Please wait a minute...
Journal of Integrative Agriculture  2021, Vol. 20 Issue (1): 191-200    DOI: 10.1016/S2095-3119(20)63231-2
Special Issue: 昆虫合辑Plant Protection—Entomolgy
Plant Protection Advanced Online Publication | Current Issue | Archive | Adv Search |
InvasionDB: A genome and gene database of invasive alien species
HUANG Cong1, 2*, LANG Kun3*, QIAN Wan-qiang2*, WANG Shu-ping4, CAO Xiao-mei5, HE Rui6, ZHAN An-ran3, CHEN Meng-yao3, YANG Nian-wan1, LI Fei3 
1 Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
2 Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120,
3 Minstry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, P.R.China
4 Technical Centre for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, P.R.China
5 Chinese Academy of Inspection and Quarantine, Beijing 100176, P.R.China
6 China National Center for Biotechnology Development, Beijing 100039, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      

外来入侵物种是指被引入到其原产地范围以外的地区,并对当地的经济、生物多样性和生态环境造成了严重危害的物种。明确入侵性的遗传机制对于开发生态友好型的方法来防控外来入侵物种至关重要,同时,揭示外来物种的基因组特征有利于准确预测其入侵性潜能。然而,尽管已经有大量外来入侵物种的基因组被测序,但这些数据存放零散,缺少一个综合的外来入侵物种基因组数据管理与分析平台。因此,我们通过文献调研和数据库检索,收集了已完成基因组测序的外来入侵物种的组学相关数据,构建了InvasionDB数据库。该数据库包含131个外来入侵物种(100种入侵动物和31种入侵植物)的基因组和转录组数据,其中,76个物种的基因组被详细注释,并提供基因功能(包括Pfam、KEGG和NR注释信息)查询、序列比对和基因组可视化,以及全部数据下载功能。为了提供更多与入侵性相关的信息,我们进一步分析了19个与入侵昆虫的入侵性相关的基因家族,以及非编码RNAs(包括135494 个miRNAs, 89294 个rRNAs和2671941 个tRNAs)。因此,InvasionDB对于从基因组水平来研究外来入侵物种的入侵性,以及发展新的防控技术具有重要指导意义。

Invasive alien species (IAS) are species whose introduction to areas outside of their native range cause harm to economics, biodiversity, and the environment.  Understanding the genetic basis of invasiveness is critical for preventing invasion by an alien species and managing IAS with eco-friendly control methods.  In addition, uncovering the genomic features of IAS is essential for accurately predicting invasiveness.  However, even though increasing efforts have been devoted to sequencing the genomes of IAS, there is still not an integrated genome database for the invasive biology community.  Here, we first determined a list of invasive plants and animals by mining references and databases.  Then, we retrieved the genomic and gene data of these IAS, and constructed a database, InvasionDB.  InvasionDB encompasses 131 IAS genomes, 76 annotated IAS assemblies, and links these data to conventional functions such as searching for gene coding sequences and Pfam, KEGG, NR annotations, BLAST server, JBrowse, and downloads services.  Next, we analyzed 19 invasiveness-related gene families which confer invasiveness in insects.  To study the roles of noncoding RNA in invasiveness, we also annotated 135 494 miRNAs, 89 294 rRNAs, and 2 671 941 tRNAs from these IAS.  In summary, InvasionDB is useful for studying the invasiveness at the genomic level, and thus helps to develop novel management strategies to control IAS.
Keywords:  database        invasive alien species        genomic        gene family        non-coding RNA  
Received: 30 December 2019   Accepted:
Fund: This work was supported by the National Key Research and Development Program of China (2017YFC1200600 and 2016YFC1200602), the Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences (caascx-2017-2021-IAS) and the Shenzhen Science and Technology Program, China (KQTD20180411143628272).
Corresponding Authors:  Correspondence YANG Nian-wan, Tel: +86-10-82109572, E-mail:    
About author:  HUANG Cong, Mobile: +86-18040634335, E-mail: huangcong16; LANG Kun, Mobile: +86-18715170767, E-mail:; QIAN Wan-qiang, E-mail:; * These authors contributed equally to this study.

Cite this article: 

HUANG Cong, LANG Kun, QIAN Wan-qiang, WANG Shu-ping, CAO Xiao-mei, HE Rui, ZHAN An-ran, CHEN Meng-yao, YANG Nian-wan, LI Fei. 2021. InvasionDB: A genome and gene database of invasive alien species. Journal of Integrative Agriculture, 20(1): 191-200.

