Abstract
Plant growth and development is usually characterized by chronological age over the plants’ lifetimes. Age-related changes actually originate with meristems because they control if, where, when, and how new tissues are formed along the axis of the shoot. The “time-keeping” of plant meristem development is a complex process. To uncover the post-transcriptional regulation underlying the chronological development of Larix kaempferi (Japanese larch) meristems, we investigated the miRNA-mediated regulatory network in the defoliated, uppermost main stems of 1-, 2-, 5-, 10-, 25-, and 50-year-old L. kaempferi using RNA-seq methods. We identified 29 high-confidence miRNAs, three of which were defined, age-related miRNAs whose expression changed depending on L. kaempferi age, and 17 showed coordinated expression patterns with three age-related miRNAs based on hierarchical correlations. All hierarchically coordinated miRNAs and their targets constituted a miRNA-mediated regulatory network. The developmental timing pathway lka-miR-1-5p-156-SBP/SPL (Squamosa Promoter Binding Protein-Like), the lignin biosynthesis pathway lka-miR-7,13-5p-397-LAC (Laccase), and an unknown pathway lka-miR-3-5p-CMSS1 (Cms1 Ribosomal Small Subunit Homolog) were age-driven, and information from auxin and light could be integrated by the lka-miR-9-5p-390-TAS/ARF (Trans-Acting siRNA3/Auxin Response Factor) and lka-miR-8-5p-IRL4 (Plant Intracellular Ras-Group-Related LRR Protein 4) pathways, respectively. Age-driven regulatory network will lead the way to understand which and how genes mutually cross-regulate their activity orchestrating development of meristems of L. kaempferi with age. We also discussed and contributed to miRNA annotation and nomenclature.
Highlights
Plant growth and development is usually characterized by chronological age at various scales over the plants’ lifetimes (Gatsuk et al 1980)
To identify with high-confidence miRNAs within the complex sRNAome, 5,945,922 unique small RNAs (sRNA) sequences were aligned to the L. kaempferi transcriptome database (Li et al 2017), and the read patterns that were predicted using the MIREAP algorithm were checked manually
Homology-based inference was used for homology detection to supplement annotation, so if sequence homology existed between putative miRNA and a known miRNA, and their targets showed significantly higher levels of sequence homology between each other, we considered them homologous
Summary
Plant growth and development is usually characterized by chronological age at various scales over the plants’ lifetimes (Gatsuk et al 1980). Meristem activity is a highly dynamic process which must be coordinately controlled by both extrinsic and intrinsic regulatory networks responding to environmental and organismal cues, such as temperature, light, hormones, carbohydrates, and age (Poethig 1990, 2013; Adrian et al 2009; Amasino 2010; Srikanth and Schmid 2011; Huijser and Schmid 2011; Nieminen et al 2015; Ye and Zhong 2015). WUSCLV and miR156-SPL pathways play critical roles in the control of shoot apical meristem (SAM) (Lenhard and Laux 1999; Schoof et al 2000; Fouracre and Poethig 2019). Thousands of genes which constitute a complex molecular regulatory network are involved in meristematic activity
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