Rosaceae phylogenomic studies provide insights into the evolution of new genes

Jiang, Lan; Li, Xiaoxu; Lyu, Kun; Wang, Han; Li, Zhiyuan; Qi, Wang; Zhang, Lin; Cao, Yunpeng

doi:10.1016/j.hpj.2024.02.002

Horticultural Plant Journal

2024

DOI: 10.1016/j.hpj.2024.02.002

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Rosaceae phylogenomic studies provide insights into the evolution of new genes

Lan Jiang,

Xiaoxu Li,

Kun Lyu

et al.

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Cited by 5 publications

References 114 publications

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VfLRR-RLK1 benefiting resistance to Fusarium oxysporum reveals infection and defense mechanisms in tung tree

Wu,

Mo,

et al. 2024

Physiol Mol Biol Plants

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VfLRR-RLK1 benefiting resistance to Fusarium oxysporum reveals infection and defense mechanisms in tung tree

Wu,

Mo,

et al. 2024

Physiol Mol Biol Plants

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Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation

Ding,

Hu,

Cao

et al. 2024

Horticultural Plant Journal

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De novo gene integration into regulatory networks via interaction with conserved genes in peach

Cao,

Hong,

Zhao

et al. 2024

Horticulture Research

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De novo genes can evolve “from scratch” from noncoding sequences, acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits. However, identifying de novo genes is challenging, as it requires high-quality genomes from closely related species. According to the comparison with nine closely related Prunus genomes, we determined at least 178 de novo genes in P. persica “baifeng”. The distinct differences were observed between de novo and conserved genes in gene characteristics and expression patterns. Gene ontology enrichment analysis suggested that Type I de novo genes originated from sequences related to plastid modification functions, while Type II genes were inferred to have derived from sequences related to reproductive functions. Finally, transcriptome sequencing across different tissues and developmental stages suggested that de novo genes have been evolutionarily recruited into existing regulatory networks, playing important roles in plant growth and development, which was also supported by WGCNA analysis and quantitative trait loci data. This study lays the groundwork for future research on the origins and functions of genes in Prunus and related taxa.

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Rosaceae phylogenomic studies provide insights into the evolution of new genes

Cited by 5 publications

References 114 publications

VfLRR-RLK1 benefiting resistance to Fusarium oxysporum reveals infection and defense mechanisms in tung tree

VfLRR-RLK1 benefiting resistance to Fusarium oxysporum reveals infection and defense mechanisms in tung tree

Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation

De novo gene integration into regulatory networks via interaction with conserved genes in peach

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