Abstract: ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) genes are a family of plant specific transcription factors, which play an important role in the regulation of plant lateral organ development and metabolism. However, a genome-wide analysis of the AS2/LOB gene family is still not available for barley. In the present study, 24 AS2-like (ASL)/LOB domain (LBD) genes were identified based on the barley (Hordeum vulgare L.) genome sequence. A phylogenetic tree of ASL/LBD proteins from barley, Arabidopsis, maize, and rice was constructed. The ASL/LBD genes were classified into two classes, class I and class II, which were divided into five and two subgroups, respectively. Genes homologous in barley and Arabidopsis were analyzed. In addition, the structure and chromosomal locations of the genes were analyzed. Expression profiles indicated that barley HvASL/LBD genes exhibit a variety of expression patterns, suggesting that they are involved in various aspects of physiological and developmental processes. This genome-wide analysis of the barley AS2/LOB gene family contributes to our understanding of the functions of the AS2/LOB gene family.

大麦ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES（AS2/LOB）基因家族的全基因组分析

[1]Artimo, P., Jonnalagedda, M., Arnold, K., et al., 2012. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res., 40(W1):W597-W603.

[2]Bailey, T.L., Elkan, C., 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Altman, R., Brutlag, D., Karp, P., et al. (Eds.), Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. American Association for Artificial Intelligence, Stanford, CA, USA, p.28-36.

[3]Borghi, L., Bureau, M., Simon, R., 2007. Arabidopsis JAGGED LATERAL ORGANS is expressed in boundaries and coordinates KNOX and PIN activity. Plant Cell, 19(6):1795-1808.

[4]Bortiri, E., Chuck, G., Vollbrecht, E., et al., 2006. ramosa2 encodes a LATERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristems of maize. Plant Cell, 18(3):574-585.

[5]Byrne, M.E., Barley, R., Curtis, M., et al., 2000. Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature, 408(6815):967-971.

[6]Byrne, M.E., Simorowski, J., Martienssen, R.A., 2002. ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis. Development, 129(8):1957-1965.

[7]Evans, M.M.S., 2007. The indeterminate gametophyte1 gene of maize encodes a LOB domain protein required for embryo sac and leaf development. Plant Cell, 19(1):46-62.

[8]Guo, M.J., Thomas, J., Collins, G., et al., 2008. Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis. Plant Cell, 20(1):48-58.

[9]Hetz, W., Hochholdinger, F., Schwall, M., et al., 1996. Isolation and characterization of rtcs, a maize mutant deficient in the formation of nodal roots. Plant J., 10(5):845-857.

[10]Hu, B., Jin, J.P., Guo, A.Y., et al., 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8):1296-1297.

[11]Husbands, A., Bell, E.M., Shuai, B., et al., 2007. LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins. Nucleic Acids Res., 35(19):6663-6671.

[12]International Barley Genome Sequencing Consortium, Mayer, K.F., Waugh, R., et al., 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature, 491(7426):711-716.

[13]Inukai, Y., Sakamoto, T., Ueguchi-Tanaka, M., et al., 2005. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling. Plant Cell, 17(5):1387-1396.

[14]Iwakawa, H., Ueno, Y., Semiarti, E., et al., 2002. The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana, required for formation of a symmetric flat leaf lamina, encodes a member of a novel family of proteins characterized by cysteine repeats and a leucine zipper. Plant Cell Physiol., 43(5):467-478.

[15]Iwakawa, H., Iwasaki, M., Kojima, S., et al., 2007. Expression of the ASYMMETRIC LEAVES2 gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves. Plant J., 51(2):173-184.

[16]Iwasaki, M., Takahashi, H., Iwakawa, H., et al., 2013. Dual regulation of ETTIN (ARF3) gene expression by AS1-AS2, which maintains the DNA methylation level, is involved in stabilization of leaf adaxial-abaxial partitioning in Arabidopsis. Development, 140(9):1958-1969.

[17]Keta, S., Iwakawa, H., Ikezaki, M., et al., 2012. Roles of the ASYMMETRIC LEAVES2 gene in floral organ development in Arabidopsis thaliana. Plant Biotechnol., 29(1):1-8.

