生物技术通报 ›› 2021, Vol. 37 ›› Issue (7): 3-13.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0710
彭焕1(), 赵薇1, 姚珂1,2, 蒋陈1, 黄文坤1, 孔令安1, 郑经武2, 彭德良1()
收稿日期:
2021-06-02
出版日期:
2021-07-26
发布日期:
2021-08-13
作者简介:
彭 焕,男,博士,副研究员,研究方向:植物与线虫互作机制;E-mail:基金资助:
PENG Huan1(), ZHAO Wei1, YAO Ke1,2, JIANG Chen1, HUANG Wen-kun1, KONG Ling-an1, ZHENG Jing-wu2, PENG De-liang1()
Received:
2021-06-02
Published:
2021-07-26
Online:
2021-08-13
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。
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.
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 | [ |
马铃薯金线虫 G. rostochiensis | 2n=18 | 95.9 | 4377 | 88.7 | 93.55 | 57.7 | 14378 | 36.1 | [ |
艾灵顿孢囊线虫G. ellingtonae | 2n=18 | 119 | 2248 | 360 | 92 | NA | 14309 | 37 | [ |
大豆孢囊线虫 Heterodera glycines(TN10) | NA | 123.8 | 738 | 304.1 | NA | 54.0 | 29769 | NA | [ |
大豆孢囊线虫 H. glycines(X12) | 18 | 141.01 | 267 | 16265.6 | NA | 52.7 | 11882 | 36.89 | [ |
南方根结线虫Meloidogyne incognita(Morelos) | NA | 86.1 | 2817 | 62.5 | 94.76 | 88.5 | 19212 | 31.4 | [ |
南方根结线虫 M. incognita(W1) | NA | 121.96 | 33735 | 16.5 | 82.66 | 80.2 | 24714 | 30.6 | [ |
南方根结线虫 M. incognita(V3) | NA | 183.53 | 12091 | 38.6 | 97.0 | 71.3 | 45351 | 29.8 | [ |
北方根结线虫 M. hapla | 2n=32 | 53.58 | 1523 | 83.65 | 93.55 | 87.4 | 14420 | 27.4 | [ |
爪哇根结线虫 M. javanica(Avignon) | NA | 235.8 | 31341 | 10.4 | 96.0 | 90.1 | 98578 | 29.9 | [ |
爪哇根结线虫 M. javanica(VW4) | NA | 142.6 | 34394 | 14.1 | 89.52 | 87.5 | 26917 | 30.2 | [ |
花生根结线虫 M. arenaria(Guadeloupe) | NA | 258.07 | 26196 | 16.5 | 94.76 | 87.1 | 103001 | 29.8 | [ |
花生根结线虫 M. arenaria(A2-O) | NA | 284.05 | 2224 | 204.6 | 94.76 | 87.1 | NA | 30 | [ |
花生根结线虫M. arenaria(HarA) | NA | 163.7 | 46509 | 10.5 | 91.53 | 78.2 | 30308 | 30.3 | [ |
象耳豆根结线虫 M. enterolobii(Swiss) | NA | 240 | 4437 | 143 | 94.76 | 87.5 | 14414 | 30 | [ |
象耳豆根结线虫M. enterolobii(L30) | NA | 162.3 | 46090 | 9.28 | 81.45 | 79.9 | 31051 | 30.2 | [ |
佛罗里达根结线虫 M. floridensis(JB5) | NA | 99.89 | 81111 | 3.52 | 60.08 | 54.1 | NA | 29.7 | [ |
佛罗里达根结线虫M. floridensis(SJF1) | NA | 74.8 | 9134 | 13.3 | 84.0 | 76.5 | 14144 | 30.3 | [ |
拟禾本根结线虫M. graminicola(IARI) | NA | 38.18 | 4304 | 20.4 | 84.27 | 73.6 | 10196 | 23.1 | [ |
鲁克根结线虫M. luci | NA | 209.16 | 327 | 1711 | 88.1 | NA | NA | 30.2 | [ |
松材线虫 Bursaphelenchus xylophilus | 2n=12 | 74.6 | 1231 | 1158 | 97.6 | 75.8 | 18074 | 40.4 | [ |
拟松材线虫B. mucronatus | 2n=12 | 73 | 72 | 11500 | 77.4 | 74.0 | 13696 | NA | [ |
香蕉穿孔线虫Radopholus similis(Rv) | NA | 50.5 | 5194 | 27.8 | NA | 59.9 | 13120 | 47.06 | [ |
香蕉穿孔线虫R. similis(Rd) | NA | 50.0 | 6195 | 20.07 | NA | 60.4 | 12452 | 47.11 | [ |
腐烂茎线虫Ditylenchus destructor | NA | 112 | 1761 | 570.4 | 87.1 | 76.1 | 13938 | 36.6 | [ |
鳞球茎线虫D. dipsaci | NA | 227.2 | 1394 | 287 | 87.9 | 57.4 | 26428 | 37.5 | [ |
