GigaScience最新文献

{"title":"Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa).","authors":"Antonio Starcevic, Rayline T A Figueredo, Juliana Naldoni, Lincoln L Corrêa, Beth Okamura, Edson A Adriano, Paul F Long","doi":"10.1093/gigascience/giaf014","DOIUrl":"10.1093/gigascience/giaf014","url":null,"abstract":"<p><p>Oxford-Nanopore PromethION sequencing is a PCR-free method that retains epigenetic markers and provides direct quantitative information about DNA methylation. Using this long-read sequencing technology, we successfully assembled 5 myxozoan genomes free from discernible host DNA contamination, surpassing previous studies in both quality and completeness. Genome assembly revealed DNA methylation patterns within myxozoan genomes, particularly in GC-rich regions within gene bodies. The findings not only refute the notion of myxozoans lacking DNA methylation capability but also offer a new perspective on gene regulation in these parasites. The high-quality genome assemblies lay a solid foundation for future research on myxozoans, including new strategies to control these commercially significant fish pathogens.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624339","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":"Unlocking the power of AI for phenotyping fruit morphology in Arabidopsis.","authors":"Kieran Atkins, Gina A Garzón-Martínez, Andrew Lloyd, John H Doonan, Chuan Lu","doi":"10.1093/gigascience/giae123","DOIUrl":"10.1093/gigascience/giae123","url":null,"abstract":"<p><p>Deep learning can revolutionise high-throughput image-based phenotyping by automating the measurement of complex traits, a task that is often labour-intensive, time-consuming, and prone to human error. However, its precision and adaptability in accurately phenotyping organ-level traits, such as fruit morphology, remain to be fully evaluated. Establishing the links between phenotypic and genotypic variation is essential for uncovering the genetic basis of traits and can also provide an orthologous test of pipeline effectiveness. In this study, we assess the efficacy of deep learning for measuring variation in fruit morphology in Arabidopsis using images from a multiparent advanced generation intercross (MAGIC) mapping family. We trained an instance segmentation model and developed a pipeline to phenotype Arabidopsis fruit morphology, based on the model outputs. Our model achieved strong performance with an average precision of 88.0% for detection and 55.9% for segmentation. Quantitative trait locus analysis of the derived phenotypic metrics of the MAGIC population identified significant loci associated with fruit morphology. This analysis, based on automated phenotyping of 332,194 individual fruits, underscores the capability of deep learning as a robust tool for phenotyping large populations. Our pipeline for quantifying pod morphological traits is scalable and provides high-quality phenotype data, facilitating genetic analysis and gene discovery, as well as advancing crop breeding research.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11816797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143407006","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 and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spiders.","authors":"Guoqing Zhang, Yiru Wang, Hongcen Jiang, Yi Wang","doi":"10.1093/gigascience/giaf019","DOIUrl":"10.1093/gigascience/giaf019","url":null,"abstract":"<p><strong>Background: </strong>Research on the mechanism of starvation resistance can help reveal how animals adjust their physiology and behavior to adapt to the uncertainty of food resources. A low metabolic rate is a significant characteristic of spider physiological activity and can increase spider starvation resistance and adapt to complex ecological environments.</p><p><strong>Results: </strong>We sequenced the genome of Heteropoda venatoria and discovered significant expansions in gene families related to lipid metabolism, such as cytochrome P450 and steroid hormone biosynthesis genes, through comparative genomic analysis. We also systematically analyzed the gene expression characteristics of H. venatoria at different starvation resistance stages and reported that the fat body plays a crucial role during starvation in spiders. This study indicates that during the early stages of starvation, H. venatoria relies on glucose metabolism to meet its energy demands. In the middle stage, gene expression stabilizes, whereas in the late stage of starvation, pathways for fatty acid metabolism and protein degradation are significantly activated, and autophagy is increased, serving as a survival strategy under extreme starvation. Notably, analysis of expanded P450 gene families revealed that H. venatoria has many duplicated CYP3 clan genes that are highly expressed in the fat body, which may help maintain a low-energy metabolic state, allowing H. venatoria to endure longer periods of starvation. We also observed that the motifs of P450 families in H. venatoria are less conserved than those in insects are, which may be related to the greater polymorphism of spider genomes.</p><p><strong>Conclusions: </strong>This research not only provides important genetic and transcriptomic evidence for understanding the starvation mechanisms of spiders but also offers new insights into the adaptive evolution of arthropods.