植物寄生线虫基因组学研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2021-0710

摘要/Abstract

摘要：

植物寄生线虫是农作物主要病原物之一,每年造成作物大幅度减产和严重的经济损失。植物寄生线虫基因组学研究在揭示植物线虫与寄主互作分子机制和作物抗线虫品种的培育中发挥着不可替代的作用。随着高通量测序技术的广泛应用,多种重要的植物寄生线虫的基因组被破解和报道。在此基础上,通过比较基因组学进一步揭示了植物寄生线虫的起源和进化,功能基因组学的研究也取得了一系列重要的进展。本文对目前已报道的植物寄生线虫基因组的研究进展进行总结,在各基因组的基本特征、染色体组变异、串联重复序列、基因表达调控与基因协同表达、水平基因转移、效应蛋白发现和功能研究及基因家族扩张等方面进行综述,以期为植物线虫致病分子机制研究及防控新策略制定提供参考。

关键词: 植物寄生线虫, 基因组学, 水平基因转移, 效应蛋白, 基因家族扩张

Abstract:

Plant-parasitic nematodes parasitize various plants,resulting in crop yield reduction and serious economic losses. Genomics study of plant parasitic nematode play an irreplaceable role in revealing the molecular mechanism of interaction between parasitic nematodes and plants,as well as breeding nematode-resistant varieties. With the continuous development of high-throughput sequencing technology,the genome of multiple important plant parasitic nematodes has been revealed and reported. The evolution and origin of plant-parasitic nematodes have been more clearly defined by the development of comparative genomics,and some progress has been made in functional genomics of plant parasitic nematodes. This paper gives a brief review on the major research advances of plant-parasitic nematode genomes,including general features,genome variation,sequences of tandem repeat genes,gene regulation and gene co-expression,horizontal gene transfer,effectors discovery and gene family expansions,aiming at providing a reference for the research on the pathogenic molecular mechanism of plant nematodes and the development of new control strategies.

Key words: plant-parasitic nematode, genome, horizontal gene transfer, effectors, gene family expansion

彭焕, 赵薇, 姚珂, 蒋陈, 黄文坤, 孔令安, 郑经武, 彭德良. 植物寄生线虫基因组学研究进展[J]. 生物技术通报, 2021, 37(7): 3-13.

PENG Huan, ZHAO Wei, YAO Ke, JIANG Chen, HUANG Wen-kun, KONG Ling-an, ZHENG Jing-wu, PENG De-liang. Research Progress on the Genomics of Plant-Parasitic Nematode[J]. Biotechnology Bulletin, 2021, 37(7): 3-13.

图/表 1

参考文献 59

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线虫种类（种群） Species（population）	染色体数 Chromosome number	组装大小 Assembly size/Mb	Scaffold数目 No. of Scaffolds	Scaffolds N50值 Scaffold N50/kb	CEGMA完整性 CEGMA complete/%	BUSCO完整性 BUSCO complete/%	基因数 Genes	GC含量 GC%	参考文献 References
马铃薯白线虫Globodera pallida	2n=18	124.7	6873	122	81	43.7	16419	36.7	[8]
马铃薯金线虫 G. rostochiensis	2n=18	95.9	4377	88.7	93.55	57.7	14378	36.1	[9]
艾灵顿孢囊线虫G. ellingtonae	2n=18	119	2248	360	92	NA	14309	37	[11]
大豆孢囊线虫 Heterodera glycines（TN10）	NA	123.8	738	304.1	NA	54.0	29769	NA	[10]
大豆孢囊线虫 H. glycines（X12）	18	141.01	267	16265.6	NA	52.7	11882	36.89	[29]
南方根结线虫Meloidogyne incognita（Morelos）	NA	86.1	2817	62.5	94.76	88.5	19212	31.4	[5]
南方根结线虫 M. incognita（W1）	NA	121.96	33735	16.5	82.66	80.2	24714	30.6	[28]
南方根结线虫 M. incognita（V3）	NA	183.53	12091	38.6	97.0	71.3	45351	29.8	[17]
北方根结线虫 M. hapla	2n=32	53.58	1523	83.65	93.55	87.4	14420	27.4	[6]
爪哇根结线虫 M. javanica（Avignon）	NA	235.8	31341	10.4	96.0	90.1	98578	29.9	[17]
爪哇根结线虫 M. javanica（VW4）	NA	142.6	34394	14.1	89.52	87.5	26917	30.2	[28]
花生根结线虫 M. arenaria（Guadeloupe）	NA	258.07	26196	16.5	94.76	87.1	103001	29.8	[17]
花生根结线虫 M. arenaria（A2-O）	NA	284.05	2224	204.6	94.76	87.1	NA	30	[16]
花生根结线虫M. arenaria（HarA）	NA	163.7	46509	10.5	91.53	78.2	30308	30.3	[28]
象耳豆根结线虫 M. enterolobii（Swiss）	NA	240	4437	143	94.76	87.5	14414	30	[13]
象耳豆根结线虫M. enterolobii（L30）	NA	162.3	46090	9.28	81.45	79.9	31051	30.2	[28]
佛罗里达根结线虫 M. floridensis（JB5）	NA	99.89	81111	3.52	60.08	54.1	NA	29.7	[15]
佛罗里达根结线虫M. floridensis（SJF1）	NA	74.8	9134	13.3	84.0	76.5	14144	30.3	[28]
拟禾本根结线虫M. graminicola（IARI）	NA	38.18	4304	20.4	84.27	73.6	10196	23.1	[14]
鲁克根结线虫M. luci	NA	209.16	327	1711	88.1	NA	NA	30.2	[18]
松材线虫 Bursaphelenchus xylophilus	2n=12	74.6	1231	1158	97.6	75.8	18074	40.4	[7]
拟松材线虫B. mucronatus	2n=12	73	72	11500	77.4	74.0	13696	NA	[12]
香蕉穿孔线虫Radopholus similis（Rv）	NA	50.5	5194	27.8	NA	59.9	13120	47.06	[23]
香蕉穿孔线虫R. similis（Rd）	NA	50.0	6195	20.07	NA	60.4	12452	47.11	[23]
腐烂茎线虫Ditylenchus destructor	NA	112	1761	570.4	87.1	76.1	13938	36.6	[19]
鳞球茎线虫D. dipsaci	NA	227.2	1394	287	87.9	57.4	26428	37.5	[20]
咖啡短体线虫Pratylenchus coffeae	2n=14	19.7	5821	10	NA	NA	6712	38.1	[21]
秀丽隐杆线虫Caenorhabditis elegans	2n=12	100.3	7	17494	98.4	98.6	20317	35.4	[4]

