Identification, isolation and expression analysis of auxin response factor (ARF) genes in Solanum lycopersicum

Abstract

Auxin response factors (ARFs) encode transcriptional factors that bind specifically to the TGTCTC-containing auxin response elements found in the promoters of primary/early auxin response genes that regulate plant development. In this study, investigation of the tomato genome revealed 21 putative functional ARF genes (SlARFs), a number comparable to that found in Arabidopsis (23) and rice (25). The full cDNA sequences of 15 novel SlARFs were isolated and delineated by sequencing of PCR products. A comprehensive genome-wide analysis of this gene family is presented, including the gene structures, chromosome locations, phylogeny, and conserved motifs. In addition, a comparative analysis between ARF family genes in tomato and maize was performed. A phylogenetic tree generated from alignments of the full-length protein sequences of 21 OsARFs, 23 AtARFs, 31 ZmARFs, and 21 SlARFs revealed that these ARFs were clustered into four major groups. However, we could not find homologous genes in rice, maize, or tomato with AtARF12-15 and AtARF20-23. The expression patterns of tomato ARF genes were analyzed by quantitative real-time PCR. Our comparative analysis will help to define possible functions for many of these newly isolated ARF-family genes in plant development.

Genome-wide analysis of the auxin response factor gene family in cucumber

“…Similar to findings in rice (Wang et al, 2007) and Solamum lycopersicum (Wu et al, 2011), the 15 CsARF members could be classified into three classes (I-III), each containing 6, 5 and 4 members, respectively ( Figure 1). Class III seemed more divergent compared with those grouped into classes I and II.…”

“…To investigate the evolutionary relations of cucumber ARFs with those in other species, a phylogenetic tree was built from alignments of the complete protein sequences of 15 CsARFs, 25 rice OsARFs, 23 Arabidopsis AtARFs and 31 maize ZmARFs (Figure 2). According to the Wu et al (2011) classification criterion, all these 94 ARFs were grouped into I-IV classes. Class I contained 31 members and could be divided into groups Ia (23 members) and Ib (8 members), where group Ia could be further classified into subgroup Ia-1(15 members) and Ia-2 (8 members).…”

Irrepressible, truncated Auxin Response Factors

“…To date, these have been identified in four species, and it seems that the numbers of C-terminally truncated ARFs increased during evolution, as flowering plants tend to encode more of them than nonflowering plants. [14][15][16] With one exception, all of the naturally occurring truncated ARFs appear to contain repression middle domains. 16 In at least one case during early angiosperm evolution, in Amborellales and Nymphaeales, mutations leading to apparent C-terminal truncations of ARF3/ ETTIN and ARF4 have occurred, but the functional consequences are unknown.…”

“…[14][15][16] With one exception, all of the naturally occurring truncated ARFs appear to contain repression middle domains. 16 In at least one case during early angiosperm evolution, in Amborellales and Nymphaeales, mutations leading to apparent C-terminal truncations of ARF3/ ETTIN and ARF4 have occurred, but the functional consequences are unknown. 17 When analyzed in Arabidopsis, the ARF3 truncation might be gratuitous, as ARF3's ability to rescue the ett-1 mutation was reduced in dominant iaa12/bodenlos(bdl) mutants, 21 consistent with MP being a target of repression by IAA12/BDL.…”

A standard nomenclature for gene designation in the Rosaceae

“…For example, ETHYLENE INSENSITIVE 5 has also been published as AIN1 and XRN4 (Olmedo et al 2006). In tomato, the ARF gene family was independently named by two different research groups, resulting in each gene having two names (Kumar et al 2011;Wu et al 2011). whereon the other hand, in some cases, the same three letter abbreviation has been given to different genes, such as CELL NUMBER REGULATOR (CNR) in cherry (De Franceschi et al 2013) and COLORLESS NON RIPENING (CNR) in tomato (Manning et al 2006).…”