Dataset of the HOX1 gene sequences of the wheat polyploids and their diploid relatives

The TaHOX-1 gene of common wheat Triticum aestivum L. (BAD-genome) encodes transcription factor (HD-Zip I) which is characterized by the presence of a DNA-binding homeodomain (HD) with an adjacent Leucine zipper (LZ) motif. This gene can play a role in adapting plant to a variety of abiotic stresses, such as drought, cold, salinity etc., which strongly affect wheat production. However, it's both functional role in stress resistance and divergence during wheat evolution has not yet been elucidated. This data in brief article is associated with the research paper “Structural and functional divergence of homoeologous copies of the TaHOX-1 gene in polyploid wheats and their diploid ancestors”. The data set represents a recent survey of the primary HOX-1 gene sequences isolated from the first wheat allotetraploids (BA-genome) and their corresponding Triticum and Aegilops diploid relatives. Specifically, we provide detailed information about the HOX-1 nucleotide sequences of the promoter region and both nucleotide and amino acid sequences of the gene. The sequencing data used here is available at DDBJ/EMBL/GenBank under the accession numbers MG000630-MG000698.


a b s t r a c t
The TaHOX-1 gene of common wheat Triticum aestivum L. (BADgenome) encodes transcription factor (HD-Zip I) which is characterized by the presence of a DNA-binding homeodomain (HD) with an adjacent Leucine zipper (LZ) motif. This gene can play a role in adapting plant to a variety of abiotic stresses, such as drought, cold, salinity etc., which strongly affect wheat production. However, it's both functional role in stress resistance and divergence during wheat evolution has not yet been elucidated. This data in brief article is associated with the research paper "Structural and functional divergence of homoeologous copies of the TaHOX-1 gene in polyploid wheats and their diploid ancestors". The data set represents a recent survey of the primary HOX-1 gene sequences isolated from the first wheat allotetraploids (BA-genome) and their corresponding Triticum and Aegilops diploid relatives. Specifically, we provide detailed information about the HOX-1 nucleotide sequences of the promoter region and both nucleotide and amino acid sequences of the gene. Non-treated seedlings

Experimental features
Total genomic DNA was extracted from one week old etiolated seedlings grown at room temperature from seeds placed in wet filter paper in Petri dishes. Using genomic DNA as a template, PCR amplification of the HOX-1 gene fragments was performed followed by their sequencing and computer analysis.

Data
The data include a list of species/accessions used in this study (Table 1), a multiple sequence alignment of the studied protein HOX-1 sequences with indication of basic structural domains ( Fig. 1), schematic representation of 0.7 kb promoter region of HOX-1 in diploid species with A-and S-genomes and corresponding genomes of polyploid wheats (Fig. 2), the neighbor-joining tree based on the alignment of the nucleotide HOX-1 promoter sequences (Fig. 3). The nucleotide and amino acid HOX-1 sequences from different accessions are available in fasta-format as Supplementary material 1.

Isolation and sequencing of PCR products
The PCR products were excised from the gel and purified using a QIAquick PCR purification kit (QIAGEN, Germany), then directly sequenced in both directions using an ABI PRISM Dye Terminator Cycle Sequencing ready reaction kit (Perkin Elmer Cetus, USA). Sequencing was conducted using resources of SB RAS Genomics Core Facilities (Novosibirsk, Russia, http://sequest.niboch.nsc.ru).

Sequence analysis
The nucleotide sequences were aligned using the ClustalW program with the MEGA4 software package [2,3]. Based on the known HDZip1 protein (AMB42697), the coding HOX-1 sequences were translated with subsequent alignment of a selective set of structurally different amino acid sequences for each species (Fig. 3). The putative cis-regulatory, stress responsive elements in the gene promoter were searched using database PlantPAN 2.0 (http://plantpan2.itps.ncku.edu.tw). Fig. 2 represents the most conservative elements implicated in response to drought and/or abscisic acid (ABA) which triggers ABA signaling pathway associated with abiotic stress.
Based on the alignment of HOX-1 promoter sequences, a phylogenetic tree was constructed by the neighbor-joining method, using 500 bootstrap replicates and pairwise deletion of gaps (Fig. 3).