植物孤基因研究进展

doi:10.16288/j.yczz.22-154

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

• Review • Previous Articles Next Articles

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

Abstract

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

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.

Figures/Tables 1

Table 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]

Progress on plant orphan genes

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