[Show abstract][Hide abstract]ABSTRACT: Meiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate. Understanding meiosis will not only advance our knowledge of the mechanisms of genetic recombination, but also has substantial applications in crop improvement. Despite the tremendous progress in the past decade in other model organisms (e.g., Saccharomyces cerevisiae and Drosophila melanogaster), the global identification of meiotic genes in flowering plants has remained a challenge due to the lack of efficient methods to collect pure meiocytes for analyzing the temporal and spatial gene expression patterns during meiosis, and for the sensitive identification and quantitation of novel genes.
A high-throughput approach to identify meiosis-specific genes by combining isolated meiocytes, RNA-Seq, bioinformatic and statistical analysis pipelines was developed. By analyzing the studied genes that have a meiosis function, a pipeline for identifying meiosis-specific genes has been defined. More than 1,000 genes that are specifically or preferentially expressed in meiocytes have been identified as candidate meiosis-specific genes. A group of 55 genes that have mitochondrial genome origins and a significant number of transposable element (TE) genes (1,036) were also found to have up-regulated expression levels in meiocytes.
These findings advance our understanding of meiotic genes, gene expression and regulation, especially the transcript profiles of MGI genes and TE genes, and provide a framework for functional analysis of genes in meiosis.
[Show abstract][Hide abstract]ABSTRACT: Supplementary Table S3. Table S3. A list of differentially expressed TEs in meiocytes and anthers. The list of differentially expressed TEs in meiocytes and anthers, the label of "--" refers to zero (0) reads from anther. In addition to the mRNA signal intensity of read counts (normalized as reads per million reads), this table also provides gene ID, transposon ID, transposon family and super family. The shaded rows are genes that down-regulated in meiocytes and preferentially expressed in anthers. M = meiocyte, A = anther.
[Show abstract][Hide abstract]ABSTRACT: Figure S4. Distribution of expressed TEs in meiocytes among gene function categories. Treemaps of expressed TEs in meiocytes generated by REVIGO. In each category, the size of the rectangle is proportional to the population of functional groups. A. Biological process. B. Cellular component. C. Molecular function.
[Show abstract][Hide abstract]ABSTRACT: Supplementary Figure S2. Figure S2. Scatterplot matrix to demonstrate the correlations among all samples. The pairs plots show the correlations among all samples. Anther_control = anthers; Anther_meiosis = meiocytes.
[Show abstract][Hide abstract]ABSTRACT: Figure S1. Parallel plot to demonstrate the similarity of technical replicates. Showing high similarity of technical replicates. Red--anther; green--meiocyte; blue--seedling. In this figure, no technical replicates for seedlings were presented.
[Show abstract][Hide abstract]ABSTRACT: Figure S3. Distribution of expressed mRNAs in meiocytes among gene function categories. Percentage of gene distribution and raw data are presented next to each category.
[Show abstract][Hide abstract]ABSTRACT: Table S4. A list of differentially expressed TEs in meiocytes and seedlings. The list of differentially expressed TEs in meiocytes and seedlings, the label of "--" refers to zero (0) reads from seedling. The shaded rows are genes that down-regulated in meiocytes and preferentially expressed in seedlings. M = meiocyte, S = seedling.
[Show abstract][Hide abstract]ABSTRACT: Table S1. Transcript profiling of genes that function in meiosis. Transcript profiling of 68 previously reported genes that function in meiosis. Showing the signal intensity by reads per million reads. M = meiocyte, A = anther, S = seedling.
[Show abstract][Hide abstract]ABSTRACT: Table S2. A list of MGI genes that are preferentially expressed in meiocytes. SN = serial number, MGI = mitochondrial genomic insertion, M = meiocyte, A = anther.
[Show abstract][Hide abstract]ABSTRACT: Whole transcriptome sequencing (RNA-seq) technologies were used to profile gene expression in dissected Arabidopsis stage 5-7 anthers and isolated male meiocytes. Previously, we reported the discovery of over 1,000 coding genes that were specifically expressed in meiocytes, some 50 genes on a large mitochondrial genome insertion on chromosome-2 pericentromeric region, and 1036 transposable element genes were up-regulated in isolated male meiocytes in comparison to the anthers. Here we present the secondary data analysis, focusing on genes that were preferentially expressed in anthers, which are likely up-regulated in anther wall cells. To assess differential expression between isolated male meiocytes and stage 5-7 anthers undergoing meiosis, we performed a negative binomial test in DESeq on the 25,881 genes expressed at a minimum of 5 reads per million in at least one sample; we identified 490 genes differentially expressed (adjusted p-value of 0.001) that had 4-fold greater expression in anthers versus meiocytes, 2 of which were only expressed in anthers. 88 genes (18%) encode unknown proteins; 27 genes are annotated coding transcription factors. In addition, well-studied anther-wall specific genes such as DYT1 (At4G21330) and ATA1 (At3G42960) are presented in this gene list. The results have advanced our understanding on the transcriptome landscapes of anthers that undergo meiosis.