{"id":311449,"date":"2025-08-02T08:27:15","date_gmt":"2025-08-02T08:27:15","guid":{"rendered":"https:\/\/www.europesays.com\/uk\/311449\/"},"modified":"2025-08-02T08:27:15","modified_gmt":"2025-08-02T08:27:15","slug":"how-new-genes-help-peaches-evolve-the-secret-inside-their-dna-2","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/uk\/311449\/","title":{"rendered":"How new genes help peaches evolve: the secret inside their DNA"},"content":{"rendered":"

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\"Identification<\/p>\n

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image:\u00a0<\/p>\n

Identification of recently emerged\u00a0de novo\u00a0genes during diversification in the genus\u00a0Prunus. (A) Through BLAT searches of\u00a0P. persica \u201cbaifeng\u201d\u00a0against sibling\u00a0Prunus\u00a0species, 178\u00a0De novo\u00a0genes were determined in\u00a0P. persica \u201cbaifeng\u201d.\u00a0Three cultivars,\u00a0P. persica\u00a0\u201cCN14\u201d,\u00a0P. persica\u00a0\u201cBatsch\u201d and\u00a0P. persica\u00a0\u201cChinese Cling\u201d, and three wild relatives,\u00a0P. ferganensis,\u00a0P. davidiana, and\u00a0P. kansuensis, were referred to as an in-group, while\u00a0P. mira\u00a0and\u00a0P. dulcis\u00a0were defined as an out-group. (B) Three types of\u00a0de novo\u00a0genes are shown in the diagram.<\/p>\n

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\n view more\u00a0<\/a><\/p>\n

Credit: Horticulture Research<\/p>\n

A new genomic study has uncovered 178 de novo genes in peach that originated from previously noncoding DNA regions. Unlike conserved genes inherited across species, these de novo genes have evolved from scratch and were found to integrate into existing regulatory networks. Many of these genes are expressed in reproductive tissues and contribute to important biological functions such as plastid modification and developmental regulation. This research provides new insight into how novel genes can arise, diversify, and become essential parts of plant growth and evolution, offering a framework for future exploration of gene innovation across related species.<\/p>\n

The emergence of new genes plays a critical role in driving species-specific traits and adaptive evolution. While gene duplication and fusion are well-known mechanisms, de novo gene birth\u2014where functional genes evolve from noncoding sequences\u2014is gaining recognition for its contribution to genetic novelty. These genes often have short lengths, low expression levels, and unique sequences, making them challenging to detect. Identifying them requires high-quality genome assemblies and comparative analysis with closely related species. Understanding their characteristics and integration into regulatory systems is essential for deciphering how new traits and functions evolve. Due to these challenges, deeper investigation into de novo genes is urgently needed.<\/p>\n

Researchers from the Wuhan Botanical Garden of the Chinese Academy of Sciences and collaborating institutions published a new study (DOI: 10.1093\/hr\/uhae252)<\/a> on September 5, 2024, in Horticulture Research<\/a>. The study identified 178 de novo genes in Prunus persica \u2018baifeng\u2019 by comparing its genome to those of related Prunus species. Transcriptome analysis confirmed that 158 of these genes are actively expressed in various tissues. The findings shed light on how de novo genes integrate into plant regulatory networks and influence key processes such as growth, reproduction, and stress response.<\/p>\n

The team used transcriptome sequencing and comparative genomics to identify de novo genes\u2014those without orthologs in related species\u2014that have emerged uniquely in peach. Out of 178 candidates, 158 genes were confirmed to be expressed in at least one tissue. These de novo genes showed distinct structural features compared to conserved genes: they were shorter, had fewer exons, and exhibited lower GC content and expression levels. Based on origin, they were divided into two types: Type I genes arose entirely from noncoding sequences and are enriched in plastid-related functions; Type II genes incorporated fragments of existing genes and were associated with development.<\/p>\n

Gene ontology enrichment, cis-regulatory binding site analysis, and co-expression network mapping revealed that many de novo genes functionally integrate into the peach regulatory framework. Notably, some were co-expressed with conserved genes involved in stress response and development, and 25 were located within QTLs or MTLs associated with agronomic traits. This suggests that de novo genes are not only expressed but also biologically relevant, contributing to phenotypic variation and adaptive evolution in peach.<\/p>\n

\u201cOur study demonstrates that de novo genes, once considered genetic noise, are in fact critical players in plant biology,\u201d said Dr. Yuepeng Han, senior author of the study. \u201cBy mapping their origin and function in peach, we show that these genes can quickly integrate into existing networks and potentially regulate key developmental traits. This research provides a template for exploring de novo gene evolution in other crops and highlights the dynamic nature of plant genomes.\u201d<\/p>\n

This research marks the first comprehensive identification of de novo genes in peach and opens new avenues for crop improvement and evolutionary biology. By linking novel genes to regulatory pathways and agronomic traits such as fruit quality and stress tolerance, breeders may one day harness de novo genes for targeted breeding. Moreover, the findings contribute to our understanding of how plant genomes evolve new functions, offering valuable insights into the molecular basis of phenotypic diversity and adaptation across fruit species. Continued exploration could also reveal how these genes influence unique peach traits not seen in other Prunus relatives.<\/p>\n

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References<\/p>\n

DOI<\/strong><\/p>\n

10.1093\/hr\/uhae252<\/a><\/p>\n

Original Source URL<\/strong><\/p>\n

https:\/\/doi.org\/10.1093\/hr\/uhae252<\/a><\/p>\n

Funding information<\/strong><\/p>\n

This research was funded by the National Natural Science Foundation of China (Grant No. U23A20206 and Grant No. 32201602), the Natural Science Fund of Hubei Province (Grant No. 2023AFB1036 and Grant No. 2022CFB932), the Beijing Life Science Academy Project (Grant No. 2023200CC0270), the Key Special Project of Intergovernmental International Cooperation of the National Key R&D Program of China (Grant No. 2023YFE0125100), the Knowledge Innovation Program of Wuhan Basic Research (Grant No. 2022020801010167), and the China Agriculture Research System (Grant No. CARS-30).<\/p>\n

About Horticulture Research <\/a><\/strong><\/p>\n

Horticulture Research <\/a>is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports \u2122 from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.<\/p>\n

Journal<\/p>\n

Horticulture Research<\/p>\n

Subject of Research<\/p>\n

Not applicable<\/p>\n

Article Title<\/p>\n

De novo gene integration into regulatory networks via interaction with conserved genes in peach<\/p>\n

Article Publication Date<\/p>\n

5-Sep-2024<\/p>\n

COI Statement<\/p>\n

The authors declare that they have no competing interests.<\/p>\n

Disclaimer:<\/strong> AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.<\/p>\n","protected":false},"excerpt":{"rendered":"image:\u00a0 Identification of recently emerged\u00a0de novo\u00a0genes during diversification in the genus\u00a0Prunus. (A) Through BLAT searches of\u00a0P. persica \u201cbaifeng\u201d\u00a0against…\n","protected":false},"author":2,"featured_media":311450,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3846],"tags":[267,70,16,15],"class_list":{"0":"post-311449","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-genetics","8":"tag-genetics","9":"tag-science","10":"tag-uk","11":"tag-united-kingdom"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@uk\/114958227733873299","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/311449","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/comments?post=311449"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/311449\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media\/311450"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media?parent=311449"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/categories?post=311449"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/tags?post=311449"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}