Moso bamboo (Phyllostachys edulis) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8,045 differentially expressed genes (DEGs) and 1,053 differentially expressed proteins (DEPs) were identified in our analyses. Gene ontology and KEGG enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs, and three significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein-protein interaction (PPI) network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.
Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.
Cuttage propagation involves adventitious root formation induced by auxin. In our previous study, Larix kaempferi BABY BOOM 1 (LkBBM1), which is known to regulate adventitious root formation, was affected by auxin. However, the relationship between LkBBM1 and auxin remains unclear. Auxin response factors (ARFs) are a class of important transcription factors in the auxin signaling pathway and modulate the expression of early auxin-responsive genes by binding to auxin response elements. In the present study, we identified 14 L. kaempferi ARFs (LkARFs), and found LkARF7 and LkARF19 bound to LkBBM1 promoter and enhanced its transcription using yeast one-hybrid, ChIP-qPCR, and dual-luciferase assays. In addition, the treatment with naphthalene acetic acid promoted the expression of LkARF7 and LkARF19. We also found that overexpression of these two genes in poplar promoted adventitious root formation. Furthermore, LkARF19 interacted with the DEAD-box ATP-dependent RNA helicase 53-like protein to form a heterodimer to regulate adventitious root formation. Altogether, our results reveal an additional regulatory mechanism underlying the control of adventitious root formation by auxin.
The radial change (RC) of tree stem is the process of heartwood formation involved in complex molecular mechanism. Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.), an evergreen species, is an important fast-growing timber tree in southern China. In this study, the top four stable genes (IDH, UBC2, RCA and H2B) were selected in RC tissues of 15 years old Chinese fir stem (RC15) and the genes (H2B, 18S, TIP41 and GAPDH) were selected in RC tissues of 30 years old Chinese fir stem (RC30). The stability of the reference genes is higher in RC30 than in RC15. Sixty-one MYB transcripts were obtained on the PacBio Sequel platform from woody tissues of one 30 years old Chinese fir stem. Based on the number of MYB DNA-binding domain and phylogenetic relationships, the ClMYB transcripts contained 21 transcripts of MYB-related proteins (1R-MYB), 39 transcripts of R2R3-MYB proteins (2R-MYB), one transcript of R1R2R3-MYB protein (3R-MYB) belonged to 18 function-annotated clades and two function-unknown clades. In RC woody tissues of 30 years old Chinese fir stem, ClMYB22 was the transcript with the greatest fold change detected by both RNA-seq and qRT-PCR. Reference genes selected in this study will be helpful for further verification of transcript abundance patterns during the heartwood formation of Chinese fir.
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