遗传 ›› 2020, Vol. 42 ›› Issue (7): 691-702.doi: 10.16288/j.yczz.20-022
收稿日期:
2020-02-20
修回日期:
2020-05-11
出版日期:
2020-07-20
发布日期:
2020-06-01
通讯作者:
杜萌泽
E-mail:du_mengze@foxmail.com
作者简介:
刘硕,在读博士研究生,专业方向:微生物基因组学。E-mail: 基金资助:
Shuo Liu1, Zhi Zeng1, Fancai Zeng2, Mengze Du2()
Received:
2020-02-20
Revised:
2020-05-11
Online:
2020-07-20
Published:
2020-06-01
Contact:
Du Mengze
E-mail:du_mengze@foxmail.com
Supported by:
摘要:
随着测序技术的不断发展,产生了海量的基因组测序数据,极大地丰富了公共遗传数据资源。同时为了应对大量基因组数据的产生,基因组比较和注释算法、工具不断更新,使得联合多种注释工具得到更准确的蛋白编码基因的注释信息成为可能。目前公共数据库的原核生物基因组测序和装配有些是10多年前的,存在大量预测的功能未知的编码基因。为了提升美国国家生物信息中心(National Center for Biotechnology Information, NCBI)数据库中基因组的注释质量,本研究联合使用多种原核基因识别算法/软件和基因表达数据重注释1587个细菌和古细菌基因组。首先,利用Z曲线的33个变量从177个基因组原注释中识别获得3092个被过度注释为蛋白编码基因的序列;其次,通过同源比对为939个基因组中的4447个功能未知的蛋白编码基因注释上具体功能;最后,通过联合采用ZCURVE 3.0和Glimmer 3.02以及Prodigal这3种高精度的、广泛使用且基于算法不同而互补的基因识别软件来寻找漏注释基因。最终,从9个基因组中找到了2003个被漏注释的蛋白编码基因,这些基因属于多个蛋白质直系同源簇(clusters of orthologous groups of proteins, COG)。本研究使用新的工具并结合多组学数据重新注释早期测序的细菌和古细菌基因组,不仅为新测序菌株提供注释方法参考,而且这些重注释后得到的细菌基因序列也会对后续基础研究有所帮助。
刘硕, 曾志, 曾凡才, 杜萌泽. 基于序列相似性和Z曲线方法重注释原核生物蛋白编码基因[J]. 遗传, 2020, 42(7): 691-702.
Shuo Liu, Zhi Zeng, Fancai Zeng, Mengze Du. Comprehensive re-annotation of protein-coding genes for prokaryotic genomes by Z-curve and similarity-based methods[J]. Hereditas(Beijing), 2020, 42(7): 691-702.
表1
识别出过度注释的ORFs多于20的菌株基因组的信息"
菌株 | NC序列号 | 数量 | 菌株 | NC序列号 | 数量 |
---|---|---|---|---|---|
慢性型大豆根瘤菌(B. japonicum USDA 110) | NC_004463 | 147 | 金黄色葡萄球菌 (S. aureus subsp. Aureus MW2) | NC_003923 | 36 |
哈氏弧菌(Vibrio harveyi ATCC BAA-1116) | NC_009784 | 133 | 黑海甲烷袋状菌 (Methanoculleus marisnigri JR1) | NC_009051 | 34 |
大肠杆菌(E. coli CFT073) | NC_004431 | 119 | 双叶钩端螺旋体血清型Patoc菌株 (Leptospira biflexa serovar Patoc strain 'Patoc 1) | NC_010602 | 34 |
织片草螺菌 (Herbaspirillum seropedicae SmR1) | NC_014323 | 109 | 拟杆菌属 (Bacteroides salanitronis DSM 18170) | NC_015164 | 34 |
结核分枝杆菌 (Mycobacterium tuberculosis CDC1551) | NC_002755 | 98 | 巴尔通体杆菌(Bartonella clarridgeiae 73) | NC_014932 | 33 |
多形类杆菌 (Bacteroides thetaiotaomicron VPI-5482) | NC_004663 | 84 | 梅毒螺旋体梅毒亚种 (Treponema pallidum subsp. pallidum SS14) | NC_010741 | 32 |
鞘脂菌(Sphingobium japonicum UT26S) | NC_014006 | 80 | 梅毒螺旋体 (Treponema paraluiscuniculi Cuniculi A) | NC_015714 | 32 |
生丝微菌属(Hyphomicrobium sp. MC1) | NC_015717 | 70 | 鼠疫杆菌(Yersinia pestis CO92) | NC_003143 | 31 |
长双歧杆菌(B. longum NCC2705) | NC_004307 | 69 | 台湾贪铜菌 (Cupriavidus taiwanensis LMG 19424) | NC_010528 | 31 |
大肠杆菌(E. coli O157:H7 str. Sakai) | NC_002695 | 55 | 噬纤维素菌属 (Cellulophaga algicola DSM 14237) | NC_014934 | 31 |
哈维弧菌(V. harveyi ATCC BAA-1116) | NC_009783 | 53 | 结核分枝杆菌(M. tuberculosis H37Rv) | NC_000962 | 30 |
溶血葡萄球菌(S. haemolyticus JCSC1435) | NC_007168 | 51 | 沙漠自然球菌(Deinococcus deserti VCD115) | NC_012526 | 30 |
