Characterization the coding and non-coding RNA components in the transcriptome of invasion weed Alternanthera philoxeroides
Abstract
Alternanthera philoxeroides is a notorious invasive weed worldwide, but it still lacks a genome information currently. In this study, we collected 4 groups of A. philoxeroides Illumina RNA-seq data (62.5 Gb) and performed a comprehensive de novo assembling. Totally, 421,372 unigenes were obtained with a total length of 230,842,460 bp, with 43,430 (10.31%) unigenes longer than 1000 bp. Then 119,222 (28.3%) unigenes were functional annotated and 235,885 (56.0%) were grouped into reliable lncRNAs reservoir. Besides, 534 tRNA and 234 rRNAs were identified in assembly sequences. Additionally, 131,624 microsatellites were characterized in 106,761 sequences. Then SSR primers were developed for the amplification of 40,752 microsatellites in 36,329 sequences. The miRNAs are key post-transcriptional regulators, about 86 candidate miRNA sequences were detected from A. philoxeroides assembly, and miRNA target genes prediction revealed possible functions of them in growth and development as well as stress responding processes. These results provide a vital basis for sequence-based studies of A. philoxeroides in the future, especially gene function analysis.
Metrics
References
Axtell MJ (2013). Shortstack: Comprehensive annotation and quantification of small RNA genes. RNA 19:740-751. https://doi.org/10.1261/rna.035279.112
Bai C, Wang P, Fan Q, Fu W, Wang L, Zhang Z, … Wu J (2017). Analysis of the role of the drought-induced gene DRI15 and salinity-induced gene SI1 in Alternanthera philoxeroides plasticity using a virus-based gene silencing tool. Frontiers in Plant Science 8:1579. https://doi.org/10.3389/fpls.2017.01579
Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017). MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583-2585. https://doi.org/10.1093/bioinformatics/btx198
Chan PP, Lowe TM (2008). GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucleic Acids Research 37:D93-D97. https://doi.org/10.1093/nar/gkn787
Fang Z, Sun C, Lu T, Xu Z, Huang W, Ma D, Yin J (2019). Molecular mapping of stripe rust resistance gene Yrh922 in a derivative of wheat (Triticum aestivum)–Psathyrostachys huashanica. Crop Pasture Science 70:939-945. https://doi.org/10.1071/CP19317
Gao L, Geng Y, Yang H, Hu Y, Yang J (2015). Gene expression reaction norms unravel the molecular and cellular processes underpinning the plastic phenotypes of Alternanthera philoxeroides in contrasting hydrological conditions. Frontiers in Plant Science 6:991. https://doi.org/10.3389/fpls.2015.00991
Geng Y, van Klinken RD, Sosa A, Li B, Chen J, Xu CY (2016). The relative importance of genetic diversity and phenotypic plasticity in determining invasion success of a clonal weed in the USA and China. Frontiers in Plant Science 7:213. https://doi.org/10.3389/fpls.2016.00213
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, … Regev A (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols 8:1494-1512. https://doi.org/10.1038/nprot.2013.084
Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, … Chinnaiyan AM (2015). The landscape of long noncoding RNAs in the human transcriptome. Nature Genetics 47(3):199. https://doi.org/10.1038/ng.3192
Karst SM, Dueholm MS, McIlroy SJ, Kirkegaard RH, Nielsen PH, Albertsen M (2018). Retrieval of a million high-quality, full-length microbial 16s and 18s rRNA gene sequences without primer bias. Nature Biotechnology 36:190-195. https://doi.org/10.1038/nbt.4045
Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G (2007). CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research 35:W345-W349. https://doi.org/10.1093/nar/gkm391
