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

Overview of attention for article published in BMC Genomics, November 2016
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Title
Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas
Published in
BMC Genomics, November 2016
DOI 10.1186/s12864-016-3270-5
Pubmed ID
Authors

Bianca Baccili Zanotto Vigna, Fernanda Ancelmo de Oliveira, Guilherme de Toledo-Silva, Carla Cristina da Silva, Cacilda Borges do Valle, Anete Pereira de Souza

Abstract

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. 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. 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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 49 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Argentina 1 2%
Slovenia 1 2%
Unknown 47 96%

Demographic breakdown

Readers by professional status Count As %
Student > Master 8 16%
Researcher 6 12%
Student > Ph. D. Student 6 12%
Student > Bachelor 5 10%
Unspecified 5 10%
Other 11 22%
Unknown 8 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 26 53%
Unspecified 5 10%
Nursing and Health Professions 3 6%
Biochemistry, Genetics and Molecular Biology 2 4%
Psychology 1 2%
Other 3 6%
Unknown 9 18%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 13 November 2016.
All research outputs
#20,353,668
of 22,901,818 outputs
Outputs from BMC Genomics
#9,300
of 10,674 outputs
Outputs of similar age
#268,653
of 310,683 outputs
Outputs of similar age from BMC Genomics
#166
of 222 outputs
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