GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae024
Justin Chu, Jiazhen Rong, Xiaowen Feng, Heng Li
{"title":"ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection.","authors":"Justin Chu, Jiazhen Rong, Xiaowen Feng, Heng Li","doi":"10.1093/gigascience/giae024","DOIUrl":"10.1093/gigascience/giae024","url":null,"abstract":"<p><strong>Background: </strong>Due to human error, sample swapping in large cohort studies with heterogeneous data types (e.g., mix of Oxford Nanopore Technologies, Pacific Bioscience, Illumina data, etc.) remains a common issue plaguing large-scale studies. At present, all sample swapping detection methods require costly and unnecessary (e.g., if data are only used for genome assembly) alignment, positional sorting, and indexing of the data in order to compare similarly. As studies include more samples and new sequencing data types, robust quality control tools will become increasingly important.</p><p><strong>Findings: </strong>The similarity between samples can be determined using indexed k-mer sequence variants. To increase statistical power, we use coverage information on variant sites, calculating similarity using a likelihood ratio-based test. Per sample error rate, and coverage bias (i.e., missing sites) can also be estimated with this information, which can be used to determine if a spatially indexed principal component analysis (PCA)-based prescreening method can be used, which can greatly speed up analysis by preventing exhaustive all-to-all comparisons.</p><p><strong>Conclusions: </strong>Because this tool processes raw data, is faster than alignment, and can be used on very low-coverage data, it can save an immense degree of computational resources in standard quality control (QC) pipelines. It is robust enough to be used on different sequencing data types, important in studies that leverage the strengths of different sequencing technologies. In addition to its primary use case of sample swap detection, this method also provides information useful in QC, such as error rate and coverage bias, as well as population-level PCA ancestry analysis visualization.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11148594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237337","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae053
Paulene S Pineda, Ester B Flores, Lilian P Villamor, Connie Joyce M Parac, Mehar S Khatkar, Hien To Thu, Timothy P L Smith, Benjamin D Rosen, Paolo Ajmone-Marsan, Licia Colli, John L Williams, Wai Yee Low
{"title":"Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project.","authors":"Paulene S Pineda, Ester B Flores, Lilian P Villamor, Connie Joyce M Parac, Mehar S Khatkar, Hien To Thu, Timothy P L Smith, Benjamin D Rosen, Paolo Ajmone-Marsan, Licia Colli, John L Williams, Wai Yee Low","doi":"10.1093/gigascience/giae053","DOIUrl":"10.1093/gigascience/giae053","url":null,"abstract":"<p><p>More people in the world depend on water buffalo for their livelihoods than on any other domesticated animals, but its genetics is still not extensively explored. The 1000 Buffalo Genomes Project (1000BGP) provides genetic resources for global buffalo population study and tools to breed more sustainable and productive buffaloes. Here we report the most contiguous swamp buffalo genome assembly (PCC_UOA_SB_1v2) with substantial resolution of telomeric and centromeric repeats, ∼4-fold more contiguous than the existing reference river buffalo assembly and exceeding a recently published male swamp buffalo genome. This assembly was used along with the current reference to align 140 water buffalo short-read sequences and produce a public genetic resource with an average of ∼41 million single nucleotide polymorphisms per swamp and river buffalo genome. Comparison of the swamp and river buffalo sequences showed ∼1.5% genetic differences, and estimated divergence time occurred 3.1 million years ago (95% CI, 2.6-4.9). The open science model employed in the 1000BGP provides a key genomic resource and tools for a species with global economic relevance.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11382405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153663","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae079
Niklas Birth, Nicolina Leppich, Julia Schirmacher, Nina Andreae, Rasmus Steinkamp, Matthias Blanke, Peter Meinicke
