Abstract
BackgroundThe B3 DNA binding domain includes five families: auxin response factor (ARF), abscisic acid-insensitive3 (ABI3), high level expression of sugar inducible (HSI), related to ABI3/VP1 (RAV) and reproductive meristem (REM). The release of the complete genomes of the angiosperm eudicots Arabidopsis thaliana and Populus trichocarpa, the monocot Orysa sativa, the bryophyte Physcomitrella patens,the green algae Chlamydomonas reinhardtii and Volvox carteri and the red algae Cyanidioschyzon melorae provided an exceptional opportunity to study the evolution of this superfamily.MethodologyIn order to better understand the origin and the diversification of B3 domains in plants, we combined comparative phylogenetic analysis with exon/intron structure and duplication events. In addition, we investigated the conservation and divergence of the B3 domain during the origin and evolution of each family.ConclusionsOur data indicate that showed that the B3 containing genes have undergone extensive duplication events, and that the REM family B3 domain has a highly diverged DNA binding. Our results also indicate that the founding member of the B3 gene family is likely to be similar to the ABI3/HSI genes found in C. reinhardtii and V. carteri. Among the B3 families, ABI3, HSI, RAV and ARF are most structurally conserved, whereas the REM family has experienced a rapid divergence. These results are discussed in light of their functional and evolutionary roles in plant development.
Highlights
Our data indicate that showed that the B3 containing genes have undergone extensive duplication events, and that the reproductive meristem (REM) family B3 domain has a highly diverged DNA binding
Our results indicate that the founding member of the B3 gene family is likely to be similar to the ABI3/high level expression of sugar inducible (HSI) genes found in C. reinhardtii and V. carteri
The B3 domain was first identified in the VIVIPAROUS (VP1) gene from Zea mays, which contains three basic regions designated as B1, B2 and B3 [1] and the VP1 orthologue ABI3 (ABSCISIC ACIDINSENSITIVE3) from Arabidopsis thaliana [2]
Summary
The B3 domain was first identified in the VIVIPAROUS (VP1) gene from Zea mays, which contains three basic regions designated as B1, B2 and B3 [1] and the VP1 orthologue ABI3 (ABSCISIC ACIDINSENSITIVE3) from Arabidopsis thaliana [2]. Five major classes of genes containing the B3 domain have been identified to date based on their similarities and domain structures. These include proteins from the ABI3/VP1 [1], HSI (High-level expression of sugarinducible gene) [3,4], RAV (Related to ABI3/VP1) [5], ARF (Auxin Response Factor) [6] and REM (Reproductive Meristem) [7] families. The B3 DNA binding domain includes five families: auxin response factor (ARF), abscisic acid-insensitive (ABI3), high level expression of sugar inducible (HSI), related to ABI3/VP1 (RAV) and reproductive meristem (REM). The release of the complete genomes of the angiosperm eudicots Arabidopsis thaliana and Populus trichocarpa, the monocot Orysa sativa, the bryophyte Physcomitrella patens,the green algae Chlamydomonas reinhardtii and Volvox carteri and the red algae Cyanidioschyzon melorae provided an exceptional opportunity to study the evolution of this superfamily
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