MOS4-Associated Complex subunits 3A and 3B modulate FLM splicing to repress floral transition in short day

MOS4 Associated Complex subunits 3A and 3B modulate FLM splicing to repress floral transition in a short day. To investigate the underlying mechanisms of the early flowering trait of mac3amac3b double mutants, we performed RNA sequencing with 40dayold leaves of mac3amac3b mutants and Col-0, which were still in the vegetative phase under short days. The RNA sequencing libraries of triple replicates of both Col-0 and mac3amac3b were prepared by Genomic Technology Core at the Institute of Plant and Microbial Biology in Academia Sinica with the Illumina TrueSeq toolkit. The paired end reads sequencing data were trimmed with Trimmomatic to remove undesired Illumina adaptor sequences and repetitive poly-G sequences. For the alternative splicing event analysis, the following procedures were performed. Firstly, the reads were mapped onto the coordinate of transcripts indexed from Araport11 201606 released with Bowtie2 with a filtering identity threshold of 0.95, and the coordinates of reads passing the filter were translated into coordinates on the genome TAIR10. To enhance the identification efficiency toward alternative splicing events, the unmapped reads were mapped onto the coordinate of the genome with BLAT with a filtering identity threshold as 0.9 and at least 8 bases matched on both sides of reads. The resulting mapped sequences by both methods were collected together as input of the RackJ pipeline.