{"title":"CoCoPyE: feature engineering for learning and prediction of genome quality indices.","authors":"Niklas Birth, Nicolina Leppich, Julia Schirmacher, Nina Andreae, Rasmus Steinkamp, Matthias Blanke, Peter Meinicke","doi":"10.1093/gigascience/giae079","DOIUrl":"https://doi.org/10.1093/gigascience/giae079","url":null,"abstract":"<p><strong>Background: </strong>The exploration of the microbial world has been greatly advanced by the reconstruction of genomes from metagenomic sequence data. However, the rapidly increasing number of metagenome-assembled genomes has also resulted in a wide variation in data quality. It is therefore essential to quantify the achieved completeness and possible contamination of a reconstructed genome before it is used in subsequent analyses. The classical approach for the estimation of quality indices solely relies on a relatively small number of universal single-copy genes. Recent tools try to extend the genomic coverage of estimates for an increased accuracy.</p><p><strong>Results: </strong>We developed CoCoPyE, a fast tool based on a novel 2-stage feature extraction and transformation scheme. First, it identifies genomic markers and then refines the marker-based estimates with a machine learning approach. In our simulation studies, CoCoPyE showed a more accurate prediction of quality indices than the existing tools. While the CoCoPyE web server offers an easy way to try out the tool, the freely available Python implementation enables integration into existing genome reconstruction pipelines.</p><p><strong>Conclusions: </strong>CoCoPyE provides a new approach to assess the quality of genome data. It complements and improves existing tools and may help researchers to better distinguish between low-quality draft and high-quality genome assemblies in metagenome sequencing projects.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498590","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae004
Ye Xu, Ling Ma, Shanlin Liu, Yanxin Liang, Qiaoqiao Liu, Zhixin He, Li Tian, Yuange Duan, Wanzhi Cai, Hu Li, Fan Song
{"title":"Chromosome-level genome of the poultry shaft louse Menopon gallinae provides insight into the host-switching and adaptive evolution of parasitic lice.","authors":"Ye Xu, Ling Ma, Shanlin Liu, Yanxin Liang, Qiaoqiao Liu, Zhixin He, Li Tian, Yuange Duan, Wanzhi Cai, Hu Li, Fan Song","doi":"10.1093/gigascience/giae004","DOIUrl":"10.1093/gigascience/giae004","url":null,"abstract":"<p><strong>Background: </strong>Lice (Psocodea: Phthiraptera) are one important group of parasites that infects birds and mammals. It is believed that the ancestor of parasitic lice originated on the ancient avian host, and ancient mammals acquired these parasites via host-switching from birds. Here we present the first chromosome-level genome of Menopon gallinae in Amblycera (earliest diverging lineage of parasitic lice). We explore the transition of louse host-switching from birds to mammals at the genomic level by identifying numerous idiosyncratic genomic variations.</p><p><strong>Results: </strong>The assembled genome is 155 Mb in length, with a contig N50 of 27.42 Mb. Hi-C scaffolding assigned 97% of the bases to 5 chromosomes. The genome of M. gallinae retains a basal insect repertoire of 11,950 protein-coding genes. By comparing the genomes of lice to those of multiple representative insects in other orders, we discovered that gene families of digestion, detoxification, and immunity-related are generally conserved between bird lice and mammal lice, while mammal lice have undergone a significant reduction in genes related to chemosensory systems and temperature. This suggests that mammal lice have lost some of these genes through the adaption to environment and temperatures after host-switching. Furthermore, 7 genes related to hematophagy were positively selected in mammal lice, suggesting their involvement in the hematophagous behavior.</p><p><strong>Conclusions: </strong>Our high-quality genome of M. gallinae provides a valuable resource for comparative genomic research in Phthiraptera and facilitates further studies on adaptive evolution of host-switching within parasitic lice.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 1","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10904027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139899653","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae007
Filipi Miranda Soares, Luís Ferreira Pires, Maria Carolina Garcia, Yamine Bouzembrak, Lidio Coradin, Natalia Pirani Ghilardi-Lopes, Rubens Rangel Silva, Aline Martins de Carvalho, Benildes Coura Moreira Dos Santos Maculan, Sheina Koffler, Uiara Bandineli Montedo, Debora Pignatari Drucker, Raquel Santiago, Anand Gavai, Maria Clara Peres de Carvalho, Ana Carolina da Silva Lima, Hillary Dandara Elias Gabriel, Stephanie Gabriele Mendonça de França, Karoline Reis de Almeida, Bárbara Junqueira Dos Santos, Antonio Mauro Saraiva
