Characterization the coding and non-coding RNA components in the transcriptome of invasion weed Alternanthera philoxeroides

  • Yongxing ZHU Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434000, Hubei (CN)
  • Xinchen JIANG Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434000, Hubei (CN)
  • Xiaowen HAN Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434000, Hubei (CN)
  • Shuo HAN Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434000, Hubei (CN)
  • Zhongyi CHEN Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434000, Hubei (CN)
  • Junliang YIN Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434000, Hubei; Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Hubei Academy of Agricultural Sciences, 430064, Wuhan (CN)
  • Yiqing LIU Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434000, Hubei (CN)
Keywords: alligator weed; invasive plant; reference unigenes; expression pattern profiling; function annotation; SSR marker

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.

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Published
2021-03-01
How to Cite
ZHU, Y., JIANG, X., HAN, X., HAN, S., CHEN, Z., YIN, J., & LIU, Y. (2021). Characterization the coding and non-coding RNA components in the transcriptome of invasion weed Alternanthera philoxeroides. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 49(1), 12242. https://doi.org/10.15835/nbha49112242
Section
Research Articles
CITATION
DOI: 10.15835/nbha49112242