Plant Pan-Genomics: Opportunities, Advances, and Challenges | Journal of Data Science and Intelligent Systems

<!DOCTYPE html> <html lang="en" xml:lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title> Plant Pan-Genomics: Opportunities, Advances, and Challenges | Journal of Data Science and Intelligent Systems </title> <link rel="icon" href="https://ojs.bonviewpress.com/public/journals/7/favicon_en_US.png"> <meta name="generator" content="Open Journal Systems 3.4.0.7"> <meta name="gs_meta_revision" content="1.1"/> <meta name="citation_journal_title" content="Journal of Data Science and Intelligent Systems"/> <meta name="citation_journal_abbrev" content="JDSIS"/> <meta name="citation_issn" content="2972-3841"/> <meta name="citation_author" content="Mingjun Hou"/> <meta name="citation_author_institution" content="College of Life Science, Northeast Forestry University, China"/> <meta name="citation_author" content="Shaozi Pang"/> <meta name="citation_author_institution" content="College of Life Science, Northeast Forestry University, China"/> <meta name="citation_title" content="Plant Pan-Genomics: Opportunities, Advances, and Challenges"/> <meta name="citation_language" content="en"/> <meta name="citation_date" content="2024/06/13"/> <meta name="citation_doi" content="10.47852/bonviewJDSIS42023107"/> <meta name="citation_abstract_html_url" content="https://ojs.bonviewpress.com/index.php/jdsis/article/view/3107"/> <meta name="citation_abstract" xml:lang="en" content="The pan-genome concept encompasses all individual genome sequences within a species, comprising both core and variable genes. In recent years, it has emerged as a promising avenue for advancing plant genetic evolution and cultivating desirable traits. This review delves into the methodologies for constructing the pan-genome, encompassing various assembly techniques and strategies for representing this data in graphical or linear formats. Emphasis is placed on the critical aspects of high-quality genome assembly, precise annotation, homologous gene identification, and judicious sample selection in pan-genome analysis. Furthermore, we investigate the pan genome's applications in plant genomics, particularly in elucidating genetic transformations during domestication, uncovering genetic variations linked to agronomic traits, and offering insights to guide breeding endeavors. 聽 Received: 14 April 2024聽| Revised: 13 May 2024| Accepted: 4 June 2024 聽 Conflicts of Interest The authors declare that they have no conflicts of interest to this work. 聽 Data Availability Statement Data sharing is not applicable to this article as no new data were created or analyzed in this study. 聽 Author Contribution Statement Mingjun Hou: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing - original draft, Writing - review &amp; editing, Visualization, Supervision, Project administration. Shaozi Pang: Writing - review &amp; editing, Visualization, Supervision."/> <meta name="citation_keywords" xml:lang="en" content="pan-genomics"/> <meta name="citation_keywords" xml:lang="en" content="crop breeding"/> <meta name="citation_keywords" xml:lang="en" content="core genes"/> <meta name="citation_keywords" xml:lang="en" content="variable genes"/> <meta name="citation_pdf_url" content="https://ojs.bonviewpress.com/index.php/jdsis/article/download/3107/973"/> <link rel="schema.DC" href="http://purl.org/dc/elements/1.1/" /> <meta name="DC.Creator.PersonalName" content="Mingjun Hou"/> <meta name="DC.Creator.PersonalName" content="Shaozi Pang"/> <meta name="DC.Date.created" scheme="ISO8601" content="2024-06-13"/> <meta name="DC.Date.dateSubmitted" scheme="ISO8601" content="2024-04-14"/> <meta name="DC.Date.issued" scheme="ISO8601" content="2022-12-09"/> <meta name="DC.Date.modified" scheme="ISO8601" content="2024-11-05"/> <meta name="DC.Description" xml:lang="en" content="The pan-genome concept encompasses all individual genome sequences within a species, comprising both core and variable genes. In recent years, it has emerged as a promising avenue for advancing plant genetic evolution and cultivating desirable traits. This review delves into the methodologies for constructing the pan-genome, encompassing various assembly techniques and strategies for representing this data in graphical or linear formats. Emphasis is placed on the critical aspects of high-quality genome assembly, precise annotation, homologous gene identification, and judicious sample selection in pan-genome analysis. Furthermore, we investigate the pan genome's applications in plant genomics, particularly in elucidating genetic transformations during domestication, uncovering genetic variations linked to agronomic traits, and offering insights to guide breeding endeavors. 聽 Received: 14 April 2024聽| Revised: 13 May 2024| Accepted: 4 June 2024 聽 Conflicts of Interest The authors declare that they have no conflicts of interest to this work. 聽 Data Availability Statement Data sharing is not applicable to this article as no new data were created or analyzed in this study. 聽 Author Contribution Statement Mingjun Hou: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing - original draft, Writing - review &amp; editing, Visualization, Supervision, Project administration. Shaozi Pang: Writing - review &amp; editing, Visualization, Supervision."