{"title":"Leveraging citizen science for monitoring urban forageable plants.","authors":"Filipi Miranda Soares, Luís Ferreira Pires, Maria Carolina Garcia, Yamine Bouzembrak, Lidio Coradin, Natalia Pirani Ghilardi-Lopes, Rubens Rangel Silva, Aline Martins de Carvalho, Benildes Coura Moreira Dos Santos Maculan, Sheina Koffler, Uiara Bandineli Montedo, Debora Pignatari Drucker, Raquel Santiago, Anand Gavai, Maria Clara Peres de Carvalho, Ana Carolina da Silva Lima, Hillary Dandara Elias Gabriel, Stephanie Gabriele Mendonça de França, Karoline Reis de Almeida, Bárbara Junqueira Dos Santos, Antonio Mauro Saraiva","doi":"10.1093/gigascience/giae007","DOIUrl":"10.1093/gigascience/giae007","url":null,"abstract":"<p><p>Urbanization brings forth social challenges in emerging countries such as Brazil, encompassing food scarcity, health deterioration, air pollution, and biodiversity loss. Despite this, urban areas like the city of São Paulo still boast ample green spaces, offering opportunities for nature appreciation and conservation, enhancing city resilience and livability. Citizen science is a collaborative endeavor between professional scientists and nonprofessional scientists in scientific research that may help to understand the dynamics of urban ecosystems. We believe citizen science has the potential to promote human and nature connection in urban areas and provide useful data on urban biodiversity.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10914215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039095","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae013
Anish M S Shrestha, Mark Edward M Gonzales, Phoebe Clare L Ong, Pierre Larmande, Hyun-Sook Lee, Ji-Ung Jeung, Ajay Kohli, Dmytro Chebotarov, Ramil P Mauleon, Jae-Sung Lee, Kenneth L McNally
{"title":"RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.","authors":"Anish M S Shrestha, Mark Edward M Gonzales, Phoebe Clare L Ong, Pierre Larmande, Hyun-Sook Lee, Ji-Ung Jeung, Ajay Kohli, Dmytro Chebotarov, Ramil P Mauleon, Jae-Sung Lee, Kenneth L McNally","doi":"10.1093/gigascience/giae013","DOIUrl":"10.1093/gigascience/giae013","url":null,"abstract":"<p><strong>Background: </strong>As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources.</p><p><strong>Results: </strong>We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs.</p><p><strong>Conclusions: </strong>RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11148593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237423","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae022
Teresa Müller, Stefan Mautner, Pavankumar Videm, Florian Eggenhofer, Martin Raden, Rolf Backofen
{"title":"CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites.","authors":"Teresa Müller, Stefan Mautner, Pavankumar Videm, Florian Eggenhofer, Martin Raden, Rolf Backofen","doi":"10.1093/gigascience/giae022","DOIUrl":"10.1093/gigascience/giae022","url":null,"abstract":"<p><strong>Background: </strong>RNA-RNA interactions are key to a wide range of cellular functions. The detection of potential interactions helps to understand the underlying processes. However, potential interactions identified via in silico or experimental high-throughput methods can lack precision because of a high false-positive rate.</p><p><strong>Results: </strong>We present CheRRI, the first tool to evaluate the biological relevance of putative RNA-RNA interaction sites. CheRRI filters candidates via a machine learning-based model trained on experimental RNA-RNA interactome data. Its unique setup combines interactome data and an established thermodynamic prediction tool to integrate experimental data with state-of-the-art computational models. Applying these data to an automated machine learning approach provides the opportunity to not only filter data for potential false positives but also tailor the underlying interaction site model to specific needs.</p><p><strong>Conclusions: </strong>CheRRI is a stand-alone postprocessing tool to filter either predicted or experimentally identified potential RNA-RNA interactions on a genomic level to enhance the quality of interaction candidates. It is easy to install (via conda, pip packages), use (via Galaxy), and integrate into existing RNA-RNA interaction pipelines.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11152173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261603","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae074
Jinxin Zhao, Jiru Han, Yu-Wei Lin, Yan Zhu, Michael Aichem, Dimitar Garkov, Phillip J Bergen, Sue C Nang, Jian-Zhong Ye, Tieli Zhou, Tony Velkov, Jiangning Song, Falk Schreiber, Jian Li
