Phylogenetic tree-informed microRNAome analysis uncovers conserved and lineage-specific miRNAs inCamelliaduring floral organ development

Abstract

In plants, miRNAs are endogenous small RNAs derived from single-stranded precursors with hairpin structures. The evolution of miRNAs and their targets represents one of the most dynamic circuits directing gene expression, which may play fundamental roles in shaping the development of distinct plant organs. Here we performed high-throughput small RNA sequencing in five organ types of Camellia azalea to capture the spatial profile of small non-coding RNA. In total we obtained >227 million high-quality reads and identified 175 miRNAs with mature and precursor sequences. We aligned the miRNAs to known miRNA databases and revealed some conserved as well as 'newly evolved' miRNA genes. Twelve miRNAs were identified to be specific in the genus Camellia, supporting the lineage-specific manner of expansion of 'young' miRNAs. Through differential expression analysis, we showed that many miRNAs were preferentially abundant in certain organ types. Moreover, hierarchical clustering analysis revealed distinctive expression patterns of tissue-specific miRNAs. Gene Ontology enrichment analysis of targets of stamen- and carpel-specific miRNA subclusters showed that miRNA-target regulatory circuits were involved in many important biological processes, enabling their proper specification and organogenesis, such as 'DNA integration' and 'fruit development'. Further, quantitative PCR of key miRNAs and their target genes revealed anti-correlated patterns, and uncovered the functions of key miRNA-target pairs in different floral organs. Taken together, this work yielded valuable information on miRNA-target regulation in the control of floral organ development and sheds light on the evolution of lineage-specific miRNAs in Camellia.

Global gene expression defines faded whorl specification of double flower domestication in Camellia

“…In Arabidopsis , SPL was found to be required for anther sporogenic tissues differentiation and expressed abundantly in the anther tissues 17, 32, 33 . In Camellia , miR156 was expressed abundantly in stamen where SPL1 and SPL2 were expressed at a low level 22 . In this study, SPLs were expressed just in stamen filaments but not anther tissues (Fig.…”

“…For each small RNA sequencing library, the clean reads range from 18–30 bp were obtained and then filtered through RNA databases before miRNA identification 22 . The transcriptome assemble from C. japonica was used as reference for precursors identification.…”

“…With the increasing power of high throughput sequencing, the sequencing of small RNA and Parallel Analysis of RNA Ends (PARE, degradome) offer effective and high throughput ways in identifying miRNAs and their targets in plant species even in the absence of a reference genome 20, 21 . Indeed, in Camellia azalea , the small RNA and transcriptome sequencing were shown to be useful in identifying key regulatory genes including conserved and novel miRNAs, and evolution of miRNA genes was predictable in the context plant evolution 22, 23 . It is unclear if these miRNAs target genes are involved in the regulation of double flower development.…”

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

“…However, we also determined the frequency of the base of the mature miRNAs, the result showed that the 20bp, 21bp, and 22bp miRNAs preferentially start with 'U' at the rst base (46.96%, 55.37%, and 61.22%, respectively) (Additional le 1: Fig.S3), while 24bp miRNAs preferred 'A' (58.5%). Comparing with miRNA's rst nucleotide bias analysis in other species, we found the bias tendency in 21bp, 22bp and 24bp miRNAs is similar to Camellia japonica [34], pomegranate [35].…”

Identification of novel and conserved microRNAs involved in fruit development and ripening in Fragaria vesca

“…MiRNA was first identified in Caenorhabditis elegans and subsequently found in almost all eukaryotes [9]. In higher plants, miRNAs play important roles in different developmental stages by mediating gene silencing at transcriptional and post-transcriptional levels [10,11] and appear to be one of the most significant regulatory mechanisms [12][13][14]. Increasing evidence indicates that miRNAs are involved in plant development, signaling, abiotic stresses, and symbiotic relationship regulation [15,16].…”