/> <meta name="DC.Format" scheme="IMT" content="application/pdf"/> <meta name="DC.Identifier" content="3107"/> <meta name="DC.Identifier.DOI" content="10.47852/bonviewJDSIS42023107"/> <meta name="DC.Identifier.URI" content="https://ojs.bonviewpress.com/index.php/jdsis/article/view/3107"/> <meta name="DC.Language" scheme="ISO639-1" content="en"/> <meta name="DC.Rights" content="Copyright (c) 2024 Authors"/> <meta name="DC.Rights" content="https://creativecommons.org/licenses/by/4.0/"/> <meta name="DC.Source" content="Journal of Data Science and Intelligent Systems"/> <meta name="DC.Source.ISSN" content="2972-3841"/> <meta name="DC.Source.URI" content="https://ojs.bonviewpress.com/index.php/jdsis"/> <meta name="DC.Subject" xml:lang="en" content="pan-genomics"/> <meta name="DC.Subject" xml:lang="en" content="crop breeding"/> <meta name="DC.Subject" xml:lang="en" content="core genes"/> <meta name="DC.Subject" 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Plant Pan-Genomics: Opportunities, Advances, and Challenges </h1> <div class="row"> <div class="main_entry"> <section class="item authors"> <h2 class="pkp_screen_reader">Authors</h2> <ul class="authors"> <li> <span class="name"> Mingjun Hou </span> <span class="affiliation"> College of Life Science, Northeast Forestry University, China </span> </li> <li> <span class="name"> Shaozi Pang </span> <span class="affiliation"> College of Life Science, Northeast Forestry University, China </span> </li> </ul> </section> <section class="item doi"> <h2 class="label"> DOI: </h2> <span class="value"> <a href="https://doi.org/10.47852/bonviewJDSIS42023107"> https://doi.org/10.47852/bonviewJDSIS42023107 </a> </span> </section> <section class="item keywords"> <h2 class="label"> Keywords: </h2> <span class="value"> pan-genomics, crop breeding, core genes, variable genes </span> </section> <section class="item abstract"> <h2 class="label">Abstract</h2> <p>The pan-genome concept encompasses all individual genome sequences within a species, comprising both core and variable genes. In recent years, it has emerged as a promising avenue for advancing plant genetic evolution and cultivating desirable traits. This review delves into the methodologies for constructing the pan-genome, encompassing various assembly techniques and strategies for representing this data in graphical or linear formats. Emphasis is placed on the critical aspects of high-quality genome assembly, precise annotation, homologous gene identification, and judicious sample selection in pan-genome analysis. Furthermore, we investigate the pan genome's applications in plant genomics, particularly in elucidating genetic transformations during domestication, uncovering genetic variations linked to agronomic traits, and offering insights to guide breeding endeavors.</p> <p>聽</p> <p><strong>Received: </strong>14 April 2024聽<strong>| Revised: </strong>13 May 2024<strong>| Accepted:</strong> 4 June 2024</p> <p>聽</p> <p><strong>Conflicts of Interest</strong></p> <p>The authors declare that they have no conflicts of interest to this work.</p> <p>聽</p> <p><strong>Data Availability Statement</strong></p> <p>Data sharing is not applicable to this article as no new data were created or analyzed in this study.</p> <p>聽</p> <p><strong>Author Contribution Statement</strong></p> <p><strong>Mingjun Hou: </strong>Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing - original draft, Writing - review & editing, Visualization, Supervision, Project administration. <strong>Shaozi Pang:</strong> Writing - review & editing, Visualization, Supervision.</p> </section> <br /><div class="separator"></div><div class="item abstract" id="trendmd-suggestions"></div><script defer src='//js.trendmd.com/trendmd.min.js' data-trendmdconfig='{"website_id":"89269", "element":"#trendmd-suggestions"}'></script> </div> <div class="entry_details"> <div class="item cover_image"> <div class="sub_item"> <a href="https://ojs.bonviewpress.com/index.php/jdsis/issue/view/onlinefirst"> <img src="https://ojs.bonviewpress.com/public/journals/7/cover_issue_29_en_US.png" alt=""> </a> </div> </div> <div class="item galleys"> <h2 class="pkp_screen_reader"> Downloads </h2> <ul class="value galleys_links"> <li> <a class="obj_galley_link pdf" href="https://ojs.bonviewpress.com/index.php/jdsis/article/view/3107/973"> PDF </a> </li> </ul> </div> <div class="item published"> <section class="sub_item"> <h2 class="label"> Published </h2> <div class="value"> <span>2024-06-13</span> </div> </section> </div> <div class="item issue"> <section class="sub_item"> <h2 class="label"> Issue </h2> <div class="value"> <a class="title" href="https://ojs.bonviewpress.com/index.php/jdsis/issue/view/onlinefirst"> Online First </a> </div> </section> <section class="sub_item"> <h2 class="label"> Section </h2> <div class="value"> Review </div> </section> </div> <div class="item copyright"> <h2 class="label"> License </h2> <p>Copyright (c) 2024 Authors</p> <a rel="license" href="https://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" src="//i.creativecommons.org/l/by/4.0/88x31.png" /></a><p>This work is licensed under a <a rel="license" href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p> </div> <div class="item citation"> <section class="sub_item citation_display"> <h2 class="label"> How to Cite </h2> <div class="value"> <div id="citationOutput" role="region" aria-live="polite"> <div class="csl-bib-body"> <div class="csl-entry">Hou, M., & Pang, S. 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