Genome-wide identification and analysis of growth regulating factor genes in Brachypodium distachyon: in silico approaches

Ertuğrul FİLİZ; İbrahim KOÇ; Hüseyin TOMBULOĞLU

Makale detayları

Genome-wide identification and analysis of growth regulating factor genes in Brachypodium distachyon: in silico approaches

Yazarlar:

Ertuğrul FİLİZ | İbrahim KOÇ | Hüseyin TOMBULOĞLU

Yayıncı:

TUBITAK

Dergi:

Turkish Journal of Biology 2014 Vol.38 Issue 2, pp.296-306

Belge Tipi:

Makale

Yayın Tarihi:

5/2014

Belge Dili:

Türkçe

Document ID (Org No.):

2000812273

Sıklık:

İki Aylık

eISSN:

1303-6092

pISSN:

1300-0152

Anahtar kelimeler:

Özet:

 

Growth-regulating factor (GRF) genes may play important roles for regulating growth and development in different plant tissues and organs. Here we report the first genome-wide analysis of the GRF gene family in Brachypodium. We performed in silico comparative analysis of GRF genes, including their structure, duplication in the genome, conserved motifs, and phylogenetic relationship. At the end of the study, 10 BdGRF genes were identified. The highest number of GRF genes was identified on chromosome 1 with 5 members, whereas the least number of genes (only 1 member) was found on chromosomes 2, 4, and 5. Of those, a single segmental duplication was observed in the Brachypodium genome. Average exon and intron numbers were determined as 3 and 4, respectively. Motif analysis showed that WRC and QLQ residues were consistent in all GRF protein sequences. Gene Ontology terms showed that 10 BdGRF proteins grouped in the same biological function, biological process, and cellular component groups. In addition, we compared the new BdGRF proteins with the other monocot and dicot GRF proteins sequences. Phylogenetic analysis revealed that GRF proteins of monocot and dicot species were clustered together in a joined tree; in particular, the monocot species (Brachypodium, maize, and rice) were grouped into the same cluster with high bootstrap values. We assume that the results of this study will provide molecular insights about GRF proteins in grass species.

 

Growth-regulating factor (GRF) genes may play important roles for regulating growth and development in different plant tissues and organs. Here we report the first genome-wide analysis of the GRF gene family in Brachypodium. We performed in silico comparative analysis of GRF genes, including their structure, duplication in the genome, conserved motifs, and phylogenetic relationship. At the end of the study, 10 BdGRF genes were identified. The highest number of GRF genes was identified on chromosome 1 with 5 members, whereas the least number of genes (only 1 member) was found on chromosomes 2, 4, and 5. Of those, a single segmental duplication was observed in the Brachypodium genome. Average exon and intron numbers were determined as 3 and 4, respectively. Motif analysis showed that WRC and QLQ residues were consistent in all GRF protein sequences. Gene Ontology terms showed that 10 BdGRF proteins grouped in the same biological function, biological process, and cellular component groups. In addition, we compared the new BdGRF proteins with the other monocot and dicot GRF proteins sequences. Phylogenetic analysis revealed that GRF proteins of monocot and dicot species were clustered together in a joined tree; in particular, the monocot species (Brachypodium, maize, and rice) were grouped into the same cluster with high bootstrap values. We assume that the results of this study will provide molecular insights about GRF proteins in grass species.

Makale detayları

Genome-wide identification and analysis of growth regulating factor genes in Brachypodium distachyon: in silico approaches

Yazarlar:

Ertuğrul FİLİZ | İbrahim KOÇ | Hüseyin TOMBULOĞLU

Yayıncı:

TUBITAK

Dergi:

Turkish Journal of Biology 2014 Vol.38 Issue 2, pp.296-306

Belge Tipi:

Makale

Yayın Tarihi:

5/2014

Belge Dili:

Türkçe

Document ID (Org No.):

2000812273

Sıklık:

İki Aylık

eISSN:

1303-6092

pISSN:

1300-0152

Key words: Brachypodium distachyon

growth regulating factor

GRF

genome-wide analysis

Sayı

Makale detayları

Genome-wide identification and analysis of growth regulating factor genes in Brachypodium distachyon: in silico approaches

Yazarlar: Ertuğrul FİLİZ | İbrahim KOÇ | Hüseyin TOMBULOĞLU

Yayıncı: TUBITAK

Dergi: Turkish Journal of Biology 2014 Vol.38 Issue 2, pp.296-306

Belge Tipi: Makale

Yayın Tarihi: 5/2014

Belge Dili: Türkçe

Document ID (Org No.): 2000812273

Sıklık: İki Aylık

eISSN: 1303-6092

pISSN: 1300-0152

Key words: Brachypodium distachyon

growth regulating factor

GRF

genome-wide analysis

Sayı

Yazarlar:

Ertuğrul FİLİZ | İbrahim KOÇ | Hüseyin TOMBULOĞLU

Yayıncı:

TUBITAK

Dergi:

Turkish Journal of Biology 2014 Vol.38 Issue 2, pp.296-306

Belge Tipi:

Makale

Yayın Tarihi:

5/2014

Belge Dili:

Türkçe

Document ID (Org No.):

2000812273

Sıklık:

İki Aylık

eISSN:

1303-6092

pISSN:

1300-0152