Isolation, identification and characterization of reverse transcriptase sequence from Ty1-copia retrotransposon in <i>Avena nuda</i>

Guo Xiao-Fang; Jia Ju-Qing; Zhang Xiao-Jun; Zhang Chun-Lai; Zhang Mei-Jun; Feng Mei-Chen; Yang Wu-De

doi:10.11913/PSJ.2095-0837.2018.50721

Plant Science Journal > 2018 > 36(5): 721-728. > DOI: 10.11913/PSJ.2095-0837.2018.50721 CSTR: 32231.14.PSJ.2095-0837.2018.50721

Guo Xiao-Fang, Jia Ju-Qing, Zhang Xiao-Jun, Zhang Chun-Lai, Zhang Mei-Jun, Feng Mei-Chen, Yang Wu-De. Isolation, identification and characterization of reverse transcriptase sequence from Ty1-copia retrotransposon in Avena nuda[J]. Plant Science Journal, 2018, 36(5): 721-728. DOI: 10.11913/PSJ.2095-0837.2018.50721

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Isolation, identification and characterization of reverse transcriptase sequence from Ty1-copia retrotransposon in Avena nuda

1. College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi 030801, China;
2. Institute of Crop Science, Shanxi Academy of Agricultural Science, Taiyuan 030032, China

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This work was supported by grants from the National Natural Science Foundation of China (31101199), Project supported by the Shanxi Provincial Research Foundation for Applied Basic Research (201601D102047, 201601D102051), Key Project in the Key Research and Development Program of Shanxi Province (201703D211001-03-01), Special Program of Scientific Research for Shanxi Agriculture Valley Construction of China (SXNGJSKYZX201702), and Project for Major Improvement Supported by Shanxi Agricultural University (TSJH1406).

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Received Date: April 16, 2018
Available Online: October 31, 2022
Published Date: October 27, 2018

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Abstract

Abstract

Using degenerate oligonucleotide primers corresponding to the conserved domains of the Ty1-copia retrotransposon reverse transcriptase, 23 Ty1-copia retrotransposons reverse transcriptase sequences were isolated by polymerase chain reaction (PCR) from the genome of Avena nuda L., and characterization, phylogeny and transcriptional activities of these sequences were carried out. Results showed that the retrotransposons had high heterogeneity, with 45%-98% identity between sequences. The DNA sequences displayed mutations, including insertions, frameshifts, and stop codons, but the frequencies were not high. Phylogenetic analysis showed that the Ty1-copia retrotransposons of oats were mainly transmitted vertically during evolution. Five Ty1-copia retrotransposons with transcriptional activity were found by searching the oat gene expression database.
- Avena nuda,
- Ty1-copia retrotransposon,
- Evolution,
- Transcriptional activation

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References (31)