Agarwala R, Barrett T, Beck J, Benson D A, Bollin C, Bolton E, Bourexis D, Brister J R, Bryant S H, Canese K, Cavanaugh M, Charowhas C, Clark K, Dondoshansky I, Feolo M, Fitzpatrick L, Funk K, Geer L Y, Gorelenkov V, Graeff A, et al. 2018. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 46, D8–D13.
Anderson C J, Oakeshott J G, Tay W T, Gordon K H J, Zwick A, Walsh T K. 2018. Hybridization and gene flow in the mega-pest lineage of moth, Helicoverpa. Proceedings of the National Academy of Sciences of the United States of America, 115, 5034–5039.
Beckert A, Wiesner J, Schmidtberg H, Lehmann R, Baumann A, Vogel H, Vilcinskas A. 2016. Expression and characterization of a recombinant i-type lysozyme from the harlequin ladybird beetle Harmonia axyridis. Insect Molecular Biology, 25, 202–215.
Bradshaw C J, Leroy B, Bellard C, Roiz D, Albert C, Fournier A, Barbet-Massin M, Salles J M, Simard F, Courchamp F. 2016. Massive yet grossly underestimated global costs of invasive insects. Nature Communications, 7, 12986.
Chen W, Hasegawa D K, Kaur N, Kliot A, Pinheiro P V, Luan J, Stensmyr M C, Zheng Y, Liu W, Sun H, Xu Y, Luo Y, Kruse A, Yang X, Kontsedalov S, Lebedev G, Fisher T W, Nelson D R, Hunter W B, Brown J K, et al. 2016. The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. BMC Biology, 14, 110.
Chen X G, Jiang X T, Gu J B, Xu M, Wu Y, Deng Y H, Zhang C, Bonizzoni M, Dermauw W, Vontas J, Armbruster P, Huang X, Yang Y L, Zhang H, He W M, Peng H J, Liu Y F, Wu K, Chen J H, Lirakis M, et al. 2015. Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution. Proceedings of the National Academy of Sciences of the United States of America, 112, E5907–E5915.
Cheng T C, Wu J Q, Wu Y Q, Chilukuri R V, Huang L H, Yamamoto K, Feng L, Li W S, Chen Z W, Guo H Z, Liu J Q, Li S L, Wang X X, Peng L, Liu D L, Guo Y B, Fu B H, Li Z Q, Liu C, Chen Y H, et al. 2017. Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest. Nature Ecology & Evolution, 1, 1747–1756.
Chiu J C, Jiang X T, Zhao L, Hamm C A, Cridland J M, Saelao P, Hamby K A, Lee E K, Kwok R S, Zhang G J, Zalom F G, Walton V M, Begun D J. 2013. Genome of Drosophila suzukii, the spotted wing Drosophila. G3, 3, 2257–2271.
Deng W, Nickle D C, Learn G H, Maust B, Mullins J I. 2007. ViroBLAST: A stand-alone BLAST web server for flexible queries of multiple databases and user’s datasets. Bioinformatics, 23, 2334–2336.
Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson M D, Lawrence C J, Lushbough C, Brendel V. 2008. PlantGDB: A resource for comparative plant genomics. Nucleic Acids Research, 36, D959–D965.
Early R, Bradley B A, Dukes J S, Lawler J J, Olden J D, Blumenthal D M, Gonzalez P, Grosholz E D, Ibanez I, Miller L P, Sorte C J B, Tatem A J. 2016. Global threats from invasive alien species in the twenty-first century and national response capacities. Nature Communications, 7, 12485.
Eddy S R. 2011. Accelerated profile HMM searches. PLoS Computational Biology, 7, e1002195.
Elton C S. 1958. The Ecology of Invasions by Animals and Plants. Methuen, London.
Finn R D, Coggill P, Eberhardt R Y, Eddy S R, Mistry J, Mitchell A L, Potter S C, Punta M, Qureshi M, Sangrador-Vegas A, Salazar G A, Tate J, Bateman A. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research, 44, D279–D285.
Gauthier J P, Legeai F, Zasadzinski A, Rispe C, Tagu D. 2007. AphidBase: A database for aphid genomic resources. Bioinformatics, 23, 783–784.