缓纤维梭菌 (Clostridium lentocellum DSM 5427) | NC_015275 | 51 | 溃疡拟杆菌(Bacteroides helcogenes P 36-108) | NC_014933 | 27 |
表皮葡萄球菌(S. epidermidis RP62A) | NC_002976 | 47 | 金黄色葡萄球菌 (S. aureus subsp. Aureus Mu50) | NC_002758 | 26 |
鼠疫杆菌(Y. pestis KIM10+) | NC_004088 | 46 | 金黄色葡萄球菌 (S. aureus subsp. Aureus N315) | NC_002745 | 25 |
海单孢菌属 (Marinomonas mediterranea MMB-1) | NC_015276 | 43 | 内脏臭气杆菌 (Odoribacter splanchnicus DSM 20712) | NC_015160 | 25 |
红球菌(Rhodococcus jostii RHA1) | NC_008268 | 40 | 嗜热盐碱细菌 (Natranaerobius thermophilus JW/NM-WN-LF) | NC_010718 | 23 |
大肠杆菌(E. coli O157:H7 str. EDL933) | NC_002655 | 39 | 圆柱杆菌(Teredinibacter turnerae T7901) | NC_012997 | 23 |
固氮密螺旋体(T. azotonutricium ZAS-9) | NC_015577 | 39 | 盐孢菌属(Salinispora tropica CNB-440) | NC_009380 | 20 |
白蚁塞巴鲁德氏菌 (Sebaldella termitidis ATCC 33386) | NC_013517 | 38 | 巴西浮霉状菌 (Planctomyces brasiliensis DSM 5305) | NC_015174 | 20 |
金黄色葡萄球菌(S. aureus subsp.COL) | NC_002951 | 37 | 苜蓿根瘤菌(Sinorhizobium meliloti AK83) | NC_015590 | 20 |
肺炎衣原体 (Chlamydophila pneumoniae AR39) | NC_002179 | 36 |
表2
含有20个以上的假定ORFs被注释上准确功能的基因组的信息"
菌株 | NC序列号 | 数量 | 菌株 | NC序列号 | 数量 |
---|---|---|---|---|---|
大肠杆菌(E. coli O111:H-str. 11128) | NC_013364 | 80 | 炭疽芽孢杆菌(B. anthracis str. CDC 684) | NC_012581 | 23 |
肠道沙门氏菌(S. enterica subsp. enterica serovar Paratyphi B str. SPB7) | NC_010102 | 64 | 肠道沙门氏菌(S. enterica subsp. enterica serovar Paratyphi C strain RKS4594) | NC_012125 | 23 |
鲍氏志贺菌(Shigella boydii CDC 3083-94) | NC_010658 | 52 | 金黄色葡萄球菌(S. aureus subsp. aureus MW2) | NC_003923 | 23 |
肠道沙门氏菌(S. enterica subsp. arizonae serovar 62:z4, z23:- str. RSK2980) | NC_010067 | 45 | 蜡状芽孢杆菌(Bacillus cereus ATCC 10987) | NC_003909 | 22 |
枯草芽孢杆菌(B. subtilis subsp. subtilis str. 168) | NC_000964 | 42 | 大肠杆菌(E. coli O26:H11 str. 11368) | NC_013361 | 22 |
鼠李糖乳杆菌(Lactobacillus rhamnosus Lc 705) | NC_013199 | 38 | 肺炎链球菌(Streptococcus pneumoniae P1031) | NC_012467 | 22 |
鼠李糖乳杆菌(L. rhamnosus GG) | NC_013198 | 36 | 金黄色葡萄球菌(S. aureus subsp. aureus Mu3) | NC_009782 | 21 |
肠道沙门氏菌(S. enterica subsp. enterica serovar Paratyphi A str. AKU_12601) | NC_011147 | 35 | 金黄色葡萄球菌(S. aureus subsp. aureus JH9) | NC_009487 | 21 |
大肠杆菌(E. coli O157:H7 str. Sakai) | NC_002695 | 34 | 结核分枝杆菌(M. tuberculosis CDC1551) | NC_002755 | 20 |
大肠杆菌(E. coli O157:H7 str. EDL933) | NC_002655 | 30 | 炭疽芽孢杆菌(B. anthracis str. A0248) | NC_012659 | 20 |
肠道沙门氏菌(S. enterica subsp. enterica serovar Paratyphi A str. ATCC 9150) | NC_006511 | 30 | 大肠杆菌(E. coli O157:H7 str. EC4115) | NC_011353 | 20 |
大肠杆菌(E. coli SE11) | NC_011415 | 28 | 炭疽芽孢杆菌(B. anthracis str. Ames) | NC_003997 | 20 |
大肠杆菌(E. coli ED1a) | NC_011745 | 27 | 哈维氏弧菌(V. harveyi ATCC BAA-1116) | NC_009783 | 20 |
