Identification, characterization and expression analysis of lineage-specific genes within 'Zhongyoutao 14' peach (Prunus persica)

被引：0
作者：
Wang, Caijuan [1 ]
Feng, Beibei [1 ]
Ding, Yejun [1 ]
Liu, Qinqi [1 ]
Xia, Yukai [1 ]
Zheng, Xianbo [1 ,2 ,3 ]
Lian, Xiaodong [1 ,2 ,3 ]
Wang, Xiaobei [1 ,2 ,3 ]
Hou, Nan [1 ,2 ,3 ]
Wang, Lei [1 ,2 ,3 ]
Zhang, Haipeng [1 ,2 ,3 ]
Feng, Jiancan [1 ,2 ,3 ]
Tan, Bin [1 ,2 ,3 ]
机构：
[1] Henan Agr Univ, Coll Hort, Zhengzhou, Peoples R China
[2] Henan Engn & Technol Ctr Peach Germplasm Innovat &, Zhengzhou, Peoples R China
[3] Int Joint Lab Henan Hort Crop Biol, Zhengzhou, Peoples R China
来源：
GENE | 2025年 / 941卷
基金：
中国国家自然科学基金;
关键词：
Lineage-specific genes; Prunus persica; GA; 3; response; ORPHAN GENES; GENOME; EVOLUTION;
D O I：
10.1016/j.gene.2025.149234
中图分类号：
Q3 [遗传学];
学科分类号：
071007 ; 090102 ;
摘要：
Background: With the development of sequencing technology and the rapid increasing in the number of sequenced genomes, lineage-specific genes (LSGs) have been identified and characterized across various species. Similar to other conserved functional genes, LSGs play a crucial role in biological evolution and development. However, the understanding of LSGs remains limited. This study aims to identify significant gene expression profiles of LSGs in peach, which may contribute to the development of specific tissues and important traits. Methods: Seven peach and 341 exogenous species genomes were used in this study. Firstly, the coding sequences of CN14 peach were compared with other genomes to discover LSGs. Next, the LSGs of CN14 peach were compared with other peach genomes to identify the peach specific genes and orphan genes. Furthermore, the tissue specificity expressed PSGs and orphan genes were identified using transcriptome data. In addition, the genes specific expressed in stem might response to GA3 treatment were identified using RT-qPCR. Result: A total of 74 peach specific genes (PSGs) and 91 Orphan genes were identified. The PSGs and orphan genes had fewer exon numbers, shorter gene lengths and lower molecular weight compared with evolutionarily conserved genes (ECGs). Part of these PSGs and Orphan genes were shown an obvious tissue specificity expression pattern at stem, fruit and flower. Three PSGs and three Orphan genes were identified within the QTLs associated with temperature-sensitive semi-dwarf (TSSD), maturity date (Md), and red flesh around stone (Rfas). Three PSGs and seven Orphan genes were identified in response to GA3, these genes might play important role in stem development of peach. Conclusion: The identification and characterization of PSGs and Orphan genes not only provide valuable peach- specific genetic resources, but also might contribute to peach specific biological process.
引用
收藏
页数：7
相关论文
共 50 条
  • [21] Terpene synthase genes in Melaleuca alternifolia: comparative analysis of lineage-specific subfamily variation within Myrtaceae
    Calvert, Jed
    Baten, Abdul
    Butler, Jakob
    Barkla, Bronwyn
    Shepherd, Mervyn
    PLANT SYSTEMATICS AND EVOLUTION, 2018, 304 (01) : 111 - 121
  • [22] Characterization and expression analysis of AGAMOUS-like, SEEDSTICK-like, and SEPALLATA-like MADS-box genes in peach (Prunus persica) fruit
    Tani, Eleni
    Polidoros, Alexios N.
    Flemetakis, Emmanouil
    Stedel, Catalina
    Kalloniati, Chrissanthi
    Demetriou, Kyproula
    Katinakis, Panagiotis
    Tsaftaris, Athanasios S.
    PLANT PHYSIOLOGY AND BIOCHEMISTRY, 2009, 47 (08) : 690 - 700
  • [23] Isolation, cloning, and expression of five genes related to nitrogen metabolism in peach (Prunus persica L. Batsch)
    Zhang, C. H.
    Zhang, B. B.
    Yu, M. L.
    Ma, R. J.
    Song, Z. Z.
    Korir, N. K.
    JOURNAL OF HORTICULTURAL SCIENCE & BIOTECHNOLOGY, 2016, 91 (05) : 448 - 455
  • [24] Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana
    Lin, Haining
    Moghe, Gaurav
    Ouyang, Shu
    Iezzoni, Amy
    Shiu, Shin-Han
    Gu, Xun
    Buell, C. Robin
    BMC EVOLUTIONARY BIOLOGY, 2010, 10
  • [25] Analysis of expression in the Anopheles gambiae developing testes reveals rapidly evolving lineage-specific genes in mosquitoes
    Krzywinska, Elzbieta
    Krzywinski, Jaroslaw
    BMC GENOMICS, 2009, 10
  • [26] Identification and Characterization of Lineage-Specific Highly Conserved Noncoding Sequences in Mammalian Genomes
    Takahashi, Mahoko
    Saitou, Naruya
    GENOME BIOLOGY AND EVOLUTION, 2012, 4 (05): : 641 - 657
  • [27] A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]
    Wells, Christina E.
    Vendramin, Elisa
    Tarodo, Sergio Jimenez
    Verde, Ignazio
    Bielenberg, Douglas G.
    BMC PLANT BIOLOGY, 2015, 15
  • [28] Uncharacterized and lineage-specific accessory genes within the Proteus mirabilis pan-genome landscape
    Potter, Robert F.
    Zhang, Kailun
    Reimler, Ben
    Marino, Jamie
    Muenks, Carol E.
    Alvarado, Kelly
    Wallace, Meghan A.
    Westblade, Lars F.
    McElvania, Erin
    Yarbrough, Melanie L.
    Hunstad, David A.
    Dantas, Gautam
    Burnham, Carey-Ann D.
    MSYSTEMS, 2023, 8 (04)
  • [29] AFLP and SSR markers for genetic diversity analysis and cultivar identification in peach [Prunus persica (L.) batsch]
    Aranzana, MJ
    Arús, P
    Carbó, J
    King, GJ
    PROCEEDINGS OF THE INTERNATIONAL SYMPOSIUM ON MOLECULAR MARKERS FOR CHARACTERIZING GENOTYPES AND IDENTIFYING CULTIVARS IN HORTICULTURE, 2001, (546): : 367 - 370
  • [30] Genome-Wide Identification, Characterization, and Expression Analysis of Orphan Genes Within Coriander
    Zhang, Meidi
    Zhu, Mo
    Lang, Hong
    Wang, Weiming
    Li, Xiaonan
    Jiang, Mingliang
    PLANTS-BASEL, 2025, 14 (05):
12345