Di Genova A, Aravena A, Zapata L, Gonzalez M, Maass A, Iturra P. 2011. SalmonDB: A bioinformatics resource for Salmo salar and Oncorhynchus mykiss. Database, 2011, bar050.
Giraldo-Calderon G I, Emrich S J, MacCallum R M, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, VectorBase C, Madey G, Collins F H, Lawson D. 2015. VectorBase: An updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Research, 43, D707–D713.
Grigoraki L, Pipini D, Labbe P, Chaskopoulou A, Weill M, Vontas J. 2017. Carboxylesterase gene amplifications associated with insecticide resistance in Aedes albopictus: Geographical distribution and evolutionary origin. PLoS Neglected Tropical Diseases, 11, e0005533.
Guerra-Assuncao J A, Enright A J. 2010. MapMi: Automated mapping of microRNA loci. BMC Bioinformatics, 11, 133.
Guo Q, Tao Y L, Chu D. 2013. Characterization and comparative profiling of miRNAs in invasive Bemisia tabaci (Gennadius) B and Q. PLoS ONE, 8, e59884.
Hu J T, Chen B, Li Z H. 2014. Thermal plasticity is related to the hardening response of heat shock protein expression in two Bactrocera fruit flies. Journal of Insect Physiology, 67, 105–113.
Huang C, Li Y Z, Yang N W, Wu Q, Xing L S, Qian W Q, Xi Y, Li F, Wan F H. 2019. Progresses in invasive insect genomics. Plant Protection, 45, 112–120. (in Chinese)
Huang Q X, Cheng X Y, Mao Z C, Wang Y S, Zhao L L, Yan X, Ferris V R, Xu R M, Xie B Y. 2010. MicroRNA discovery and analysis of pinewood nematode Bursaphelenchus xylophilus by deep sequencing. PLoS ONE, 5, e13271.
Khajuria C, Williams C E, El Bouhssini M, Whitworth R J, Richards S, Stuart J J, Chen M S. 2013. Deep sequencing and genome-wide analysis reveals the expansion of microRNA genes in the gall midge Mayetiola destructor. BMC Genomics, 14, 187.
Khalfallah Y, Bouktila D, Makni M, Makni H. 2015. Tracking microRNAs with a potential for virulence regulation in the pea aphid, Acyrthosiphon pisum Harris (Hemiptera: Aphidae), and the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae). African Entomology, 23, 502–509.
Kozomara A, Griffiths-Jones S. 2014. miRBase: Annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Research, 42, D68–D73.
Liu H M, Liu T, Xie L H, Wang X M, Deng Y H, Chen C H, James A A, Chen X G. 2016. Functional analysis of Orco and odorant receptors in odor recognition in Aedes albopictus. Parasites and Vectors, 9, 363.
Lowe T M, Chan P P. 2016. tRNAscan-SE On-line: Integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research, 44, W54–W57.
McKenna D D, Scully E D, Pauchet Y, Hoover K, Kirsch R, Geib S M, Mitchell R F, Waterhouse R M, Ahn S J, Arsala D, Benoit J B, Blackmon H, Bledsoe T, Bowsher J H, Busch A, Calla B, Chao H, Childers A K, Childers C, Clarke D J, et al. 2016. Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. Genome Biology, 17, 227.
Mishra R, Chiu J C, Hua G, Tawari N R, Adang M J, Sial A A. 2018. High throughput sequencing reveals Drosophila suzukii responses to insecticides. Insect Science, 25, 928–945.
Nguyen P, Kim A Y, Jung J K, Donahue K M, Jung C, Choi M Y, Koh Y H. 2016. The biochemical adaptations of spotted wing Drosophila (Diptera: Drosophilidae) to fresh fruits reduced fructose concentrations and glutathione S-transferase activities. Journal of Economic Entomology, 109, 973–981.
Papanicolaou A, Schetelig M F, Arensburger P, Atkinson P W, Benoit J B, Bourtzis K, Castanera P, Cavanaugh J P, Chao H, Childers C, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs R A, et al. 2016. The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biology, 17, 192.
Pearce S L, Clarke D F, East P D, Elfekih S, Gordon K H J, Jermiin L S, McGaughran A, Oakeshott J G, Papanicolaou A, Perera O P, Rane R V, Richards S, Tay W T, Walsh T K, Anderson A, Anderson C J, Asgari S, Board P G, Bretschneider A, Campbell P M, et al. 2017. Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biology, 15, 63.