References

[1]	Bennetzen JL. Transposable element contributions to plant gene and genome evolution[J]. Plant Mol Biol, 2000, 42(1):251-269.
[2]	Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. The B73 maize genome:complexity, diversity, and dynamics[J]. Science, 2009, 326(5966):1112-1115.
[3]	Bennetzen JL, Wang H. The contributions of transposable elements to the structure, function, and evolution of plant genomes[J]. Annu Rev Plant Biol, 2014, 65:505-530.
[4]	Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, et al. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges[J]. Plant Cell, 2012, 24(3):1242-1255.
[5]	Xia C, Zhang LC, Zou C, Gu YQ, Duan JL, et al. A TRIM insertion in the promoter of Ms2 causes male sterility in wheat[J]. Nat Commun, 2017, 8:15407.
[6]	Angelika V, Viktorija B, Aris J, Dainis R. Stress-induced transcriptional activation of retrotransposon-like sequences in the Scots pine (Pinus sylvestris L.) genome[J]. Tree Genet Genomes, 2014, 10(4):937-951.
[7]	Woodrow P, Pontecorvo G, Fantaccione S, Fuggi A, Kafantaris I, et al. Polymorphism of a new Ty1-copia retrotransposon in durum wheat under salt and light stresses[J]. Theor Appl Genet, 2010, 121(2):311-322.
[8]	Grandbastien MA. LTR retrotransposons, handy hitchhi-kers of plant regulation and stress response[J]. BBA-GeneRegul Mech, 2015, 1849(4):403-416.
[9]	Lisch D, Bennetzen JL. Transposable element origins of epigenetic gene regulation[J]. Curr Opin Plant Biol, 2011, 14(2):156-161.
[10]	Ahmed S, Shafiuddin M, Azam MS, Islam MS, Ghosh A, Khan H. Identification and characterization of jute LTR retrotransposons:their abundance, heterogeneity and transcriptional activity[J]. Mob Genet Elements, 2011, 1(1):18-28.
[11]	范付华, 乔光, 郑思成, 文晓鹏. 火龙果Ty1-copia类反转录转座子反转录酶序列的克隆及分析[J]. 园艺学报, 2012, 39(2):265-272. Fan FH, Qiao G, Zhen SC, Wen XP. Cloning and analysis of reverse transcriptase of Ty1-copia retrotransposons in Hylocereus undatus[J]. Acta Horticulturae Sinical, 2012, 39(2):265-272.
[12]	Fan F, Wen X, Ding G, Cui B. Isolation, identification, and characterization of genomic LTR retrotransposon sequences from masson pine (Pinus massoniana)[J]. Tree Genet Genomes, 2013, 9(5):1237-1246.
[13]	Ma B, Kuang L, Xin Y, Hou F, He N. Reverse transcriptase sequences from mulberry LTR retrotransposons:characterization analysis[J]. Open Life Sci, 2017, 12(1):266-276.
[14]	Rasane P, Jha A, Sabikhi L, Kumar A, Unnikrishnan VS. Nutritional advantages of oats and opportunities for its processing as value added foods-a review[J]. J Food Sci Technol, 2015, 52(2):662-675.
[15]	Bussler WW, Dezego K, Bowen M, Buige A, Esposito D, et al. Health modifying regions in the oat (Avena sativa) genome responsible for beneficial effects on immune and gastrointestinal health[J]. Faseb J, 2017, 31(1):437.
[16]	Fu YB. Oat evolution revealed in the maternal lineages of 25Avena species[J]. Sci Rep, 2018, 8:4252.
[17]	Wu B, Hu Y, Huo P, Zhang Q, Chen X, Zhang Z. Transcriptome analysis of hexaploid hulless oat in response to salinity stress[J]. PLoS One, 2017, 12(2):e0171451.
[18]	Yan H, Martin SL, Bekele WA, Latta RG, Diederichsen A, et al. Genome size variation in the genus Avena[J]. Genome, 2016, 59(3):209-220.
[19]	Linares C, Serna A, Fominaya A. Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species[J]. Genome, 1999, 42(4):706-713.
[20]	翟志文, 柴国师, 候莎莎, 剌士潇, 靳艳婷, 贾举庆. 燕麦D基因组特异标记开发[J]. 农学学报, 2015, 5(10):88-92. Zhai ZW, Chai GS, Hou SS, La SX, Jin YT, Jia JQ. Development of D genome-specific marker in oat[J]. Journal of Agriculture, 2015, 5(10):88-92.
[21]	Linares C, Loarce Y, Serna A, Fominaya A. Isolation and characterization of two novel retrotransposons of the Ty1-copia group in oat genomes[J]. Chromosoma, 2001, 110(2):115-123.
[22]	Kimura Y, Tosa Y, Shimada S, Sogo R, Kusaba M, et al. OARE-1, a Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses[J]. Plant cell Physiol, 2001, 42(12):1345-1354.
[23]	Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison J, et al. The Ty1-copia group of retrotransposons in plants:genomic organisation, evolution, and use as molecular markers[J]. Genetica, 1997, 100(1):205-217.
[24]	Jiang B, Wu ZM, Lou QF, Wang D, Zhang WP, Chen JF. Genetic diversity of Ty1-copia retrotransposons in a wild species of Cucumis (C. hystrix)[J]. Sci Hortic, 2010, 127(1):46-53.
[25]	Gabriel A, Willems M, Mules EH, Boeke JD. Replication infidelity during a single cycle of Ty1 retrotransposition[J]. Proc Natl Acad Sci USA, 1996, 93(15):7767-7771.
[26]	Song Y, Ji D, Li S, Wang P, Li Q, Xiang F. The dynamic changes of DNA methylation and histone modifications of salt responsive transcription factor genes in soybean[J]. PLoS One, 2012, 7(7):e41274.
[27]	Diao XM, Freeling M, Lish D. Horizontal transfer of a plant transposon[J]. PLoS Biol, 2006, 4(1):120-128.
[28]	Jin Y, Li XY, Pan C, Li YY, Jiang JY, Jiang CJ. Cloning and analysis of reverse transcriptases from Ty1-copia retrotransposons in Camellia sinensis[J]. Biotechnol Biotec Eq, 2017, 31(4):663-669.
[29]	He N, Zhang C, Qi X, Zhao S, Tao Y, et al. Draft genome sequence of the mulberry tree Morus notabilis[J]. Nat Commun, 2013, 4:2445.
[30]	Sarkar D, Mahato AK, Satya P, Kundu A, Singh SJ, et al. The draft genome of Corchorus olitorius cv. JRO-524(Navin)[J]. Genomics Data, 2017, 12:151-154.
[31]	Anca IA, Fromentin J, Bui QT, Mhiri C, Grandbastien MA, Simon-Plas F. Different tobacco retrotransposons are specifically modulated by the elicitor cryptogein and reactive oxygen species[J]. J Plant Physiol, 2014, 171(16):1533-1540.

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