GigaScience最新文献

{"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":"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":"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":"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":"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":"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}

{"title":"Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants","authors":"Yiyan Yang, Keith Dufault-Thompson, Wei Yan, Tian Cai, Lei Xie, Xiaofang Jiang","doi":"10.1093/gigascience/giae017","DOIUrl":"https://doi.org/10.1093/gigascience/giae017","url":null,"abstract":"Background Phage therapy, reemerging as a promising approach to counter antimicrobial-resistant infections, relies on a comprehensive understanding of the specificity of individual phages. Yet the significant diversity within phage populations presents a considerable challenge. Currently, there is a notable lack of tools designed for large-scale characterization of phage receptor-binding proteins, which are crucial in determining the phage host range. Results In this study, we present SpikeHunter, a deep learning method based on the ESM-2 protein language model. With SpikeHunter, we identified 231,965 diverse phage-encoded tailspike proteins, a crucial determinant of phage specificity that targets bacterial polysaccharide receptors, across 787,566 bacterial genomes from 5 virulent, antibiotic-resistant pathogens. Notably, 86.60% (143,200) of these proteins exhibited strong associations with specific bacterial polysaccharides. We discovered that phages with identical tailspike proteins can infect different bacterial species with similar polysaccharide receptors, underscoring the pivotal role of tailspike proteins in determining host range. The specificity is mainly attributed to the protein’s C-terminal domain, which strictly correlates with host specificity during domain swapping in tailspike proteins. Importantly, our dataset-driven predictions of phage–host specificity closely match the phage–host pairs observed in real-world phage therapy cases we studied. Conclusions Our research provides a rich resource, including both the method and a database derived from a large-scale genomics survey. This substantially enhances understanding of phage specificity determinants at the strain level and offers a valuable framework for guiding phage selection in therapeutic applications.","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"41 1","pages":""},"PeriodicalIF":9.2,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140804820","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":"An effective strategy for assembling the sex-limited chromosome","authors":"Xiao-Bo Wang, Hong-Wei Lu, Qing-You Liu, A-Lun Li, Hong-Ling Zhou, Yong Zhang, Tian-Qi Zhu, Jue Ruan","doi":"10.1093/gigascience/giae015","DOIUrl":"https://doi.org/10.1093/gigascience/giae015","url":null,"abstract":"Background Most currently available reference genomes lack the sequence map of sex-limited (such as Y and W) chromosomes, which results in incomplete assemblies that hinder further research on sex chromosomes. Recent advancements in long-read sequencing and population sequencing have provided the opportunity to assemble sex-limited chromosomes without the traditional complicated experimental efforts. Findings We introduce the first computational method, Sorting long Reads of Y or other sex-limited chromosome (SRY), which achieves improved assembly results compared to flow sorting. Specifically, SRY outperforms in the heterochromatic region and demonstrates comparable performance in other regions. Furthermore, SRY enhances the capabilities of the hybrid assembly software, resulting in improved continuity and accuracy. Conclusions Our method enables true complete genome assembly and facilitates downstream research of sex-limited chromosomes.","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"21 1","pages":""},"PeriodicalIF":9.2,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140613961","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":"Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology","authors":"Hamid Beiki, Brenda M Murdoch, Carissa A Park, Chandlar Kern, Denise Kontechy, Gabrielle Becker, Gonzalo Rincon, Honglin Jiang, Huaijun Zhou, Jacob Thorne, James E Koltes, Jennifer J Michal, Kimberly Davenport, Monique Rijnkels, Pablo J Ross, Rui Hu, Sarah Corum, Stephanie McKay, Timothy P L Smith, Wansheng Liu, Wenzhi Ma, Xiaohui Zhang, Xiaoqing Xu, Xuelei Han, Zhihua Jiang, Zhi-Liang Hu, James M Reecy","doi":"10.1093/gigascience/giae019","DOIUrl":"https://doi.org/10.1093/gigascience/giae019","url":null,"abstract":"Background The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues. Results A total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated genes. A median of two 5′ untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as noncoding genes in fetal tissues but as protein-coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available quantitative trait loci data to study tissue–tissue interconnection involved in different traits and construct the first bovine trait similarity network. Conclusions These validated results show significant improvement over current bovine genome annotations.","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"19 1","pages":""},"PeriodicalIF":9.2,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140614176","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":"Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups","authors":"Sungwon Jeon, Hansol Choi, Yeonsu Jeon, Whan-Hyuk Choi, Hyunjoo Choi, Kyungwhan An, Hyojung Ryu, Jihun Bhak, Hyeonjae Lee, Yoonsung Kwon, Sukyeon Ha, Yeo Jin Kim, Asta Blazyte, Changjae Kim, Yeonkyung Kim, Younghui Kang, Yeong Ju Woo, Chanyoung Lee, Jeongwoo Seo, Changhan Yoon, Dan Bolser, Orsolya Biro, Eun-Seok Shin, Byung Chul Kim, Seon-Young Kim, Ji-Hwan Park, Jongbum Jeon, Dooyoung Jung, Semin Lee, Jong Bhak","doi":"10.1093/gigascience/giae014","DOIUrl":"https://doi.org/10.1093/gigascience/giae014","url":null,"abstract":"Background Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole genome–wide association analysis, making it crucial to have genome-to-phenome association information with the largest possible whole genome and matched phenome data to conduct further population-genome studies and develop health care services based on population genomics. Results Here, we present 4,157 whole genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest genomic resource of the Korean Genome Project. It encompasses most of the variants with allele frequency &amp;gt;0.001 in Koreans, indicating that it sufficiently covered most of the common and rare genetic variants with commonly measured phenotypes for Koreans. Korea4K provides 45,537,252 variants, and half of them were not present in Korea1K (1,094 samples). We also identified 1,356 new genotype–phenotype associations that were not found by the Korea1K dataset. Phenomics analyses further revealed 24 significant genetic correlations, 14 pleiotropic associations, and 127 causal relationships based on Mendelian randomization among 37 traits. In addition, the Korea4K imputation reference panel, the largest Korean variants reference to date, showed a superior imputation performance to Korea1K across all allele frequency categories. Conclusions Collectively, Korea4K provides not only the largest Korean genome data but also corresponding health check-up parameters and novel genome–phenome associations. The large-scale pathological whole genome–wide omics data will become a powerful set for genome–phenome level association studies to discover causal markers for the prediction and diagnosis of health conditions in future studies.","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"24 1","pages":""},"PeriodicalIF":9.2,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140614276","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}