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. 2005 Jul;138(3):1734-45.
doi: 10.1104/pp.105.062851. Epub 2005 Jun 17.

Profile and analysis of gene expression changes during early development in germinating spores of Ceratopteris richardii

Mari L Salmi  1 , Thomas J Bushart, Stephen C Stout, Stanley J Roux
Collaborators, Affiliations

Profile and analysis of gene expression changes during early development in germinating spores of Ceratopteris richardii

Mari L Salmi et al. Plant Physiol. 2005 Jul.

Abstract

Analysis of an expressed sequence tag library with more than 5,000 sequences from spores of the fern Ceratopteris richardii reveals that more than 3,900 of them represent distinct genes, and almost 70% of these have significant similarity to Arabidopsis (Arabidopsis thaliana) genes. Eight genes are common between three very different dormant plant systems, Ceratopteris spores, Arabidopsis seeds, and Arabidopsis pollen. We evaluated the pattern of mRNA abundance over the first 48 h of spore development using a microarray of cDNAs representing 3,207 distinct genes of C. richardii and determined the relative levels of RNA abundance for 3,143 of these genes using a Bayesian method of statistical analysis. More than 900 of them (29%) show a significant change between any of the five time points analyzed, and these have been annotated based on their sequence similarity with the Arabidopsis proteome. Novel data arising from these analyses identify genes likely to be critical for the germination and subsequent early development of diverse cells and tissues emerging from dormancy.

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Figures

Figure 1.
Figure 1.
Functional classification of gene products expressed in C. richardii spores. Ceratopteris TUGs were annotated by BLAST comparison with the Arabidopsis proteome, and the functional classification of each TUG was done according to The Arabidopsis Information Resource (TAIR) Gene Ontology database of the resulting best BLAST match. The functional classification distribution of genes expressed in Arabidopsis seed, pollen, and leaf tissue is also indicated.
Figure 2.
Figure 2.
Localization of gene products expressed in C. richardii spores. Ceratopteris TUGs were annotated by BLAST comparison with the Arabidopsis proteome, and the compartmental classification of each TUG was done according to the TAIR Gene Ontology database of the resulting best BLAST match. The compartmental distribution of genes expressed in Arabidopsis seed, pollen, and leaf tissue is also indicated.
Figure 3.
Figure 3.
Comparison of the C. richardii spore TUGs to genes expressed in Arabidopsis seeds and pollen. A, Identification of tissue-specific gene expression in Ceratopteris spores and Arabidopsis seeds and pollen. The proportion of genes present in the seed, spore, and pollen sets that were also expressed in vegetative tissue is indicated in light gray. The remaining tissue-specific genes, indicated in dark gray, are used for the expression comparisons. Numbers indicate the number of genes included in each proportion. B, Overlapping expression of genes expressed in seeds, spores, and pollen. Numbers in overlapping regions indicate number of genes shared between the respective sets. Several relatively abundant genes present in each overlap are also indicated.
Figure 4.
Figure 4.
Specific expression patterns of C. richardii TUGs. Sequences are identified by accession number. The identity of the best BLASTX match to the Ceratopteris sequence is included. Times after initial light exposure tested were 0, 6, 12, 24, and 48 h. Transcript abundance at the time point with the lowest mean expression level is presented as 1, and all other time points are relative to 1. Error bars represent 95% credible interval for relative expression levels. Significant difference in RNA abundance between time points is defined as nonoverlapping 95% credible interval. Ceratopteris accession numbers are as follows: A, Mago nashi-1 (BE641602), Mago nashi-2 (BE642256), and SIN-like family protein (BE643380); B, Ras-related GTP-binding protein (BE642932), NPH3 family protein (BE641485), and catalase 1 (BE642028).
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