植物孤基因研究进展

doi:10.16288/j.yczz.22-154

遗传 ›› 2022, Vol. 44 ›› Issue (8): 682-694.doi: 10.16288/j.yczz.22-154

植物孤基因研究进展

姜明亮¹(), 郎红¹(), 李晓楠², 祖野², 赵靖¹, 彭沈凌¹, 刘振¹, 战宗祥²(), 朴钟云²()

1. 吉林农业科技学院农学院,吉林 132101
2. 沈阳农业大学园艺学院,沈阳 110866

收稿日期:2022-05-10 修回日期:2022-07-23 出版日期:2022-08-20 发布日期:2022-08-08
通讯作者: 战宗祥,朴钟云 E-mail:jiangmingliang@jlnku.edu.cn;langhong@jlnku.edu.cn;zhanzxiang@syau.edu.cn;zypiao@syau.edu.cn
作者简介:姜明亮,博士,讲师,研究方向：蔬菜分子生物学。E-mail: jiangmingliang@jlnku.edu.cn;|郎红,博士,讲师,研究方向：植物分子生物学。E-mail: langhong@jlnku.edu.cn;
姜明亮和郎红并列第一作者。
基金资助:
第五批吉林省青年科技人才托举工程项目编号(QT202123);Supported by the Fifth Batch of Jilin Province Youth Science and Technology Talent Promotion Project No(QT202123)

Progress on plant orphan genes

Mingliang Jiang¹(), Hong Lang¹(), Xiaonan Li², Ye Zu², Jing Zhao¹, Shenling Peng¹, Zhen Liu¹, Zongxiang Zhan²(), Zhongyun Piao²()

1. School of Agriculture, Jilin Agricultural Science and Technology College, Jilin 132101, China
2. College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China

Received:2022-05-10 Revised:2022-07-23 Online:2022-08-20 Published:2022-08-08
Contact: Zhan Zongxiang,Piao Zhongyun E-mail:jiangmingliang@jlnku.edu.cn;langhong@jlnku.edu.cn;zhanzxiang@syau.edu.cn;zypiao@syau.edu.cn

摘要/Abstract

摘要：

孤基因(orphan genes)处在一个特殊的进化分支上,和其他任何已鉴定的基因没有显著的序列相似性。孤基因普遍存在于每个物种中,比较基因组学分析发现所有已测序的物种中均包含一部分孤基因,不同的筛选条件所获得的数量不等。孤基因经常与各种胁迫响应、物种特异性进化和物质代谢调节相关联。但多数孤基因没有被很好的注释,甚至没有可以被识别的功能结构域,为孤基因的功能表征带来了一定困难。相对于保守基因而言,孤基因的研究较少,这就导致了孤基因的重要性可能被“埋没”。本文从孤基因起源与进化、植物孤基因筛选及功能等方面进行了综述,并分析了目前存在的挑战和未来的研究重点与解决方案,以期为研究孤基因功能及其作用机制提供理论基础。

关键词: 植物孤基因, 起源, 进化, 筛选, 基因功能

Abstract:

Orphan genes are located in a special evolutionary branch and have no significant sequence similarity with any other identified genes. Orphan genes are prevalent in every species, comparative genomics analyses found that all sequenced species contained a portion of orphan genes, and the number of orphan genes obtained by distinct screening conditions is different. Orphan genes are often associated with various stress responses, species-specific evolution and substance metabolism regulation. However, most of the orphan genes have not been well annotated or even have no recognizable functional domains, which brings some difficulties to the functional characterization of orphan genes. Compared with conserved genes, there is less research on orphan genes, which leads to the possibility that the importance of orphan genes may be “unrewarded”. In this review, we summarize the origin and evolution of orphan genes, plant orphan gene screening and functions, and analyse the existing challenges and future research priorities and solutions, which provide theoretical basis for the study of orphan gene function and action mechanisms.

Key words: plant orphan genes, origin, evolution, screening, gene functions

姜明亮, 郎红, 李晓楠, 祖野, 赵靖, 彭沈凌, 刘振, 战宗祥, 朴钟云. 植物孤基因研究进展[J]. 遗传, 2022, 44(8): 682-694.

Mingliang Jiang, Hong Lang, Xiaonan Li, Ye Zu, Jing Zhao, Shenling Peng, Zhen Liu, Zongxiang Zhan, Zhongyun Piao. Progress on plant orphan genes[J]. Hereditas(Beijing), 2022, 44(8): 682-694.

图/表 1

表1

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物种	筛选程序	E-value	孤基因数量	孤基因占比	参考文献
拟南芥(Arabidopsis thaliana)	BLASTP和TBLASTN	1E-01	165个	~0.6%	[39]
	BLASTP、BLASTN、TBLASTN 和PSI-BLAST	1E-03	958个	~3%	[25]
	BLASTP和TBLASTN	1E-05	1324个	~5%	[20]
白菜(Brassica rapa)	BLASTP、BLASTN和TBLASTN	1E-03	529个芸薹种孤基因	~1%	[43,44]
水稻(Oryza sativa)	BLASTP和BLASTN	1E-04	1926个	~3%	[41]
	BLAST和BLAT	1E-02	37个	~0.0006%	[45]
	BLASTP和TBLASTN	1E-01	638个	~1%	[39]
杨树(Populus trichocarpa)	BLASTP和TBLASTN	1E-01	109个	~0.2%	[39]
杨树(Populus trichocarpa)	BLASTP和TBLASTN	1E-02	40个	~0.3%	[40]
豇豆(Vigna unguiculata)	BLAST和基于微阵列的基因组杂交	1E-10	578个	~2%	[46]
蜡烛果(Aegiceras corniculatum)	BLASTP和TBLASTN	1E-05	4823个	~12%	[48]
甜橙(Citrus sinensis)	BLASTP和TBLASTN	1E-05	296个柑橘属特异基因和 1039个甜橙特异基因	~1%和~4%	[49,50,51]
木豆(Cajanus cajan)	BLASTP、BLASTN和TBLASTN	1E-02	266个菜豆科孤基因	1%	[52]
高粱(Sorghum bicolor)	BLASTN和BLASTX	1E-02	3864个	—	[53]
高粱(Sorghum bicolor)	BLASTP和PSI-BLAST	1E-05	3607个	~11%	[54]
玉米(Zea mays)	BLASTP和PSI-BLAST	1E-05	20,021个	~32%	[54]
二穗短柄草 (Brachypodium distachyon)	BLASTP和PSI-BLAST	1E-05	3281个	~10%	[54]
烟草(Nicotiana benthamiana)	TBLASTX	1E-10	571个	~8%	[55]
马铃薯(Solanum tuberosum)	TBLASTX	1E-10	4825个	~13%	[54]
马铃薯(Solanum tuberosum)	BLASTP和TBLASTN	1E-05	2521个	~0.06%	[56]
番茄(Solanum lycopersicum)	TBLASTX	1E-10	3151个	~10%	[55]
辣椒(Capsicum annuum)	TBLASTX	1E-10	1531个	~12%	[55]
矮牵牛(Petunia hybrida)	TBLASTX	1E-10	512个	~11%	[55]
小麦(Triticum aestivum)	BLASTN和BLASTX	1E-02	3809个	—	[53]
苹果(Malus domestica Borkh.)	BLASTP	1E-10	11,444个	~20%	[57]
葡萄(Vitis vinifera)	BLASTP和TBLASTN	1E-02	2009个	~7%	[58,59]

植物孤基因研究进展

Progress on plant orphan genes

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