[18]Koppolu, R., Anwar, N., Sakuma, S., et al., 2013. Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. PNAS, 110(32):13198-13203.

[19]Lee, H.W., Kim, N.Y., Lee, D.J., et al., 2009. LBD18/ASL20 regulates lateral root formation in combination with LBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis. Plant Physiol., 151(3):1377-1389.

[20]Lescot, M., Déhais, P., Thijs, G., et al., 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res., 30(1):325-327.

[21]Letunic, I., Doerks, T., Bork, P., 2012. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res., 40(D1):D302-D305.

[22]Liu, R.H., Meng, J.L., 2003. MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data. Hereditas (Beijing), 25(3):317-321.

[23]Liu, H.J., Wang, S.F., Yu, X.B., et al., 2005. ARL1, a LOB-domain protein required for adventitious root formation in rice. Plant J., 43(1):47-56.

[24]Long, J.A., Moan, E.I., Medford, J.I., 1996. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature, 379(6560):66-69.

[25]Majer, C., Hochholdinger, F., 2011. Defining the boundaries: structure and function of LOB domain proteins. Trends Plant Sci., 16(1):47-52.

[26]Matsumura, Y., Iwakawa, H., Machida, Y., 2009. Characterization of genes in the ASYMMETRIC LEAVES2/ LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members. Plant J., 58(3):525-537.

[27]Okushima, Y., Fukaki, H., Onoda, M., et al., 2007. ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell, 19(1):118-130.

[28]Ori, N., Eshed, Y., Chuck, G., et al., 2000. Mechanisms that control knox gene expression in the Arabidopsis shoot. Development, 127:5523-5532.

[29]Punta, M., Coggill, P.C., Eberhardt, R.Y., et al., 2012. The Pfam protein families database. Nucleic Acids Res., 40(D1):D290-D301.

[30]Rubin, G., Tohge, T., Matsuda, F., et al., 2009. Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. Plant Cell, 21(11):3567-3584.

[31]Semiarti, E., Ueno, Y., Tsukaya, H., et al., 2001. The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana regulates formation of a symmetric lamina, establishment of venation and repression of meristem-related homeobox genes in leaves. Development, 128(10):1771-1783.

[32]Shuai, B., Reynaga-Pena, C.G., Springer, P.S., 2002. The lateral organ boundaries gene defines a novel, plant-specific gene family. Plant Physiol., 129(2):747-761.

[33]Tamura, K., Stecher, G., Peterson, D., et al., 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol., 30(12):2725-2729.

[34]Taramino, G., Sauer, M., Stauffer, J.L., et al., 2007. The maize (Zea mays L.) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and post-embryonic shoot-borne root initiation. Plant J., 50(4):649-659.

[35]Wang, X.F., Zhang, S.Z., Su, L., et al., 2013. A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES Domain) gene family in Malus domestica with a functional characterization of MdLBD11. PLOS ONE, 8(2):e57044.

[36]Xu, B., Li, Z.Y., Zhu, Y., et al., 2008. Arabidopsis genes AS1, AS2, and JAG negatively regulate boundary-specifying genes to promote sepal and petal development. Plant Physiol., 146(4):566-575.

[37]Xu, C., Luo, F., Hochholdinger, F., 2016. LOB domain proteins: beyond lateral organ boundaries. Trends Plant Sci., 21(2):159-167.

[38]Yang, Y., Yu, X.B., Wu, P., 2006. Comparison and evolution analysis of two rice subspecies LATERAL ORGAN BOUNDARIES domain gene family and their evolutionary characterization from Arabidopsis. Mol. Phylogenet. Evol., 39(1):248-262.

[39]Zhang, Y.M., Zhang, S.Z., Zheng, C.C., 2014. Genomewide analysis of LATERAL ORGAN BOUNDARIES Domain gene family in Zea mays. J. Genet., 93(1):79-91.

[40]List of electronic supplementary materials

[41]Table S1 Amino acid sequence of the ASL/LBD genes in barley

[42]Fig. S1 Promoter analysis of HvASL12/LBD12 and HvASL14/ LBD19 genes