UV-B resistance in rice. Our study reveals the complex biochemical and genetic foundations that govern the metabolite dynamics underlying the response, tolerance, and adaptive strategies of rice to UV-B stress. These findings provide new insights into the biochemical and genetic basis of the metabolome underlying the crop response, tolerance, and adaptation to UV-B stress.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":null,"pages":null},"PeriodicalIF":12.3,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142090107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs NERD-seq：纳米孔直接 RNA 测序的新方法，可扩展非编码 RNA 的代表性

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-08-28 DOI: 10.1186/s13059-024-03375-8

Luke Saville, Li Wu, Jemaneh Habtewold, Yubo Cheng, Babita Gollen, Liam Mitchell, Matthew Stuart-Edwards, Travis Haight, Majid Mohajerani, Athanasios Zovoilis

引用次数: 0

Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations 肠道微生物群有助于人类适应高海拔缺氧环境

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-08-28 DOI: 10.1186/s13059-024-03373-w

Qian Su, Dao-Hua Zhuang, Yu-Chun Li, Yu Chen, Xia-Yan Wang, Ming-Xia Ge, Ting-Yue Xue, Qi-Yuan Zhang, Xin-Yuan Liu, Fan-Qian Yin, Yi-Ming Han, Zong-Liang Gao, Long Zhao, Yong-Xuan Li, Meng-Jiao Lv, Li-Qin Yang, Tian-Rui Xia, Yong-Jun Luo, Zhigang Zhang, Qing-Peng Kong

{"title":"Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations","authors":"Qian Su, Dao-Hua Zhuang, Yu-Chun Li, Yu Chen, Xia-Yan Wang, Ming-Xia Ge, Ting-Yue Xue, Qi-Yuan Zhang, Xin-Yuan Liu, Fan-Qian Yin, Yi-Ming Han, Zong-Liang Gao, Long Zhao, Yong-Xuan Li, Meng-Jiao Lv, Li-Qin Yang, Tian-Rui Xia, Yong-Jun Luo, Zhigang Zhang, Qing-Peng Kong","doi":"10.1186/s13059-024-03373-w","DOIUrl":"https://doi.org/10.1186/s13059-024-03373-w","url":null,"abstract":"The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This stems primarily from uncertainties regarding both the potential temporal changes in the microbiota under such conditions and the existence of any dominant or core bacteria that may assist in host acclimatization. To address these issues, and to control for variables commonly present in previous studies which significantly impact the results obtained, namely genetic background, ethnicity, lifestyle, and diet, we conducted a 108-day longitudinal study on the same cohort comprising 45 healthy Han adults who traveled from lowland Chongqing, 243 masl, to high-altitude plateau Lhasa, Xizang, 3658 masl, and back. Using shotgun metagenomic profiling, we study temporal changes in gut microbiota composition at different timepoints. The results show a significant reduction in the species and functional diversity of the gut microbiota, along with a marked increase in functional redundancy. These changes are primarily driven by the overgrowth of Blautia A, a genus that is also abundant in six independent Han cohorts with long-term duration in lower hypoxia environment in Shigatse, Xizang, at 4700 masl. Further animal experiments indicate that Blautia A-fed mice exhibit enhanced intestinal health and a better acclimatization phenotype to sustained hypoxic stress. Our study underscores the importance of Blautia A species in the gut microbiota’s rapid response to high-altitude hypoxia and its potential role in maintaining intestinal health and aiding host adaptation to extreme environments, likely via anti-inflammation and intestinal barrier protection.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":null,"pages":null},"PeriodicalIF":12.3,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142085505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Contribution of homoeologous exchange to domestication of polyploid Brassica. 同源交换对多倍体芸薹属植物驯化的贡献。