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673819","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":"The telomere-to-telomere genome of flowering cherry (Prunus campanulata) reveals genomic evolution of the subgenus Cerasus.","authors":"Dongyue Jiang, Yingang Li, Fei Zhuge, Qi Zhou, Wenjin Zong, Xinhong Liu, Xin Shen","doi":"10.1093/gigascience/giaf009","DOIUrl":"10.1093/gigascience/giaf009","url":null,"abstract":"<p><strong>Background: </strong>Prunus campanulata, a species of ornamental cherry, holds significant genetic and horticultural value. Despite the availability of various cherry genomes, a fully resolved telomere-to-telomere (T2T) assembly for this species has been lacking. Recent advancements in long-read sequencing technologies have made it possible to generate gap-free genome assemblies, providing comprehensive insights into genomic structures that were previously inaccessible.</p><p><strong>Findings: </strong>We present the first T2T genome assembly for P. campanulata \"Lianmeiren\" (v2.0), achieved through the integration of PacBio HiFi, ultra-long Oxford Nanopore Technologies, Illumina, and Hi-C sequencing. The assembly resulted in a highly contiguous genome with a total size of 266.23 Mb and a contig N50 of 31.6 Mb. The genome exhibits remarkable completeness (98.9% BUSCO) and high accuracy (quality value of 48.75). Additionally, 13 telomeres and putative centromere regions were successfully identified across the 8 pseudochromosomes. Comparative analysis with the previous v1.0 assembly revealed 336,943 single nucleotide polymorphisms, 107,521 indels, and 1,413 structural variations, along with the annotation of 1,402 new genes.</p><p><strong>Conclusions: </strong>This T2T genome assembly of P. campanulata \"Lianmeiren\" provides a critical reference for understanding the genetic architecture of the species. It enhances our ability to study structural variations, gene function, and evolutionary biology within the Prunus genus.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: \"UDE DIATOMS in the Wild 2024\": a new image dataset of freshwater diatoms for training deep learning models.","authors":"","doi":"10.1093/gigascience/giaf043","DOIUrl":"10.1093/gigascience/giaf043","url":null,"abstract":"","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11943468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729536","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":"Benchmarking short-read metagenomics tools for removing host contamination.","authors":"Yunyun Gao, Hao Luo, Hujie Lyu, Haifei Yang, Salsabeel Yousuf, Shi Huang, Yong-Xin Liu","doi":"10.1093/gigascience/giaf004","DOIUrl":"10.1093/gigascience/giaf004","url":null,"abstract":"<p><strong>Background: </strong>The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.</p><p><strong>Results: </strong>In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.</p><p><strong>Conclusions: </strong>Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556458","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":"A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity.","authors":"Temitope Opeyemi Oriowo, Ioannis Chrysostomakis, Sebastian Martin, Sandra Kukowka, Thomas Brown, Sylke Winkler, Eugene W Myers, Astrid Böhne, Madlen Stange","doi":"10.1093/gigascience/giae116","DOIUrl":"10.1093/gigascience/giae116","url":null,"abstract":"<p><strong>Background: </strong>In this study, we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).</p><p><strong>Results: </strong>We achieved a haploid size of 940 megabase pairs (Mbp) for haplome 1 and 929 Mbp for haplome 2 with high scaffold N50 values of 36.4 Mb and 36.6 Mb and BUSCO scores of 96.9% and 97.2%, respectively, indicating a highly complete genome assembly. We detected notable heterozygosity (1.43%) and a high repeat content (approximately 54%), primarily consisting of DNA transposons, which contribute to genome rearrangements and variations. We found substantial structural variations within the genome, including insertions, deletions, inversions, and translocations. These variations affect genes enriched in functions such as dephosphorylation, developmental pigmentation, phagocytosis, immunity, and stress response. In the annotation of protein-coding genes, 30,980 messenger RNAs and 23,497 protein-coding genes were identified with a high completeness score, which further underpins the high contiguity of our genome assemblies. We performed a gene family evolution analysis by comparing our proteome to 10 other teleost species, which identified immune system gene families that prioritize histone-based disease prevention over NB-LRR-related-based immune responses. Additionally, demographic analysis indicates historical fluctuations in the effective population size of P. phoxinus, likely correlating with past climatic changes.</p><p><strong>Conclusions: </strong>This annotated, phased reference genome provides a crucial resource for resolving the taxonomic complexity within the genus Phoxinus and highlights the importance of haplotype-phased assemblies in understanding haplotype diversity in species characterized by high heterozygosity.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058682","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":"Unveiling patterns in spatial transcriptomics data: a novel approach utilizing graph attention autoencoder and multiscale deep subspace clustering network.","authors":"Liqian Zhou, Xinhuai Peng, Min Chen, Xianzhi He, Geng Tian, Jialiang Yang, Lihong Peng","doi":"10.1093/gigascience/giae103","DOIUrl":"10.1093/gigascience/giae103","url":null,"abstract":"<p><strong>Background: </strong>The accurate deciphering of spatial domains, along with the identification of differentially expressed genes and the inference of cellular trajectory based on spatial transcriptomic (ST) data, holds significant potential for enhancing our understanding of tissue organization and biological functions. However, most of spatial clustering methods can neither decipher complex structures in ST data nor entirely employ features embedded in different layers.