Poelchau M, Childers C, Moore G, Tsavatapalli V, Evans J, Lee C Y, Lin H, Lin J W, Hackett K. 2015. The i5k Workspace@NAL-enabling genomic data access, visualization and curation of arthropod genomes. Nucleic Acids Research, 43, D714–D719.
Qin Z D, Chen J S, Jin L L, Duns G J, Ouyang P K. 2015. Differential expression of miRNAs under salt stress in Spartina alterniflora leaf tissues. Journal of Nanoscience and Nanotechnology, 15, 1554–1561.
Reynolds J A, Poelchau M F, Rahman Z, Armbruster P A, Denlinger D L. 2012. Transcript profiling reveals mechanisms for lipid conservation during diapause in the mosquito, Aedes albopictus. Journal of Insect Physiology, 58, 966–973.
Seebens H, Blackburn T M, Dyer E E, Genovesi P, Hulme P E, Jeschke J M, Pagad S, Pysek P, Winter M, Arianoutsou M, Bacher S, Blasius B, Brundu G, Capinha C, Celesti-Grapow L, Dawson W, Dullinger S, Fuentes N, Jager H, Kartesz J, et al. 2017. No saturation in the accumulation of alien species worldwide. Nature Communications, 8, 14435.
Seemann T, Booth T. 2018. BARNAP: Basic rapid ribosomal RNA predictor. [2018-05-03].
Smith C D, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie C R, Elhaik E, Elsik C G, Fave M J, Fernandes V, Gadau J, Gibson J D, Graur D, Grubbs K J, Hagen D E, Helmkampf M, Holley J A, Hu H, et al. 2011. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proceedings of the National Academy of Sciences of the United States of America, 108, 5673–5678.
Sparks J T, Dickens J C. 2017. Mini review: Gustatory reception of chemicals affecting host feeding in aedine mosquitoes. Pesticide Biochemistry and Physiology, 142, 15–20.
Tang W Q, Yu L Y, He W Y, Yang G, Ke F S, Baxter S W, You S J, Douglas C J, You M S. 2014. DBM-DB: The diamondback moth genome database. Database, 2014, bat087.
Tian L, Song T, He R, Zeng Y, Xie W, Wu Q, Wang S, Zhou X, Zhang Y J. 2017. Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci. BMC Genomics, 18, 330.
Vogel H, Schmidtberg H, Vilcinskas A. 2017. Comparative transcriptomics in three ladybird species supports a role for immunity in invasion biology. Developmental and Comparative Immunology, 67, 452–456.
Wan F H, Yang N W. 2016. Invasion and management of agricultural alien insects in China. Annual Review of Entomology, 61, 77–98.
Wang X R, Wang C, Ban F X, Zhu D T, Liu S S, Wang X W. 2017. Genome-wide identification and characterization of HSP gene superfamily in whitefly (Bemisia tabaci) and expression profiling analysis under temperature stress. Insect Science, 26, 44–57.
Wang X R, Wang C, Wang X W, Qian L X, Chi Y, Liu S S, Liu Y Q, Wang X W. 2018. The functions of caspase in whitefly Bemisia tabaci apoptosis in response to UV irradiation. Insect Molecular Biology, 27, 739–751.
Wu N, Zhang S, Li X, Cao Y, Liu X, Wang Q, Liu Q, Liu H, Hu X, Zhou X J. 2018. Fall webworm genomes yield insights into rapid adaptation of invasive species. Nature Ecology & Evolution, 3, 105–115.
Wu Z Z, Bin S Y, He H L, Wang Z B, Li M, Lin J T. 2016a. Differential expression analysis of chemoreception genes in the striped flea beetle Phyllotreta striolata using a transcriptomic approach. PLoS ONE, 11, e0153067.
Wu Z Z, Zhang H, Bin S Y, Chen L, Han Q X, Lin J T. 2016b. Antennal and abdominal transcriptomes reveal chemosensory genes in the Asian citrus psyllid, Diaphorina citri. PLoS ONE, 11, e0159372.
Wurm Y, Uva P, Ricci F, Wang J, Jemielity S, Iseli C, Falquet L, Keller L. 2009. Fourmidable: A database for ant genomics. BMC Genomics, 10, 5.