IF 10.1 1区生物学

Genome Biology Pub Date : 2024-08-27 DOI: 10.1186/s13059-024-03370-z

Tianpeng Wang, Aalt D J van Dijk, Ranze Zhao, Guusje Bonnema, Xiaowu Wang

{"title":"Contribution of homoeologous exchange to domestication of polyploid Brassica.","authors":"Tianpeng Wang, Aalt D J van Dijk, Ranze Zhao, Guusje Bonnema, Xiaowu Wang","doi":"10.1186/s13059-024-03370-z","DOIUrl":"10.1186/s13059-024-03370-z","url":null,"abstract":"Background: Polyploidy is widely recognized as a significant evolutionary force in the plant kingdom, contributing to the diversification of plants. One of the notable features of allopolyploidy is the occurrence of homoeologous exchange (HE) events between the subgenomes, causing changes in genomic composition, gene expression, and phenotypic variations. However, the role of HE in plant adaptation and domestication remains unclear.Results: Here we analyze the whole-genome resequencing data from Brassica napus accessions representing the different morphotypes and ecotypes, to investigate the role of HE in domestication. Our findings demonstrate frequent occurrence of HEs in Brassica napus, with substantial HE patterns shared across populations, indicating their potential role in promoting crop domestication. HE events are asymmetric, with the A genome more frequently replacing C genome segments. These events show a preference for specific genomic regions and vary among populations. We also identify candidate genes in HE regions specific to certain populations, which likely contribute to flowering-time diversification across diverse morphotypes and ecotypes. In addition, we assemble a new genome of a swede accession, confirming the HE signals on the genome and their potential involvement in root tuber development. By analyzing HE in another allopolyploid species, Brassica juncea, we characterize a potential broader role of HE in allopolyploid crop domestication.Conclusions: Our results provide novel insights into the domestication of polyploid Brassica species and highlight homoeologous exchange as a crucial mechanism for generating variations that are selected for crop improvement in polyploid species.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11350971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections 从大型基因组集合中实时识别 SARS-CoV-2 中的表观相互作用

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-08-22 DOI: 10.1186/s13059-024-03355-y

Gabriel Innocenti, Maureen Obara, Bibiana Costa, Henning Jacobsen, Maeva Katzmarzyk, Luka Cicin-Sain, Ulrich Kalinke, Marco Galardini

{"title":"Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections","authors":"Gabriel Innocenti, Maureen Obara, Bibiana Costa, Henning Jacobsen, Maeva Katzmarzyk, Luka Cicin-Sain, Ulrich Kalinke, Marco Galardini","doi":"10.1186/s13059-024-03355-y","DOIUrl":"https://doi.org/10.1186/s13059-024-03355-y","url":null,"abstract":"The emergence of the SARS-CoV-2 virus has highlighted the importance of genomic epidemiology in understanding the evolution of pathogens and guiding public health interventions. The Omicron variant in particular has underscored the role of epistasis in the evolution of lineages with both higher infectivity and immune escape, and therefore the necessity to update surveillance pipelines to detect them early on. In this study, we apply a method based on mutual information between positions in a multiple sequence alignment, which is capable of scaling up to millions of samples. We show how it can reliably predict known experimentally validated epistatic interactions, even when using as little as 10,000 sequences, which opens the possibility of making it a near real-time prediction system. We test this possibility by modifying the method to account for the sample collection date and apply it retrospectively to multiple sequence alignments for each month between March 2020 and March 2023. We detected a cornerstone epistatic interaction in the Spike protein between codons 498 and 501 as soon as seven samples with a double mutation were present in the dataset, thus demonstrating the method’s sensitivity. We test the ability of the method to make inferences about emerging interactions by testing candidates predicted after March 2023, which we validate experimentally. We show how known epistatic interaction in SARS-CoV-2 can be detected with high sensitivity, and how emerging ones can be quickly prioritized for experimental validation, an approach that could be implemented downstream of pandemic genome sequencing efforts.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":null,"pages":null},"PeriodicalIF":12.3,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142022189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Current limitations in predicting mRNA translation with deep learning models. 目前利用深度学习模型预测 mRNA 翻译的局限性。

IF 10.1 1区生物学

Genome Biology Pub Date : 2024-08-20 DOI: 10.1186/s13059-024-03369-6

Niels Schlusser, Asier González, Muskan Pandey, Mihaela Zavolan

{"title":"Current limitations in predicting mRNA translation with deep learning models.","authors":"Niels Schlusser, Asier González, Muskan Pandey, Mihaela Zavolan","doi":"10.1186/s13059-024-03369-6","DOIUrl":"10.1186/s13059-024-03369-6","url":null,"abstract":"Background: The design of nucleotide sequences with defined properties is a long-standing problem in bioengineering. An important application is protein expression, be it in the context of research or the production of mRNA vaccines. The rate of protein synthesis depends on the 5' untranslated region (5'UTR) of the mRNAs, and recently, deep learning models were proposed to predict the translation output of mRNAs from the 5'UTR sequence. At the same time, large data sets of endogenous and reporter mRNA translation have become available.Results: In this study, we use complementary data obtained in two different cell types to assess the accuracy and generality of currently available models for predicting translational output. We find that while performing well on the data sets on which they were trained, deep learning models do not generalize well to other data sets, in particular of endogenous mRNAs, which differ in many properties from reporter constructs.Conclusions: These differences limit the ability of deep learning models to uncover mechanisms of translation control and to predict the impact of genetic variation. We suggest directions that combine high-throughput measurements and machine learning to unravel mechanisms of translation control and improve construct design.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes 甜瓜：利用标记基因进行基于元基因组长读数的分类鉴定和量化

