A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

Abstract

Liriodendron chinense is an economically and ecologically important deciduous tree species. Although the reference genome has been revealed, alternative polyadenylation (APA), transcription factors (TFs), long non-coding RNAs (lncRNAs), and co-expression networks of tissue-specific genes remain incompletely annotated. In this study, we used the bracts, petals, sepals, stamens, pistils, leaves, and shoot apex of L. chinense as materials for hybrid sequencing. On the one hand, we improved the annotation of the genome. We detected 13,139 novel genes, 7,527 lncRNAs, 1,791 TFs, and 6,721 genes with APA sites. On the other hand, we found that tissue-specific genes play a significant role in maintaining tissue characteristics. In total, 2,040 tissue-specific genes were identified, among which 9.2% of tissue-specific genes were affected by APA, and 1,809 tissue-specific genes were represented in seven specific co-expression modules. We also found that bract-specific hub genes were associated plant defense, leaf-specific hub genes were involved in energy metabolism. Moreover, we also found that a stamen-specific hub TF Lchi25777 may be involved in the determination of stamen identity, and a shoot-apex-specific hub TF Lchi05072 may participate in maintaining meristem characteristic. Our study provides a landscape of APA, lncRNAs, TFs, and tissue-specific gene co-expression networks in L. chinense that will improve genome annotation, strengthen our understanding of transcriptome complexity, and drive further research into the regulatory mechanisms of tissue-specific genes.

The Roles of microRNA-Long Non-coding RNA-mRNA Networks in the Regulation of Leaf and Flower Development in Liriodendron chinense

“…We used Illumina sequencing and PacBio sequencing to obtain transcriptome data; the construction of the respective libraries and the data processing were described in our previous study (Tu et al, 2020(Tu et al, , 2021. In total, 12 samples from the leaves, pistils, stamens, and petals were sequenced.…”

“…In our previous study, we identified 7,527 lncRNAs using PacBio sequencing (Tu et al, 2020(Tu et al, , 2021. To predict the target genes of lncRNAs, we used the method described by Liu S. et al (2018).…”

“…In our previous study, we identified 17,363 DEGs from the leaves, petals, pistils, and stamens of L. chinense (Supplementary Figure 1; Tu et al, 2021). To better understand the functions of these DEGs, we performed KEGG pathway enrichment analysis.…”

“…In our previous study, we identified 7,527 lncRNAs and 1,791 TFs (Tu et al, 2021). In this study, we used the τ-value to evaluate the tissue specificity of these lncRNAs.…”

Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response

“…APA can produce multiple mRNA polyadenylation isoforms through pre-mRNA endonucleolytic cleavage and poly(A) tail addition at the 3’ cleavage site end of a nascent transcript to change the length of untranslated regions (UTRs) or coding regions that may influence mRNA stability, translation efficiency, subcellular localization, or gene function gain or loss. Consequently, all these changes will result in various plant physiological and biochemical processes ( Yeh and Yong, 2016 ; Sadek et al, 2019 ; Zhang et al, 2020 ; Tu et al, 2021 ); for example, APA participates in cell wall modification, root hair development, DNA repair, and gene regulation in response to abiotic and biotic stresses ( Cao et al, 2019 ; Ye et al, 2019 ; Yan et al, 2021 ). LncRNAs longer than 200 nucleotides are epigenetic regulators that regulate gene expression by interacting with mRNAs, DNAs, proteins, and miRNAs to participate in biological processes such as plant growth and development and biotic and abiotic stress responses ( Budak et al, 2020 ; Yu et al, 2020 ; Tu et al, 2021 ; Urquiaga et al, 2021 ).…”