Gao Fan, Nan Fangru, Feng Jia, Xie Shulian
School of Life Science, Shanxi University, Wucheng Road No. 92, Taiyuan 030006, P. R. China.
Iran J Biotechnol. 2021 Oct 1;19(4):e2868. doi: 10.30498/ijb.2021.247164.2868. eCollection 2021 Oct.
MicroRNA (miRNA) is a key regulator at the gene posttranscriptional regulation level. We have previously identified miRNAs and their putative targets in 3 representative red algae, , and .
In this study, unique molecular and evolutionary characterization of miRNAs were revealed in the 3 red algae based on the comparative miRNAs profiling.
Genome locations of small RNAs (sRNAs), miRNAs and () in the 3 red algae were shown by collinearity analysis. Characterization of miRNAs and were profiled via bioinformatics analysis. Taken and miR156s for examples, red algae miRNAs evolutionary features were demonstrated via phylogenetic and evolutionary information analysis. MiRNA targets main inhibition type was validated via performing data statistics and RLM-RACE PCR. Key target genes and their function were predicted by the common Gene Ontolgoy (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis.
Quantity, nucleotide bias and common sequences of miRNAs were analyzed in the 3 red algae. Four typical precursor structures and primary molecular features of red algae miRNAs were profiled. Genome-wide collinearity analysis of sRNAs, miRNAs and in the 3 red algae was performed to show their distribution and interrelation based on the deep sequencing data. Taken red algae for example, their family members and sequences divergence were demonstrated. The whole evolutionary processes of miR156s and pre-miR156s in red algae were steady with negative selected pressure though diverse phylogenetic relationships and evolutionary parameters showed. Through 3 red algae miR156 targets validation, cleavage was validated as their main miRNA targets inhibition type. The common target genes (GO:0009536) enriched significantly for plastid formation will provide important insights for red algal biopigment research. The common KEGG pathways (ko01100) enriched significantly were predicted without a detailed reference metabolic map.
MiRNA plays an essential role in gene expression regulation involved in diverse biological processes of red algae. Comprehensive molecular and evolutionary features of miRNAs in the 3 red algae will provide insights for further utilizing the algae resources at the molecular level.
微小RNA（miRNA）是基因转录后调控水平的关键调节因子。我们之前已在3种代表性红藻（ 、 和 ）中鉴定出miRNA及其潜在靶标。
本研究基于比较性miRNA分析，揭示了3种红藻中miRNA独特的分子和进化特征。
通过共线性分析展示了3种红藻中小RNA（sRNA）、miRNA和（ ）的基因组位置。通过生物信息学分析对miRNA和（ ）进行了特征分析。以（ ）和miR156s为例，通过系统发育和进化信息分析展示了红藻miRNA的进化特征。通过数据统计和RLM-RACE PCR验证了miRNA靶标的主要抑制类型。通过通用基因本体论（GO）和京都基因与基因组百科全书（KEGG）通路富集分析预测了关键靶基因及其功能。
分析了3种红藻中miRNA的数量、核苷酸偏好和共有序列。描绘了红藻miRNA的四种典型前体结构和主要分子特征。基于深度测序数据，对3种红藻中的sRNA、miRNA和（ ）进行了全基因组共线性分析，以展示它们的分布和相互关系。以红藻（ ）为例，展示了其家族成员和序列差异。尽管显示出不同的系统发育关系和进化参数，但红藻中miR156s和前体miR156s的整个进化过程在负选择压力下是稳定的。通过对3种红藻miR156靶标的验证，证实切割是其主要的miRNA靶标抑制类型。显著富集的共同靶基因（GO:0009536）参与质体形成，这将为红藻生物色素研究提供重要见解。预测了显著富集的共同KEGG通路（ko01100），但没有详细的参考代谢图谱。
miRNA在参与红藻多种生物学过程的基因表达调控中起重要作用。3种红藻中miRNA的综合分子和进化特征将为在分子水平上进一步利用藻类资源提供见解。