Xie W, Yang X, Chen C, Yang Z, Guo L, Wang D, Huang J, Zhang H, Wen Y, Zhao J, Wu Q, Wang S, Coates B S, Zhou X, Zhang Y. 2018. The invasive MED/Q Bemisia tabaci genome: A tale of gene loss and gene gain. BMC Genomics, 19, 68.
Yang S, Zhang J H, Wang S, Zhang X X, Liu Y, Xi J H. 2017. Identification and profiling of miRNAs in overwintering Lissorhoptrus oryzophilus via next-generation sequencing. Cryobiology, 74, 68–76.
Yin C L, Shen G Y, Guo D H, Wang S P, Ma X Z, Xiao H M, Liu J D, Zhang Z, Liu Y, Zhang Y Q, Yu K X, Huang S Q, Li F. 2016. InsectBase: A resource for insect genomes and transcriptomes. Nucleic Acids Research, 44, D801–D807.
Yuan X, Jiang Y D, Wang G Y, Yu H, Zhou W W, Liu S, Yang M F, Cheng J, Gurr G M, Way M O, Zhu Z R. 2016. Odorant-binding proteins and chemosensory proteins from an invasive pest Lissorhoptrus oryzophilus (Coleoptera: Curculionidae). Environmental Entomology, 45, 1276–1286.
[1] HOU Qian-dong, HONG Yi, WEN Zhuang, SHANG Chun-qiong, LI Zheng-chun, CAI Xiao-wei, QIAO Guang, WEN Xiao-peng. Molecular characterization of the SAUR gene family in sweet cherry and functional analysis of PavSAUR55 in the process of abscission[J]. >Journal of Integrative Agriculture, 2023, 22(6): 1720-1739.
[2] FENG Xi-kang, XIE Chun-di, LI Yong-yao, WANG Zi-shuai, BAI Li-jing. SCSMRD: A database for single-cell skeletal muscle regeneration[J]. >Journal of Integrative Agriculture, 2023, 22(3): 864-871.
[3] LI Zhi-qi, Xie Qian, YAN Jia-hui, CHEN Jian-qing, CHEN Qing-xi. Genome-wide identification and characterization of the abiotic-stress-responsive lipoxygenase gene family in diploid woodland strawberry (Fragaria vesca)[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1982-1996.
[4] Jing WAN, HUANG Cong, LI Chang-you, ZHOU Hong-xu, REN Yong-lin, LI Zai-yuan, XING Long-sheng, ZHANG Bin, QIAO Xi, LIU Bo, LIU Cong-hui, XI Yu, LIU Wan-xue, WANG Wen-kai, QIAN Wan-qiang, Simon MCKIRDY, WAN Fang-hao . Biology, invasion and management of the agricultural invader: Fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae)[J]. >Journal of Integrative Agriculture, 2021, 20(3): 646-663.
[5] FANG Zheng-wu, HE Yi-qin, LIU Yi-ke, JIANG Wen-qiang, SONG Jing-han, WANG Shu-ping, MA Dong-fang, YIN Jun-liang. Bioinformatic identification and analyses of the non-specific lipid transfer proteins in wheat[J]. >Journal of Integrative Agriculture, 2020, 19(5): 1170-1185.
[6] Mundla SRILATHA, Naina PATYAL, Madhu Sudhana SADDALA. Functional analysis and screening small molecules to RpfF protein in Xanthomonas oryzae involved in rice bacterial blight disease[J]. >Journal of Integrative Agriculture, 2020, 19(3): 735-747.
[7] ZHENG Xing-wei, YI Deng-xia, SHAO Lin-hui, LI Cong . In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula[J]. >Journal of Integrative Agriculture, 2017, 16(07): 1576-1591.
[8] JIANG Rui, WANG Tong-tong, SHAO Jin, GUO Sheng, ZHU Wei, YU Ya-jun, CHEN Shao-lin, HATANO Ryusuke. Modeling the biomass of energy crops: Descriptions, strengths and prospective[J]. >Journal of Integrative Agriculture, 2017, 16(06): 1197-1210.
[9] DONG Chun-juan, CAO Ning, ZHANG Zhi-gang, SHANG Qing-mao. Phenylalanine ammonia-lyase gene families in cucurbit species: Structure, evolution, and expression[J]. >Journal of Integrative Agriculture, 2016, 15(06): 1239-1255.
No Suggested Reading articles found!