大肠杆菌(E. coli UTI89) | NC_007946 | 26 | 结核分枝杆菌(M. tuberculosis KZN 1435) | NC_012943 | 20 |
枯草芽孢杆菌(B. subtilis BSn5) | NC_014976 | 25 | 大肠杆菌(E. coli O55:H7 str. CB9615) | NC_013941 | 20 |
肠道沙门氏菌 (S. enterica subsp. enterica serovar Typhi str. Ty2) | NC_004631 | 25 | 牛型分枝杆菌 (Mycobacterium bovis AF2122/97) | NC_002945 | 20 |
大肠杆菌(E. coli CFT073) | NC_004431 | 23 |
表3
大肠杆菌(E.coli str. K-12 substr. MG1655)满足宽松阈值的新基因"
正/负链(在基因组上位置) | 同源序列来源 | 功能 | E值 | 覆盖度 (%) | 一致性 (%) |
---|---|---|---|---|---|
负链(190551~191603) | 肠道沙门菌 (S. enterica subsp. enterica) | 亮氨酸操纵子先导肽 (leu operon leader peptide) | 8e-139 | 79 | 74.01 |
负链(2228549~2228758) | 志贺氏菌属(Shigella) | 多药耐药外膜蛋白MdtQ (multidrug resistance outer membrane protein MdtQ) | 1e-27 | 72 | 100 |
负链(4322661~4323281) | 志贺氏菌属(Shigella) | Pn转运体膜通道蛋白组分(membrane channel protein component of Pn transporter) | 4e-108 | 77 | 98.74 |
负链(4500432~4500791) | 猪布鲁氏杆菌(Brucella suis) | 磷酸乙醇胺转移酶(MULTISPECIES: phosphoethanolamine transferase) | 3e-45 | 69 | 91.57 |
正链(1465410~1467950) | 宋内志贺菌(Shigella sonnei) | 包含蛋白质的自转运体结构域 (autotransporter domain-containing protein) | 0.0 | 74 | 87.03 |
正链(1470858~1474013) | 福氏志贺氏菌 (Shigella flexneri) | 自转运体外膜β管(MULTISPECIES: autotransporter outer membrane beta-barrel) | 0.0 | 76 | 100 |
正链(2070501~2071211) | 双歧杆菌 (Bifidobacterium longum) | GTPase家族蛋白(GTPase family protein) | 4e-129 | 77 | 99.45 |
正链(3993850~3994335) | 痢疾志贺氏菌 (Shigella dysenteriae 1617) | CyaX蛋白(CyaX protein) | 9e-67 | 63 | 96.12 |
负链(4506626~4506883) | 红树杆菌属 (Mangrovibacter plantisponsor) | 表皮粘着蛋白E (surface-adhesin protein E) | 1e-28 | 98 | 60 |
表4
9个菌株的名称、NC序列号、基因组大小、基因总数和新注释基因的数目"
菌株 | NC序列号 | 基因组大小(bp) | 基因总数 | 新基因的数目 |
---|---|---|---|---|
枯草芽孢杆菌(B. subtilis subsp. subtilis str. 168) | NC_000964 | 4215606 | 4175 | 52 |
金黄色葡萄球菌(S. aureus subsp. aureus NCTC 8325) | NC_007795 | 2821361 | 2767 | 61 |
酿脓链球菌(S. pyogenes SF370) | NC_002737 | 1852441 | 1696 | 104 |
流感嗜血杆菌(H. influenzae Rd KW20) | NC_000907 | 1830138 | 1610 | 123 |
嗜酸氧化亚铁硫杆菌(A. ferrooxidans ATCC 23270) | NC_011761 | 2982397 | 3147 | 143 |
大肠杆菌(E. coli str. K-12 substr. MG1655) | NC_000913 | 4641652 | 4140 | 246 |
脑膜炎奈瑟球菌(N. meningitidis MC58) | NC_003112 | 2272360 | 1953 | 279 |
炭疽芽孢杆菌(B. anthracis str. Ames) | NC_003997 | 5227293 | 5039 | 418 |
肠道沙门氏菌(S. enterica subsp. enterica serovar Typhi str. CT18) | NC_003198 | 4809037 | 4111 | 577 |
图4
特定同源簇对应的新基因占全部新基因的比例 A:RNA加工和修饰;B:染色质结构和动力学;Y:核结构;Z:细胞骨架;W:细胞外结构;D:细胞周期控制,细胞分裂,染色体分裂;O:翻译后修饰,蛋白反转,伴侣;Q:次生代谢产物的生物合成、运输和分解代谢;I:脂质转运与代谢;J:翻译,核糖体结构和生物发生;H:辅酶运输与代谢;F:核苷酸转运与代谢;V:防卫机制;N:细胞迁移;C:能量产生和转化;U:细胞内传输,分泌和囊泡转运;P:无机离子转运与代谢;T:信号转导机制;K:转录;E:氨基酸转运和代谢;M:细胞壁和细胞膜的生物发生;G:碳水化合物运输和代谢;S:功能未知;R:只能预测大致功能;L:复制重组和修复。"
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