</p><p><strong>Results: </strong>This article introduces STMSGAL, a novel framework for analyzing ST data by incorporating graph attention autoencoder and multiscale deep subspace clustering. First, STMSGAL constructs ctaSNN, a cell type-aware shared nearest neighbor graph, using Louvian clustering exclusively based on gene expression profiles. Subsequently, it integrates expression profiles and ctaSNN to generate spot latent representations using a graph attention autoencoder and multiscale deep subspace clustering. Lastly, STMSGAL implements spatial clustering, differential expression analysis, and trajectory inference, providing comprehensive capabilities for thorough data exploration and interpretation. STMSGAL was evaluated against 7 methods, including SCANPY, SEDR, CCST, DeepST, GraphST, STAGATE, and SiGra, using four 10x Genomics Visium datasets, 1 mouse visual cortex STARmap dataset, and 2 Stereo-seq mouse embryo datasets. The comparison showcased STMSGAL's remarkable performance across Davies-Bouldin, Calinski-Harabasz, S_Dbw, and ARI values. STMSGAL significantly enhanced the identification of layer structures across ST data with different spatial resolutions and accurately delineated spatial domains in 2 breast cancer tissues, adult mouse brain (FFPE), and mouse embryos.</p><p><strong>Conclusions: </strong>STMSGAL can serve as an essential tool for bridging the analysis of cellular spatial organization and disease pathology, offering valuable insights for researchers in the field.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11727722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142978066","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":"Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes.","authors":"Yang Zhou, Jiazheng Jin, Xuemei Li, Gregory Gedman, Sarah Pelan, Arang Rhie, Chuan Jiang, Olivier Fedrigo, Kerstin Howe, Adam M Phillippy, Erich D Jarvis, Frank Grutzner, Qi Zhou, Guojie Zhang","doi":"10.1093/gigascience/giae112","DOIUrl":"10.1093/gigascience/giae112","url":null,"abstract":"<p><strong>Background: </strong>A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology. However, they also exhibit rearrangements in several chromosomes, especially in the sex chromosome chain. Therefore, the lack of a chromosome-level echidna genome has limited insights into genome evolution in monotremes, in particular the multiple sex chromosomes complex.</p><p><strong>Results: </strong>Here, we present a new long reads-based chromosome-level short-beaked echidna (Tachyglossus aculeatus) genome, which allowed the inference of chromosomal rearrangements in the monotreme ancestor (2n = 64) and each extant species. Analysis of the more complete sex chromosomes uncovered homology between 1 Y chromosome and multiple X chromosomes, suggesting that it is the ancestral X that has undergone reciprocal translocation with ancestral autosomes to form the complex. We also identified dozens of ampliconic genes on the sex chromosomes, with several ancestral ones expressed during male meiosis, suggesting selective constraints in pairing the multiple sex chromosomes.</p><p><strong>Conclusion: </strong>The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11710854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947512","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":"IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning","authors":"Hengchuang Yin, Shufang Wu, Jie Tan, Qian Guo, Mo Li, Jinyuan Guo, Yaqi Wang, Xiaoqing Jiang, Huaiqiu Zhu","doi":"10.1093/gigascience/giae018","DOIUrl":"https://doi.org/10.1093/gigascience/giae018","url":null,"abstract":"Background The virome obtained through virus-like particle enrichment contains a mixture of prokaryotic and eukaryotic virus-derived fragments. Accurate identification and classification of these elements are crucial to understanding their roles and functions in microbial communities. However, the rapid mutation rates of viral genomes pose challenges in developing high-performance tools for classification, potentially limiting downstream analyses. Findings We present IPEV, a novel method to distinguish prokaryotic and eukaryotic viruses in viromes, with a 2-dimensional convolutional neural network combining trinucleotide pair relative distance and frequency. Cross-validation assessments of IPEV demonstrate its state-of-the-art precision, significantly improving the F1-score by approximately 22% on an independent test set compared to existing methods when query viruses share less than 30% sequence similarity with known viruses. Furthermore, IPEV outperforms other methods in accuracy on marine and gut virome samples based on annotations by sequence alignments. IPEV reduces runtime by at most 1,225 times compared to existing methods under the same computing configuration. We also utilized IPEV to analyze longitudinal samples and found that the gut virome exhibits a higher degree of temporal stability than previously observed in persistent personal viromes, providing novel insights into the resilience of the gut virome in individuals. Conclusions IPEV is a high-performance, user-friendly tool that assists biologists in identifying and classifying prokaryotic and eukaryotic viruses within viromes. The tool is available at https://github.com/basehc/IPEV.","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"46 1","pages":""},"PeriodicalIF":9.2,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140804753","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}