Kozomara A, Birgaoanu M, Griffiths-Jones S (2018). miRBase: from microRNA sequences to function. Nucleic Acids Research, 47, D155-D162. https://doi.org/10.1093/nar/gky1141
Lakhotia N, Joshi G, Bhardwaj AR, Katiyar-Agarwal S, Agarwal M, Jagannath A, ... Kumar A (2014). Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing. BMC Plant Biology, 14:6. https://doi.org/10.1186/1471-2229-14-6
Li B, Dewey CN (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323-323. https://doi.org/ 10.1186/1471-2105-12-323
Li J, Ye W (2006). Genetic diversity of alligator weed ecotypes is not the reason for their different responses to biological control. Aquatic Botany 85:155-158. https://doi.org/10.1016/j.aquabot.2006.02.006
Li L, Xu L, Wang X, Pan G, Lu L (2015). De novo characterization of the alligator weed (Alternanthera philoxeroides) transcriptome illuminates gene expression under potassium deprivation. Journal of Genetics 94:95-104. https://doi.org/10.1007/s12041-015-0493-1
Liu D, Horvath D, Li P, Liu W (2019). RNA sequencing characterizes transcriptomes differences in cold response between northern and southern Alternanthera philoxeroides and highlight adaptations associated with northward expansion. Frontiers in Plant Science 10:24. https://doi.org/10.3389/fpls.2019.00024
Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenashuertero C, Chua NH (2012). Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24:4333-4345. https://doi.org/10.1105/tpc.112.102855
Lowe TM, Eddy SR (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25:955-964. https://doi.org/10.1093/nar/25.5.955
Phookaew P, Netrphan S, Sojikul P, Narangajavana J (2014). Involvement of miR164- and miR167-mediated target gene expressions in responses to water deficit in cassava. Biologia Plantarum 58:469-478. https://doi.org/10.1007/s10535-014-0410-0
Severing E, Faino L, Jamge S, Busscher M, Kuijer-Zhang Y, Bellinazzo F, … Pajoro A (2018). Arabidopsis thaliana ambient temperature responsive lncRNAs. BMC Plant Biology 18:145. https://doi.org/10.1186/s12870-018-1362-x
Song JB, Gao S, Wang Y, Li BW, Zhang YL, Yang ZM (2016). miR394 and its target gene LCR are involved in cold stress response in Arabidopsis. Plant Gene 5:56-64. https://doi.org/10.1016/j.plgene.2015.12.001
Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C,... Zhao Y (2013). Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Research 41:e166. https://doi.org/10.1093/nar/gkt646
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012). Primer3-new capabilities and interfaces. Nucleic Acids Research 40:e115. https://doi.org/10.1093/nar/gks596
Vašek J, Čílová D, Melounová M, Svoboda P, Vejl P, Štikarová R, ... Ovesná J (2020). New EST-SSR markers for individual genotyping of opium poppy cultivars (Papaver somniferum L.). Plants 9:10. https://doi.org/10.3390/plants9010010
Vitiello A, Rao R, Corrado G, Chiaiese P, Digilio MC, Cigliano RA, D’Agostino N (2018). De novo transcriptome assembly of Cucurbita pepo L. leaf tissue infested by Aphis gossypii. Data 3(3):36. https://doi.org/10.3390/data3030036
Wang B, Li W, Wang J (2005). Genetic diversity of Alternanthera philoxeroides in China. Aquatic Botany 81(3):277-283. https://doi.org/10.1016/j.aquabot.2005.01.004
Wang J (2014). Regulation of flowering time by the miR156-mediated age pathway. Journal of Experimental Botany 65:4723-4730. https://doi.org/10.1093/jxb/eru246
Wang T, Hu J, Wang R, Liu C, Yu D (2018). Tolerance and resistance facilitate the invasion success of Alternanthera philoxeroides in disturbed habitats: a reconsideration of the disturbance hypothesis in the light of phenotypic variation. Environmental and Experimental Botany 153:135-142. https://doi.org/10.1016/j.envexpbot.2018.05.011
