Genome sequencing of eggplant reveals Eggplant mild leaf mottle virus existence with associated two endogenous viruses in diseased eggplant in Iraq

References

• Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N. 2009. Next‐generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol. 10(4):537–545.
   PubMed Web of Science ®Google Scholar
• Adams MJ, Antoniw JF. 2005. DPVweb: An open access internet resource on plant viruses and virus diseases. Outlook Pest Man. 16(6):268–270.
   Google Scholar
• Al-Ani RA, Adhab MA, Hassan KA. 2011. Antiviral activity of Vit-org, 2-nitromethyl phenol and Thuja extract against Eggplant blister mottled virus (EBMV). Afr J Microbiol Res. 5(21):3555–3558.
   Google Scholar
• Al-Ani RA, Adhab MA, Ismail KA. 2011. Eggplant blister mottled virus (EBMV): A possible new potyvirus characterized from Iraq. J Gener Mol Virol. 3(3):49–54.
   Google Scholar
• Alisawi ON. 2019. Virus integration and tandem repeats in the genomes of Petunia [Doctoral dissertation]. UK: University of Leicester.
   Google Scholar
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410.
   PubMed Web of Science ®Google Scholar
• Barchi L, Pietrella M, Venturini L, Minio A, Toppino L, Acquadro A, Andolfo G, Aprea G, Avanzato C, Bassolino L, et al. 2019. A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Sci Rep. 9(1):1–13.
   PubMedGoogle Scholar
• Bester R, Cook G, Breytenbach JH, Steyn C, De Bruyn R, Maree HJ. 2021. Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids. Virol J. 18(1):1–19.
   PubMed Web of Science ®Google Scholar
• D’Arcy WG. 1991. The Solanaceae since 1976 with a review of its biogeography. In: Hawkes JG, Lester RN, Nee M, Estrada N, editors. Solanaceae III. London: Royal Botanic Gardens/Kew; p. 75–138.
   Google Scholar
• Dombrovsky A, Sapkota R, Lachman O, Antignus Y. 2012. Eggplant mild leaf mottle virus (EMLMV), a new putative member of the genus Ipomovirus that harbors an HC-Pro gene. Virus Genes. 44(2):329–337.
   PubMed Web of Science ®Google Scholar
• Dombrovsky A, Sapkota R, Lachman O, Pearlsman M, Antignus Y. 2013. A new aubergine disease caused by a whitefly‐borne strain of Tomato mild mottle virus (TomMMoV). Plant Pathol. 62(4):750–759.
   Web of Science ®Google Scholar
• Doyle J, Doyle J. 1990. Isolation of DNA from small amounts of plant tissues. BRL Focus. 12:V15.
   Google Scholar
• Geering AD, Maumus F, Copetti D, Choisne N, Zwickl DJ, Zytnicki M, ... , Teycheney PY 2014. Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nat. Commun. 5(1):1–11.
   Google Scholar
• Gilbert W. 1986. The RNA world superlattices point ahead. Nature. 319(6055):618–618.
   PubMed Web of Science ®Google Scholar
• Goodrich D, Tao X, Bohrer C, Lonczak A, Xing T, Zimmerman R, Zhan Y, Scott Jr RT, Treff NR. 2016. A randomized and blinded comparison of qPCR and NGS-based detection of aneuploidy in a cell line mixture model of blastocyst biopsy mosaicism. J Assist Reprod Genet. 33(11):1473–1480.
   PubMed Web of Science ®Google Scholar
• Hansen CN, Harper G, Heslop-Harrison JS. 2005. Characterisation of pararetrovirus-like sequences in the genome of potato (Solanum tuberosum). Cytogenet. Genome Res. 110(1-4):559–565.
   PubMed Web of Science ®Google Scholar
• Heslop-Harrison JS. 2000. RNA, genes, genomes and chromosomes: repetitive DNA sequences in plants. In: Ettore Olmo, Carlo Alberto Redi (Eds.), Chromosomes today. Vol. 13; p. 45–56.
   Google Scholar
• Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, et al. 2014. Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res. 21(6):649–660.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17(8):754–755.
   PubMed Web of Science ®Google Scholar
• Huggett JF, O’Grady J, Bustin S. 2015. qPCR, dPCR, NGS–a journey. Biomol Detect Quantif. 3:A1–A5.
   PubMedGoogle Scholar
• Jones S, Baizan-Edge A, MacFarlane S, Torrance L. 2017. Viral diagnostics in plants using next generation sequencing: computational analysis in practice. Front Plant Sci. 8:1770.
   PubMed Web of Science ®Google Scholar
• Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110(1–4):462–467.
   PubMed Web of Science ®Google Scholar
• Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649.
   PubMed Web of Science ®Google Scholar
• Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering ADW. 2018. Ortervirales: New virus order unifying five families of reverse-transcribing viruses. J Virol. 92:1–5.
   Web of Science ®Google Scholar
• Krupovic M, Koonin EV. 2017. Homologous capsid proteins testify to the common ancestry of retroviruses, caulimoviruses, pseudoviruses, and metaviruses. J. Virol. 91:e210–e217.
   Web of Science ®Google Scholar
• Mustafa SI, Schwarzacher T, Heslop-Harrison J. 2018. Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors. Mitochondrial DNA Part A. UK: Taylor and Francis Online, 1–14.
   PubMed Web of Science ®Google Scholar
• Mustafa SI. 2018. Mitochondrial and repetitive DNA defining the sheep genome landscape [Doctoral dissertation]. University of Leicester, 298 pages.
   Google Scholar
• Novák P, Neumann P, Pech J, Steinhaisl J, Macas J. 2013. RepeatExplorer: a Galaxy based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 29(6):792–793.
   PubMed Web of Science ®Google Scholar
• Richert‐Pöggeler KR, Noreen F, Schwarzacher T, Harper G, Hohn T. 2003. Induction of infectious Petunia vein clearing (pararetro) virus from endogenous provirus in petunia. Embo J. 22(18):4836–4845.
   PubMed Web of Science ®Google Scholar
• Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. 2021. Broken, silent, and in hiding: Tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). Ann Bot. 128(3):281–299.
   PubMed Web of Science ®Google Scholar
• Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science. 326(5956):1112–1115.
   PubMed Web of Science ®Google Scholar
• Serfraz S, Sharma V, Maumus F, Aubriot X, Geering AD, Teycheney PY. 2021. Insertion of badnaviral DNA in the late blight resistance gene (R1a) of brinjal eggplant (Solanum melongena). Front Plant Sci. 12
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30(12):2725–2729.
   PubMed Web of Science ®Google Scholar
• Wei Q, Wang J, Wang W, Hu T, Hu H, Bao C. 2020. A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant. Hortic Res. 7(1):1–15.
   PubMed Web of Science ®Google Scholar
• Wu F, Eannetta NT, Xu Y, Tanksley SD. 2009. A detailed synteny map of the eggplant genome based on conserved ortholog set II (COSII) markers. Theor Appl Genet. 118(5):927–935.
   PubMed Web of Science ®Google Scholar
• Yang H, Liu M, Jiang H, Zeng Y, Jin L, Luan T, Deng Y, He N, Zhang G, Zeng X. 2017. Copy number variation analysis based on gold magnetic nanoparticles and fluorescence multiplex ligation-dependent probe amplification. J Biomed Nanotechnol. 13(6):655–664.
   Web of Science ®Google Scholar