Detailed analysis of putative genes encoding small proteins in legume genomes
Por:
Guillen, G, Diaz-Camino, C, Loyola-Torres, CA, Aparicio-Fabre, R, Hernandez-Lopez, A, Diaz-Sanchez, M, Sanchez, F
Publicada:
20 jun 2013
Categoría:
Plant Science
Resumen:
Diverse plant genome sequencing projects coupled with powerful
bioinformatics tools have facilitated massive data analysis to construct
specialized databases classified according to cellular function.
However, there are still a considerable number of genes encoding
proteins whose function has not yet been characterized. Included in this
category are small proteins (SPs, 30-150 amino acids) encoded by short
open reading frames (sORFs). SPs play important roles in plant
physiology, growth, and development. Unfortunately, protocols focused on
the genome-wide identification and characterization of sORFs are scarce
or remain poorly implemented. As a result, these genes are
underrepresented in many genome annotations. In this work, we exploited
publicly available genome sequences of Phaseolus vulgaris, Medicago
truncatula, Glycine max, and Lotus japonicus to analyze the abundance of
annotated SPs in plant legumes. Our strategy to uncover bona fide sORFs
at the genome level was centered in bioinformatics analysis of
characteristics such as evidence of expression (transcription), presence
of known protein regions or domains, and identification of orthologous
genes in the genomes explored. We collected 6170, 10,461, 30,521, and
23,599 putative sORFs from P. vulgaris, G. max, M. truncatula, and L.
japonicus genomes, respectively. Expressed sequence tags (ESTs)
available in the DFCI Gene Index database provided evidence that similar
to one-third of the predicted legume sORFs are expressed. Most potential
SPs have a counterpart in a different plant species and counterpart
regions or domains in larger proteins. Potential functional sORFs were
also classified according to a reduced set of GO categories, and the
expression of 13 of them during P. vulgaris nodule ontogeny was
confirmed by qPCR. This analysis provides a collection of sORFs that
potentially encode for meaningful SPs, and offers the possibility of
their further functional evaluation.
Filiaciones:
Guillen, G:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Biol Mol Plantas, Cuernavaca 62210, Morelos, Mexico
Diaz-Camino, C:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Biol Mol Plantas, Cuernavaca 62210, Morelos, Mexico
Loyola-Torres, CA:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Biol Mol Plantas, Cuernavaca 62210, Morelos, Mexico
Aparicio-Fabre, R:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Biol Mol Plantas, Cuernavaca 62210, Morelos, Mexico
Hernandez-Lopez, A:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Biol Mol Plantas, Cuernavaca 62210, Morelos, Mexico
Diaz-Sanchez, M:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Biol Mol Plantas, Cuernavaca 62210, Morelos, Mexico
Sanchez, F:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Biol Mol Plantas, Cuernavaca 62210, Morelos, Mexico
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