Phylogenesis Of The Plant-specific Transcription Factor Family LBD

LBD is a new plant-specific transcription factor family that contains conserved LOB(lateral organ boundaries) domain,it plays an important role in the formation anddevelopment of plant lateral organ. LOB gene was firstly identified expressing in the lateralorgan boundaries of Arabidopsis thaliana. Then by using amino acid sequence of LOBdomain as a probe to search in Arabidopsis genome database, there are43similar memberswere found. The encoding product of the member contains a conserved domain with length of100amino acid-LOB domain, named as LOB genes which are referred to those containing LOBdomain. LBD genes were involved in the formation and development of root, stem, leaves,and flowers, Participated in plant metabolism, regulating and secondary growth as well. Thefunction of LBD genes are of vital importance to plants. Research in this area is mainlyfocused on exploration of new members and identification of the function of LBD genes, fewresearch focused on how LBD genes were originated and evolved.In this study, based on18species with whole genome sequence. we identified allpotential LBD genes from these species, then analyzed them from sequence similarity,multiple sequence alignment, phylogeny, introns insertion pattern, conserved motifarrangement patterns, and so on. Try to describe the origination and evolution of LBD genefamily, illuminate characteristic of every subfamily and latent function of LBD gene family.The main results obtained are as follows:1.There are622members of LBD family gene in the18species we found. There is noLBD family gene in species Chlamydomonas reinhardtii and Volvox carteri.26members ofLBD genes were found in Bryophyte Physcomitrella patens. Selaginella moellendorrffiiLycopodiophyta contains15members. There are21to72LBD members in other14species.As plants evolved from lower to higher, the number of LBD gene family increasescontinuously.2.We divided LBD transcription factor family into seven subfamilies named A、B、C、D、E、F、and G by using maximum likelihood method. Earlier research divided LBD proteinsinto two families, Class II is corresponding to G subfamily we described, A、B、C、D、E andF could be considered as detailed classification of Class I. There is only one member of Selaginella moellendorrffii in sub-family B, while6to20members in other higher plantspecies we selected. LBD gene in higher plants involved in regulation of initiation of lateralroot, is located in downstream of auxin signal. The root of Selaginella moellendorrffii is ofgreat difference with higher plants which differentiated from the top of the grassroots lowerepidermis cell. This maybe the reason why the LBD members of sub-family B are so differentfrom higher plants. There is no LBD member of Physcomitrella patens and Selaginellamoellendorrffii belonged to sub-family D, but every angiosperm we selected contains1~3members of sub-family D. The function of sub-family D is still unknown.3.The insertion site of introns varies with LBD gene in different subfamilies. Theinsertion site and phase position are conserved within the same subfamily. There is oneinsertion site in47with the phase position0in sub-family A、D、E. Sub-family B were foundhas one insertion site at87with the phase position0, while sub-family G’s insertion site is at60with the phase1. Intron insertion site of sub-family C is outside the LOB domain at105site with phase0. Sub-family F has a insertion site at position251, but there are still a fewsequences with the insertion site at25inside the LOB domain, phase position is0. Theconservation of the intron insertion site of LBD gene support the result of classification ofLBD gene family, suggesting angiosperm-specific class D might be divided from Class A or E.Ten conserved motifs were found from different LBD domains use software MEME. Motif1,2,3are shared with all LBD sub-family, motif5is only show up in class G and motif8isonly show up in class F, motif4appears in all subclass. The result of similarity of differentmotif in sub-family certified sub-family A or E is ancestor of sub-family D.4.Green plants are originated from algae. Although there are no LBD gene inChlamydomonas reinhardtii and Volvox carteri, several LBD members were found by blastsearching EST database and the transcriptome sequencing data of algae. There are4,1,1LBD members were found from CharalesNitella mirabilis, Coleochaete Orbicularis andSpirogyra pratensis, they belong to sub-family A, F and G separately, but no one belongs tosub-family B which involved in root formation and angiosperm-specific sub-family D.Charales is the closet ancestor of higher Embryo plants. The fact that there are several LBDmembers in Charales suggests that LBD proteins were already exist before algae evolvedtowards terrestrial plants.Our research has an in-depth exploration in the origination and evolution of LBDtranscription factor family, and system analyzation of structure and function of everysubfamily. Our work laid the foundation for related research in the future.