Cell-type-specific alternative splicing in the Arabidopsis germline.

During sexual reproduction in flowering plants, the two haploid sperm cells (SCs) embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome levels. While the transcriptome of pollen and SCs in Arabidopsis (Arabidopsis thaliana) is well documented, previous analyses have mostly been based on gene-level expression. In-depth transcriptome analysis, particularly the extent of alternative splicing (AS) at the resolution of SC and vegetative nucleus (VN), is still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis SCs and VN isolated from mature pollen grains. Based on our de novo transcriptome assembly, we identified 58,039 transcripts, including 9,681 novel transcripts, of which 2,091 were expressed in SCs and 3,600 in VN. Four hundred and sixty-eight genes were regulated both at gene and splicing levels, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides insights into a gamete-specific AS landscape at unprecedented resolution.

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants.

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

Transcriptomics of Arabidopsis sperm cells at single-cell resolution.

KEY MESSAGE: We present a detailed protocol for isolation of single sperm cells and transcriptome analysis to study variation in gene expression between sperm cells. Male gametophyte development in flowering plants begins with a microspore mother cell, which upon two consecutive cell divisions forms a mature pollen grain containing a vegetative nucleus and two sperm cells. Pollen development is a highly dynamic process, involving changes at both the transcriptome and epigenome levels of vegetative nuclei and the pair of sperm cells that have their own cytoplasm and nucleus. While the overall transcriptome of Arabidopsis pollen development is well documented, studies at single-cell level, in particular of sperm cells, are still lacking. Such studies would be essential to understand whether and how the two sperm cells are transcriptionally different, in particular once the pollen tube grows through the transmitting tissue of the pistil. Here we describe a detailed protocol for isolation of single sperm cells from growing pollen tubes and analysis of their transcriptome.

Characterization of lignin-degrading enzymes (LDEs) from a dimorphic novel fungus and identification of products of enzymatic breakdown of lignin.

Lignin is a major component of all plants, the degradation of which remains a major challenge to date owing to its recalcitrant nature. Several classes of fungi have been studied to carry out this process to some extent, but overall the process remains inefficient. We have isolated a novel alkalophilic dimorphic lignin-degrading Deuteromycete from soil, identified as "uncultured" and coded as MVI.2011. Supernatant from 12-h culture of MVI.2011 in optimized mineral medium containing lignin pH 9.0 was analysed for Lignin Peroxidase, Manganese Peroxidase and Laccase. Enzyme purification was carried out by standard protocols using ammonium sulphate precipitation followed by further purification by Gel Permeation Chromatography. Analysis of total protein, specific enzyme activity and molecular weight of the GPC-purified LiP, MnP and Laccase showed 93.83 µg/ml, 5.27 U/mg, 42 kDa; 78.13 µg/ml, 13.18 U/mg, 45 kDa and 85.81 µg/ml, 4.77 U/mg, 62 kDa, respectively. The purified enzymes possessed high activity over a wide range of pH (4-11), and temperature (30-55 °C). The optimum substrate concentration was 20 µg/ml of lignin for all the three enzymes. CD spectra suggested that the predominant secondary structure was helix in LiP, and, turns in MnP and Laccase. The breakdown products of lignin degradation by MVI.2011 and the three purified enzymes were detected and identified by FTIR and GC-MS. They were oxalic acid, hentriacontane, derivatives of octadecane, nonane, etc. These vital compounds are certain to find application as biofuels, an alternate energy source in various industries.