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BMC Genomics

, 18:318

Plant genomics

Abstract

BackgroundPaspalum 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.

ResultsWe 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 physically-supported 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.

ConclusionsThe 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.

KeywordsApomixis Next generation sequencing Plant reproduction Sexual reproduction Transcriptomics AbbreviationsACLApomixis controlling locus

AFLPAmplified fragment length polymorphism

APOApomictic

BACBacterial artificial chromosome

BLASTBasic local alignment search tool

DDDifferential display

ESTExpressed sequence tag

EST-SSRExpressed sequence tag-simple sequence repeat

E-valueExpect value

FDRFalse discovery rate

GOGene ontology

IDIdentity

logCPMLogarithm transformed counts per million mapped reads

logFCLogarithm transformed fold change

NGSNext generation sequencing

PCRPolymerase chain reaction

p-valueProbability value

RACERandom amplification of cDNA ends

RNA-SeqRNA-sequencing

SEXSexual

UTRUntranslated region

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-017-3700-z contains supplementary material, which is available to authorized users.





Autor: Juan Pablo A. Ortiz - Santiago Revale - Lorena A. Siena - Maricel Podio - Luciana Delgado - Juliana Stein - Olivier Lebl

Fuente: https://link.springer.com/







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