Abstract
The KNOX gene family codes for transcriptional regulators with a variety of functions in plant developmental and physiological processes. In this study, a genome-wide comparative analysis of KNOX genes in Poplar (Populustrichocarpa) and rice (Oryza sativa L. ssp. japonica) was carried out. With comprehensive computational analyses, which take into account the gene structures, phylogeny and conserved motifs, 15 and 13 KNOX genes in Poplar and rice were identified, respectively. These KNOX genes were further divided into 3 groups. The Poplar gene POPTR_0012s04040 and the rice genes LOC_Os03g47042 and LOC_Os03g47022 were classified to a new group of KNOX genes without ahomeobox domain together with KNATM, which were proposed to play potential role in plant development and pluripotency. The identification of KNATM homolog in monocotyledons (rice) provided a strong support for proposing an ancient shuffling of HOMEOBOX gene with MEINOX gene took place in the KNOX phylogeny. Using subcellular location information, GO (gene ontology) and expression profile analysis, KNOX genes in rice and poplar were proposed to function similarly to the members in Arabidopsis. Our observations may lay the foundation for future functional analysis of KNOX genes in rice and poplar to unravel their biological roles in cellular pluripotency.
Highlights
Homeobox genes are key regulators in plant and animal development
Our observations may lay the foundation for future functional analysis of KNOX genes in rice and poplar to unravel their biological roles in cellular pluripotency
Class I subfamily consists of 4 members, SHOOT MERISTEMLESS (STM), KNAT1, KNAT2 and KNAT6 which are characteristically expressed in the shoot apical meristem (SAM)
Summary
Homeobox genes are key regulators in plant and animal development. In plants, homeobox genes are divided into several groups according to their sequences, one of which is the KNOX (knotted-like homeobox) family [1] [2]. In Arabidopsis, members of the KNOX genes are divided into three classes depending on their sequences and expression patterns, class I, class II and class M [7]. Class I subfamily consists of 4 members, SHOOT MERISTEMLESS (STM), KNAT1, KNAT2 and KNAT6 which are characteristically expressed in the shoot apical meristem (SAM). They play important roles in meristem, control of leaf shape and hormone homeostasis and act as either transcriptional activators or repressors [8] [9]. KNAT6 is expressed in the embryonic SAM, the SAM boundaries [15] and the phloem tissue of roots [18]
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