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-08-19 DOI: 10.1186/s13059-024-03363-y

Xi Chen, Xiaole Yin, Xianghui Shi, Weifu Yan, Yu Yang, Lei Liu, Tong Zhang

引用次数: 0

Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets 测序数据中被忽视的劣质患者样本损害了已发布的临床相关数据集的可重复性

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-08-16 DOI: 10.1186/s13059-024-03331-6

Maximilian Sprang, Jannik Möllmann, Miguel A. Andrade-Navarro, Jean-Fred Fontaine

{"title":"Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets","authors":"Maximilian Sprang, Jannik Möllmann, Miguel A. Andrade-Navarro, Jean-Fred Fontaine","doi":"10.1186/s13059-024-03331-6","DOIUrl":"https://doi.org/10.1186/s13059-024-03331-6","url":null,"abstract":"Reproducibility is a major concern in biomedical studies, and existing publication guidelines do not solve the problem. Batch effects and quality imbalances between groups of biological samples are major factors hampering reproducibility. Yet, the latter is rarely considered in the scientific literature. Our analysis uses 40 clinically relevant RNA-seq datasets to quantify the impact of quality imbalance between groups of samples on the reproducibility of gene expression studies. High-quality imbalance is frequent (14 datasets; 35%), and hundreds of quality markers are present in more than 50% of the datasets. Enrichment analysis suggests common stress-driven effects among the low-quality samples and highlights a complementary role of transcription factors and miRNAs to regulate stress response. Preliminary ChIP-seq results show similar trends. Quality imbalance has an impact on the number of differential genes derived by comparing control to disease samples (the higher the imbalance, the higher the number of genes), on the proportion of quality markers in top differential genes (the higher the imbalance, the higher the proportion; up to 22%) and on the proportion of known disease genes in top differential genes (the higher the imbalance, the lower the proportion). We show that removing outliers based on their quality score improves the resulting downstream analysis. Thanks to a stringent selection of well-designed datasets, we demonstrate that quality imbalance between groups of samples can significantly reduce the relevance of differential genes, consequently reducing reproducibility between studies. Appropriate experimental design and analysis methods can substantially reduce the problem.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":null,"pages":null},"PeriodicalIF":12.3,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Benchmarking computational methods for single-cell chromatin data analysis 单细胞染色质数据分析计算方法基准测试

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-08-16 DOI: 10.1186/s13059-024-03356-x

Siyuan Luo, Pierre-Luc Germain, Mark D. Robinson, Ferdinand von Meyenn

{"title":"Benchmarking computational methods for single-cell chromatin data analysis","authors":"Siyuan Luo, Pierre-Luc Germain, Mark D. Robinson, Ferdinand von Meyenn","doi":"10.1186/s13059-024-03356-x","DOIUrl":"https://doi.org/10.1186/s13059-024-03356-x","url":null,"abstract":"Single-cell chromatin accessibility assays, such as scATAC-seq, are increasingly employed in individual and joint multi-omic profiling of single cells. As the accumulation of scATAC-seq and multi-omics datasets continue, challenges in analyzing such sparse, noisy, and high-dimensional data become pressing. Specifically, one challenge relates to optimizing the processing of chromatin-level measurements and efficiently extracting information to discern cellular heterogeneity. This is of critical importance, since the identification of cell types is a fundamental step in current single-cell data analysis practices. We benchmark 8 feature engineering pipelines derived from 5 recent methods to assess their ability to discover and discriminate cell types. By using 10 metrics calculated at the cell embedding, shared nearest neighbor graph, or partition levels, we evaluate the performance of each method at different data processing stages. This comprehensive approach allows us to thoroughly understand the strengths and weaknesses of each method and the influence of parameter selection. Our analysis provides guidelines for choosing analysis methods for different datasets. Overall, feature aggregation, SnapATAC, and SnapATAC2 outperform latent semantic indexing-based methods. For datasets with complex cell-type structures, SnapATAC and SnapATAC2 are preferred. With large datasets, SnapATAC2 and ArchR are most scalable.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":null,"pages":null},"PeriodicalIF":12.3,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases StaVia：利用高阶随机游走为细胞图谱绘制时空感知地图

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-08-16 DOI: 10.1186/s13059-024-03347-y

Shobana V. Stassen, Minato Kobashi, Edmund Y. Lam, Yuanhua Huang, Joshua W. K. Ho, Kevin K. Tsia

引用次数: 0