Biology Reference
In-Depth Information
Embryo Sac Enriched Genes
Our strategic approach to exploring the embryo sac transcriptome was twofold:
we aimed first to identify embryo sac expressed genes; second to describe the
gametophyte enriched (male and female) transcriptome; and finally to define the
embryo sac enriched (female only) transcriptome. Although the first category does
not consider whether an embryo sac expressed gene is also expressed in the sporo-
phyte, the second class of genes are grouped for their enriched expression in the
male (pollen) and female gametophyte, but not in the sporophyte. The embryo
sac enriched transcriptome is a subset of the gametophyte enriched transcrip-
tome, wherein male gametophyte expressed genes are omitted. Of the embryo sac
expressed genes, 32% were also present in the mature pollen transcriptome, and
the vast majority (77%) were expressed in immature siliques as expected. Because
large-scale female gametophytic cell expressed transcriptome data of Arabidopsis
based on microarray or EST analyses are not yet available, we compared our data
with the publicly available cell specific ESTs from maize and wheat by basic local
alignment search tool (BLAST) analysis. Large-scale monocot ESTs are available
only for the embryo sac and egg cells but not for the central cells (only 30 central
cell derived ESTs from [54]). Therefore, we included the ESTs from immature en-
dosperm cells at 6 days after pollination in the data comparison. Of our candidate
genes, 38% were similar to the monocot embryo sac ESTs, 33% to the egg ESTs,
and 53% to the central cell and endosperm ESTs.
Genes that were enriched in both the male and female gametophytes, or
only in the embryo sac, were identified by subtracting these transcriptomes
from a vast array of plant sporophytic transcriptomes of leaves, roots, whole
seedlings, floral organs, pollen, and so on. The transcriptomes of the immature
siliques were omitted in this subtraction scheme because often the gametophyte
enriched genes are also present in the developing embryo and endosperm. We
found 129 gametophyte enriched and 108 embryo sac enriched genes, account-
ing for 10% and 8.6%, respectively, of the embryo sac expressed genes (Table
1). Among the embryo sac enriched genes, 52% are uncategorized, 17% are
enzymes or genes that are involved in metabolism, 15% are involved in cell
structure and transport, 8% are transcriptional regulators, 4% are involved in
translational initiation and modification, 3% are predicted to be involved in
RNA synthesis and modification, and 2% in signaling (Figure 1 and Table 1).
Of the embryo sac enriched transcripts, 31% were present in the immature
siliques, suggesting their expression in the embryo and endosperm (Table 1).
Furthemore, 26% of the embryo sac enriched genes were similar to monocot
ESTs from the embryo sac or egg, and 41% were similar to central cell and en-
dosperm ESTs (Table 1).