Xia Z, Xu H, Zhai J, Li D, Luo H, He C, Huang X (2011). RNA-seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Molecular Biology 77(3):299-308. https://doi.org/10.1007/s11103-011-9811-z
Xian Z, Huang W, Yang Y, Tang N, Zhang C, Ren M, Li Z (2014). miR168 influences phase transition, leaf epinasty, and fruit development via SLAGO1s in tomato. Journal of Experimental Botany 65:6655-6666. https://doi.org/10.1093/jxb/eru387
Yin J, Liu M, Ma D, Wu J, Li S, Zhu Y, Han B (2018a). Identification of circular RNAs and their targets during tomato fruit ripening. Postharvest Biology and Technology 136:90-98. https://doi.org/10.1016/j.postharvbio.2017.10.013
Yin JL, Tian J, Li G, Zhu Y, Zhou X, He Y, … Chen Z (2020). Carbohydrate, phytohormone, and associated transcriptome changes during storage root formation in Alternanthera philoxeroides. Weed Science 68:382-395. https://doi.org/10.1017/wsc.2020.37
Yin J, Fang ZW, Sun C, Zhang P, Zhang X, Lu C, … Zhu YX (2018b). Rapid identification of a stripe rust resistant gene in a space-induced wheat mutant using specific locus amplified fragment (SLAF) sequencing. Scientific Reports 8:3086. https://doi.org/10.1038/s41598-018-21489-5
Yin JL, Wang LX, Zhao J, Li YT, Huang R, Jiang XC, ... Zhu YX (2020). Genome-wide characterization of the C2H2 zinc-finger genes in Cucumis sativus and functional analyses of four CsZFPs in response to stresses. BMC Plant Biology 20: 359. https://doi.org/10.1186/s12870-020-02575-1
Yuan J, Zhang Y, Dong J, Sun Y, Lim B, Liu D, Lu Z (2016). Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. BMC Genomics 17:655. https://doi.org/10.1186/s12864-016-2929-2
Zhang X, Liu YH, Wang YH, Shen SK (2020). Genetic diversity and population structure of rhododendron rex subsp. Rex inferred from microsatellite markers and chloroplast DNA sequences. Plants 9:338. https://doi.org/10.3390/plants9030338
Zhou R, Zhu Y, Zhao J, Fang Z, Wang S, Yin J, … Ma D (2018). Transcriptome-wide identification and characterization of potato circular RNAs in response to Pectobacterium carotovorum subspecies brasiliense infection. International Journal of Molecular Sciences 19(1):71. https://doi.org/10.3390/ijms19010071
Zhu Y, Jia JH, Yang L, Xia Y, Zhang H, Jia J, … Liu L (2019a). Identification of cucumber circular RNAs responsive to salt stress. BMC Plant Biology 19:164. https://doi.org/10.1186/s12870-019-1712-3
Zhu YX, Yin J, Liang Y, Liu J, Jia J, Huo H, … Gong H (2019b). Transcriptomic dynamics provide an insight into the mechanism for silicon-mediated alleviation of salt stress in cucumber plants. Ecotoxicology and Environmental Safety 174:245-254. https://doi.org/10.1016/j.ecoenv.2019.02.075
Zhu Y, Gong HJ, Yin JL (2019c). Role of silicon in mediating salt tolerance in plants: a review. Plants 8:147. https://doi.org/10.3390/plants8060147
Zhu YX, Yang L, Liu N, Yang J, Zhou XK, Xia YC, … Yin JL (2019d). Genome-wide identification, structure characterization, and expression pattern profiling of aquaporin gene family in cucumber. BMC Plant Biology 19: 345. https://doi.org/10.1186/s12870-019-1953-1
Copyright (c) 2021 Notulae Botanicae Horti Agrobotanici Cluj-Napoca
This work is licensed under a Creative Commons Attribution 4.0 International License.
License:
Open Access Journal:
The journal allows the author(s) to retain publishing rights without restriction. Users are allowed to read, download, copy, distribute, print, search, or link to the full texts of the articles, or use them for any other lawful purpose, without asking prior permission from the publisher or the author.
.png){kind=icon}
.png)