{"title":"PhageGE: an interactive web platform for exploratory analysis and visualization of bacteriophage genomes.","authors":"Jinxin Zhao, Jiru Han, Yu-Wei Lin, Yan Zhu, Michael Aichem, Dimitar Garkov, Phillip J Bergen, Sue C Nang, Jian-Zhong Ye, Tieli Zhou, Tony Velkov, Jiangning Song, Falk Schreiber, Jian Li","doi":"10.1093/gigascience/giae074","DOIUrl":"10.1093/gigascience/giae074","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance is a serious threat to global health. Due to the stagnant antibiotic discovery pipeline, bacteriophages (phages) have been proposed as an alternative therapy for the treatment of infections caused by multidrug-resistant pathogens. Genomic features play an important role in phage pharmacology. However, our knowledge of phage genomics is sparse, and the use of existing bioinformatic pipelines and tools requires considerable bioinformatic expertise. These challenges have substantially limited the clinical translation of phage therapy.</p><p><strong>Findings: </strong>We have developed PhageGE (Phage Genome Explorer), a user-friendly graphical interface application for the interactive analysis of phage genomes. PhageGE enables users to perform key analyses, including phylogenetic analysis, visualization of phylogenetic trees, prediction of phage life cycle, and comparative analysis of phage genome annotations. The new R Shiny web server, PhageGE, integrates existing R packages and combines them with several newly developed functions to facilitate these analyses. Additionally, the web server provides interactive visualization capabilities and allows users to directly export publication-quality images.</p><p><strong>Conclusions: </strong>PhageGE is a valuable tool that simplifies the analysis of phage genome data and may expedite the development and clinical translation of phage therapy. PhageGE is publicly available at https://jason-zhao.shinyapps.io/PhageGE_Update/.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11423353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344887","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae027
Rafael Moysés Alves, Vinicius A C de Abreu, Rafaely Pantoja Oliveira, João Victor Dos Anjos Almeida, Mauro de Medeiros de Oliveira, Saura R Silva, Alexandre R Paschoal, Sintia S de Almeida, Pedro A F de Souza, Jesus A Ferro, Vitor F O Miranda, Antonio Figueira, Douglas S Domingues, Alessandro M Varani
{"title":"Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation.","authors":"Rafael Moysés Alves, Vinicius A C de Abreu, Rafaely Pantoja Oliveira, João Victor Dos Anjos Almeida, Mauro de Medeiros de Oliveira, Saura R Silva, Alexandre R Paschoal, Sintia S de Almeida, Pedro A F de Souza, Jesus A Ferro, Vitor F O Miranda, Antonio Figueira, Douglas S Domingues, Alessandro M Varani","doi":"10.1093/gigascience/giae027","DOIUrl":"10.1093/gigascience/giae027","url":null,"abstract":"<p><strong>Background: </strong>Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family.</p><p><strong>Findings: </strong>The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species.</p><p><strong>Conclusions: </strong>The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11152179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261605","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}
GigaSciencePub Date : 2024-01-02DOI: 10.1093/gigascience/giae049
Christian Gaser, Robert Dahnke, Paul M Thompson, Florian Kurth, Eileen Luders, The Alzheimer's Disease Neuroimaging Initiative
{"title":"CAT: a computational anatomy toolbox for the analysis of structural MRI data.","authors":"Christian Gaser, Robert Dahnke, Paul M Thompson, Florian Kurth, Eileen Luders, The Alzheimer's Disease Neuroimaging Initiative","doi":"10.1093/gigascience/giae049","DOIUrl":"10.1093/gigascience/giae049","url":null,"abstract":"<p><p>A large range of sophisticated brain image analysis tools have been developed by the neuroscience community, greatly advancing the field of human brain mapping. Here we introduce the Computational Anatomy Toolbox (CAT)-a powerful suite of tools for brain morphometric analyses with an intuitive graphical user interface but also usable as a shell script. CAT is suitable for beginners, casual users, experts, and developers alike, providing a comprehensive set of analysis options, workflows, and integrated pipelines. The available analysis streams-illustrated on an example dataset-allow for voxel-based, surface-based, and region-based morphometric analyses. Notably, CAT incorporates multiple quality control options and covers the entire analysis workflow, including the preprocessing of cross-sectional and longitudinal data, statistical analysis, and the visualization of results. The overarching aim of this article is to provide a complete description and evaluation of CAT while offering a citable standard for the neuroscience community.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141893242","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}