A reference floral transcriptome of sexual and apomictic Paspalum notatum
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Date
2017-04-21
Journal Title
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Publisher
BMC
Abstract
Description
Background: Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual
diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were
discovered in this species through genetic mapping and differential expression surveys. However, the scarce
information on Paspalum sequences available in public databanks limited annotations and functional
predictions for these candidates.
Results: We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets
from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential
representation in both reproductive types. Raw data originated from floral samples collected from premeiosis to anthesis
was assembled in three libraries: i) sexual (SEX), ii) apomictic (APO) and iii) global (SEX + APO). A group of physicallysupported
Paspalum mRNA and EST sequences matched with high level of confidence to both sexual and apomictic
libraries. A preliminary trial allowed discovery of the whole set of putative alleles/paralogs corresponding to 23 previously
identified apomixis-associated candidate genes. Moreover, a list of 3,732 transcripts and several co-expression and
protein –protein interaction networks associated with apomixis were identified.
Conclusions: The use of the 454/Roche FLX+ transcriptome database will allow the detailed characterization of floral
alleles/paralogs of apomixis candidate genes identified in prior and future work. Moreover, it was used to reveal
additional candidate genes differentially represented in apomictic and sexual flowers. Gene ontology (GO) analyses of
this set of transcripts indicated that the main molecular pathways altered in the apomictic genotype correspond to
specific biological processes, like biotic and abiotic stress responses, growth, development, cell death and senescence.
This data collection will be of interest to the plant reproduction research community and, particularly, to Paspalum
breeding projects.
Keywords
apomixis, Next Generation Sequencing, plant reproduction, sexual reproduction, transcriptomics