Abstract
Key message
An unambiguous nomenclature is proposed for the twenty-eight-member LOB domain transcription factor family in Brachypodium . Expression analysis provides unique transcript patterns that are characteristic of a wide range of organs and plant parts.
Abstract
LOB (lateral organ boundaries)-domain proteins define a family of plant-specific transcription factors involved in developmental processes from embryogenesis to seed production. They play a crucial role in shaping the plant architecture through coordinating cell fate at meristem to organ boundaries. Despite their high potential importance, our knowledge of them is limited, especially in the case of monocots. In this study, we characterized LOB domain protein coding genes (LBDs) of Brachypodium distachyon, a model plant for grasses, and present their phylogenetic relationships and an overall spatial expression study. In the Brachypodium genome database, 28 LBDs were found and then classified based on the presence of highly conserved LOB domain motif. Their transcript amounts were measured via quantitative real-time RT-PCR in 37 different plant parts from root tip to generative organs. Comprehensive phylogenetic analysis suggests that there are neither Brachypodium- nor monocot-specific lineages among LBDs, but there are differences in terms of complexity of subclasses between monocots and dicots. Although LBDs in Brachypodium have wide variation of tissue-specific expression and relative transcript levels, overall expression patterns show similarity to their counterparts in other species. The varying transcript profiles we observed support the hypothesis that Brachypodium LBDs have diverse but conserved functions in plant organogenesis.
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Acknowledgments
This research was supported by the Hungarian Scientific Research Foundation (OTKA-K76273 and OTKA-K109719) and the Hungarian Governmental Grant GINOP-2.3.2-15-2016-00001. The authors are grateful to Judit Györgyey Ries and John Ries for their correction of the English of the manuscript.
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299_2016_2057_MOESM1_ESM.tif
Online Resource 1 Combined phylogenetic tree of LOB-domain proteins from rice (Oryza sativa sp. Japonica) (medium blue dots), maize (Zea mays) (dark blue dots), Arabidopsis thaliana (red dots) and Brachypodium distachyon (light blue dots). The unrooted NJ tree was constructed with MEGA6 software based on amino acid sequences of conserved domain motif of 28 B. distachyon, 43 A. thaliana, 35 O. sativa and 44 maize LOB-domain proteins. The numbers on the branches are local bootstrap values calculated with 1000 replicates. Subfamilies are indicated by colour arches (TIFF 31431 kb)
299_2016_2057_MOESM2_ESM.rtf
Online Resource 2 Multiple sequence alignment of amino acid sequences of conserved domain motif of LOB-domain proteins from O. sativa, Zea mays, A. thaliana and B. distachyon. Invariant residues are marked with *. Consensus amino acid residues conserved in more than 50 % of proteins are indicated by grey background, while residues conserved in more than 75 % of proteins are indicated with withe font colour on black background. Os01g39040-A and Os01g39040-B highlighted with red font colour are two different LOB-domain motifs of the same protein, but presented in this alignment separately. The numbers mark the starting and ending position of LOB-domain motifs in each protein (RTF 1213 kb)
299_2016_2057_MOESM3_ESM.tif
Online Resource 3 The relative transcript amount of all 28 LBD genes of B. distachyon in root tip (R1), root differentiation zone (R3), 2nd leaf blade (L2), 3rd stem node (N3), flowers 1–2 days before pollination (F1), seeds 10 days after pollination (E3) and anthers. Root tips, 2nd leaf blades and 3rd stem nodes were collected from 14 DAG (days after germination) old plantlets; flowers 1–2 days before pollination and anthers were collected from 28 DAG old plantlets, seeds 10 days after pollination (10 DAP) were harvested from 40–45 DAG old plants grown under normal condition. The levels of gene expression were determined by quantitative real-time RT-PCR; at first relative to average transcript amount of EF1-α and UBC18 genes and second by relative to average transcript amount of each LBD genes. Means ±SD are shown (n = 2). Diagrams marked with black star are parts of Figure 5. Corresponding numeric data are listed in Online Resource 6 (TIFF 3727 kb)
299_2016_2057_MOESM4_ESM.xls
Online Resource 4 List of primer sequences used for quantitative real-time RT-PCR measurements. Some supporting information (genome position of BdLBD genes; length, weight and isoelectronic points of encoded proteins) are also represented (XLS 31 kb)
299_2016_2057_MOESM5_ESM.xlsx
Online Resource 5 Log10-transformed relative transcript amount data corresponding to expression profile analysis of 28 BdLBD genes in 37 different plant parts. Presented data is from one biological replicate derived from approximately 200 plants (XLSX 26 kb)
299_2016_2057_MOESM6_ESM.xlsx
Online Resource 6 Relative transcript amount data corresponding to biological replication (n = 2) of the expression pattern of 28 BdLBD genes in seven selected samples (root tip (R1), root differentiation zone (R3), 2nd leaf blade (L2), 3rd stem node (N3), flowers 1–2 days before pollination (F1), seeds 10 days after pollination (E3) and anthers) (XLSX 25 kb)
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Gombos, M., Zombori, Z., Szécsényi, M. et al. Characterization of the LBD gene family in Brachypodium: a phylogenetic and transcriptional study. Plant Cell Rep 36, 61–79 (2017). https://doi.org/10.1007/s00299-016-2057-0
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DOI: https://doi.org/10.1007/s00299-016-2057-0