咖啡短体线虫Pratylenchus coffeae | 2n=14 | 19.7 | 5821 | 10 | NA | NA | 6712 | 38.1 | [ |
秀丽隐杆线虫Caenorhabditis elegans | 2n=12 | 100.3 | 7 | 17494 | 98.4 | 98.6 | 20317 | 35.4 | [ |
表1 植物线虫和秀丽隐杆线虫基因组基本特征比较
Table 1 Comparison of basic genomic characteristics between plant nematode and C. elegans
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 | [ |
马铃薯金线虫 G. rostochiensis | 2n=18 | 95.9 | 4377 | 88.7 | 93.55 | 57.7 | 14378 | 36.1 | [ |
艾灵顿孢囊线虫G. ellingtonae | 2n=18 | 119 | 2248 | 360 | 92 | NA | 14309 | 37 | [ |
大豆孢囊线虫 Heterodera glycines(TN10) | NA | 123.8 | 738 | 304.1 | NA | 54.0 | 29769 | NA | [ |
大豆孢囊线虫 H. glycines(X12) | 18 | 141.01 | 267 | 16265.6 | NA | 52.7 | 11882 | 36.89 | [ |
南方根结线虫Meloidogyne incognita(Morelos) | NA | 86.1 | 2817 | 62.5 | 94.76 | 88.5 | 19212 | 31.4 | [ |
南方根结线虫 M. incognita(W1) | NA | 121.96 | 33735 | 16.5 | 82.66 | 80.2 | 24714 | 30.6 | [ |
南方根结线虫 M. incognita(V3) | NA | 183.53 | 12091 | 38.6 | 97.0 | 71.3 | 45351 | 29.8 | [ |
北方根结线虫 M. hapla | 2n=32 | 53.58 | 1523 | 83.65 | 93.55 | 87.4 | 14420 | 27.4 | [ |
爪哇根结线虫 M. javanica(Avignon) | NA | 235.8 | 31341 | 10.4 | 96.0 | 90.1 | 98578 | 29.9 | [ |
爪哇根结线虫 M. javanica(VW4) | NA | 142.6 | 34394 | 14.1 | 89.52 | 87.5 | 26917 | 30.2 | [ |
花生根结线虫 M. arenaria(Guadeloupe) | NA | 258.07 | 26196 | 16.5 | 94.76 | 87.1 | 103001 | 29.8 | [ |
花生根结线虫 M. arenaria(A2-O) | NA | 284.05 | 2224 | 204.6 | 94.76 | 87.1 | NA | 30 | [ |
花生根结线虫M. arenaria(HarA) | NA | 163.7 | 46509 | 10.5 | 91.53 | 78.2 | 30308 | 30.3 | [ |
象耳豆根结线虫 M. enterolobii(Swiss) | NA | 240 | 4437 | 143 | 94.76 | 87.5 | 14414 | 30 | [ |
象耳豆根结线虫M. enterolobii(L30) | NA | 162.3 | 46090 | 9.28 | 81.45 | 79.9 | 31051 | 30.2 | [ |
佛罗里达根结线虫 M. floridensis(JB5) | NA | 99.89 | 81111 | 3.52 | 60.08 | 54.1 | NA | 29.7 | [ |
佛罗里达根结线虫M. floridensis(SJF1) | NA | 74.8 | 9134 | 13.3 | 84.0 | 76.5 | 14144 | 30.3 | [ |
拟禾本根结线虫M. graminicola(IARI) | NA | 38.18 | 4304 | 20.4 | 84.27 | 73.6 | 10196 | 23.1 | [ |
鲁克根结线虫M. luci | NA | 209.16 | 327 | 1711 | 88.1 | NA | NA | 30.2 | [ |
松材线虫 Bursaphelenchus xylophilus | 2n=12 | 74.6 | 1231 | 1158 | 97.6 | 75.8 | 18074 | 40.4 | [ |
拟松材线虫B. mucronatus | 2n=12 | 73 | 72 | 11500 | 77.4 | 74.0 | 13696 | NA | [ |
香蕉穿孔线虫Radopholus similis(Rv) | NA | 50.5 | 5194 | 27.8 | NA | 59.9 | 13120 | 47.06 | [ |
香蕉穿孔线虫R. similis(Rd) | NA | 50.0 | 6195 | 20.07 | NA | 60.4 | 12452 | 47.11 | [ |
腐烂茎线虫Ditylenchus destructor | NA | 112 | 1761 | 570.4 | 87.1 | 76.1 | 13938 | 36.6 | [ |
鳞球茎线虫D. dipsaci | NA | 227.2 | 1394 | 287 | 87.9 | 57.4 | 26428 | 37.5 | [ |
咖啡短体线虫Pratylenchus coffeae | 2n=14 | 19.7 | 5821 | 10 | NA | NA | 6712 | 38.1 | [ |
秀丽隐杆线虫Caenorhabditis elegans | 2n=12 | 100.3 | 7 | 17494 | 98.4 | 98.6 | 20317 | 35.4 | [ |
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