线虫种类（种群） Species（population）	染色体数 Chromosome number	组装大小 Assembly size/Mb	Scaffold数目 No. of Scaffolds	Scaffolds N50值 Scaffold N50/kb	CEGMA完整性 CEGMA complete/%	BUSCO完整性 BUSCO complete/%	基因数 Genes	GC含量 GC%	参考文献 References
马铃薯白线虫Globodera pallida	2n=18	124.7	6873	122	81	43.7	16419	36.7	[8]
马铃薯金线虫 G. rostochiensis	2n=18	95.9	4377	88.7	93.55	57.7	14378	36.1	[9]
艾灵顿孢囊线虫G. ellingtonae	2n=18	119	2248	360	92	NA	14309	37	[11]
大豆孢囊线虫 Heterodera glycines（TN10）	NA	123.8	738	304.1	NA	54.0	29769	NA	[10]
大豆孢囊线虫 H. glycines（X12）	18	141.01	267	16265.6	NA	52.7	11882	36.89	[29]
南方根结线虫Meloidogyne incognita（Morelos）	NA	86.1	2817	62.5	94.76	88.5	19212	31.4	[5]
南方根结线虫 M. incognita（W1）	NA	121.96	33735	16.5	82.66	80.2	24714	30.6	[28]
南方根结线虫 M. incognita（V3）	NA	183.53	12091	38.6	97.0	71.3	45351	29.8	[17]
北方根结线虫 M. hapla	2n=32	53.58	1523	83.65	93.55	87.4	14420	27.4	[6]
爪哇根结线虫 M. javanica（Avignon）	NA	235.8	31341	10.4	96.0	90.1	98578	29.9	[17]
爪哇根结线虫 M. javanica（VW4）	NA	142.6	34394	14.1	89.52	87.5	26917	30.2	[28]
花生根结线虫 M. arenaria（Guadeloupe）	NA	258.07	26196	16.5	94.76	87.1	103001	29.8	[17]
花生根结线虫 M. arenaria（A2-O）	NA	284.05	2224	204.6	94.76	87.1	NA	30	[16]
花生根结线虫M. arenaria（HarA）	NA	163.7	46509	10.5	91.53	78.2	30308	30.3	[28]
象耳豆根结线虫 M. enterolobii（Swiss）	NA	240	4437	143	94.76	87.5	14414	30	[13]
象耳豆根结线虫M. enterolobii（L30）	NA	162.3	46090	9.28	81.45	79.9	31051	30.2	[28]
佛罗里达根结线虫 M. floridensis（JB5）	NA	99.89	81111	3.52	60.08	54.1	NA	29.7	[15]
佛罗里达根结线虫M. floridensis（SJF1）	NA	74.8	9134	13.3	84.0	76.5	14144	30.3	[28]
拟禾本根结线虫M. graminicola（IARI）	NA	38.18	4304	20.4	84.27	73.6	10196	23.1	[14]
鲁克根结线虫M. luci	NA	209.16	327	1711	88.1	NA	NA	30.2	[18]
松材线虫 Bursaphelenchus xylophilus	2n=12	74.6	1231	1158	97.6	75.8	18074	40.4	[7]
拟松材线虫B. mucronatus	2n=12	73	72	11500	77.4	74.0	13696	NA	[12]
香蕉穿孔线虫Radopholus similis（Rv）	NA	50.5	5194	27.8	NA	59.9	13120	47.06	[23]
香蕉穿孔线虫R. similis（Rd）	NA	50.0	6195	20.07	NA	60.4	12452	47.11	[23]
腐烂茎线虫Ditylenchus destructor	NA	112	1761	570.4	87.1	76.1	13938	36.6	[19]
鳞球茎线虫D. dipsaci	NA	227.2	1394	287	87.9	57.4	26428	37.5	[20]
咖啡短体线虫Pratylenchus coffeae	2n=14	19.7	5821	10	NA	NA	6712	38.1	[21]
秀丽隐杆线虫Caenorhabditis elegans	2n=12	100.3	7	17494	98.4	98.6	20317	35.4	[4]