Busca avançada
Ano de início
Entree
(Referência obtida automaticamente do Web of Science, por meio da informação sobre o financiamento pela FAPESP e o número do processo correspondente, incluída na publicação pelos autores.)

Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas

Texto completo
Autor(es):
Zanotto Vigna, Bianca Baccili ; de Oliveira, Fernanda Ancelmo ; de Toledo-Silva, Guilherme ; da Silva, Carla Cristina ; do Valle, Cacilda Borges ; de Souza, Anete Pereira
Número total de Autores: 6
Tipo de documento: Artigo Científico
Fonte: BMC Genomics; v. 17, NOV 11 2016.
Citações Web of Science: 2
Resumo

Background: Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi. Results: We sequenced the leaf transcriptome of Koronivia grass using an Illumina GAIIx system, which produced 13.09 Gb of data that consisted of 163,575,526 paired-end reads between the two libraries. We de novo-assembled 76,196 transcripts with an average length of 1,152 bp and filtered 35,093 non-redundant unigenes. A similarity search against the non-redundant National Center of Biotechnology Information (NCBI) protein database returned 65 % hits. We annotated 24,133 unigenes in the Phytozome database and 14,082 unigenes in the UniProtKB/Swiss-Prot database, assigned 108,334 gene ontology terms to 17,255 unigenes and identified 5,324 unigenes in 327 known metabolic pathways. Comparisons with other grasses via a reciprocal BLAST search revealed a larger number of orthologous genes for the Panicum species. The unigenes were involved in C4 photosynthesis, lignocellulose biosynthesis and flooding stress responses. A search for functional molecular markers revealed 4,489 microsatellites and 560,298 single nucleotide polymorphisms (SNPs). A quantitative real-time PCR analysis validated the RNA-seq expression analysis and allowed for the identification of transcriptomic differences between the two evaluated genotypes. Moreover, 192 unannotated sequences were classified as containing complete open reading frames, suggesting that the new, potentially exclusive genes should be further investigated. Conclusion: The present study represents the first whole-transcriptome sequencing of U. humidicola leaves, providing an important public information source of transcripts and functional molecular markers. The qPCR analysis indicated that the expression of certain transcripts confirmed the differential expression observed in silico, which demonstrated that RNA-seq is useful for identifying differentially expressed and unique genes. These results corroborate the findings from previous studies and suggest a hybrid origin for BH031. (AU)

Processo FAPESP: 13/14903-2 - Análise de transcriptoma de folha de Brachiaria humidicola e Paspalum notatum visando o desenvolvimento de marcadores funcionais para o estudo genético e genômico de gramíneas forrageiras tropicais
Beneficiário:Fernanda Ancelmo de Oliveira
Linha de fomento: Bolsas no Brasil - Doutorado
Processo FAPESP: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
Beneficiário:Anete Pereira de Souza
Linha de fomento: Auxílio à Pesquisa - Programa BIOEN - Temático
Processo FAPESP: 13/20447-0 - Análise de transcriptoma de Hevea pauciflora e Hevea benthamiana e identificação de grupos de genes ortólogos para o gênero Hevea
Beneficiário:Guilherme de Toledo e Silva
Linha de fomento: Bolsas no Brasil - Pós-Doutorado