Electronic Supplementary Material (Online Resource 1) For

Electronic Supplementary Material for:

Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L.

Hude Mao1*·Lijuan Yu2·Zhanjie Li2·Hui Liu2·Ran Han2

1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University,Yangling, Shaanxi 712100, China.

2 College of Life Sciences, Northwest A&F University, Yangling, Shanxi 712100, China.

Journal: Genetica

* Corresponding author.

Email:

Fig. S1 Phylogenetic relationships of HD-Zip proteins from five land plant species. An unrooted Neighbor-joining tree was constructed based on the sequence alignments of 207 full-length HD-Zip proteins from five species. HD-Zip protein classes I, II, III, and IV are shaded in red, blue, green, and yellow, respectively. Bootstrap values from 1,000 replicates are indicated at each node, and the scale represents branch lengths.

Maize HD-Zip proteins are labled with red dots.

Fig. S2 Correlation of fold-change values calculated with microarray and qRT-PCR for 17 selected maize HD-Zip genes. P-values represent the two-tailed probability for Pearson’s correlation (r).

Table S1 Oligonucleotide primers used in this research. The name of the primers was based on the gene name and experimental purpose.

Gene name / Forward primer / Reverse primer
ZmHDZ1 / GACCGATGCTTGGCCTTG / AGCTGCTCGTCGTAGTACTCCTC
ZmHDZ2 / CCAGGTAGCTGTTTGGTTCCA / GGCGAGTGCGTCGTAAGC
ZmHDZ3 / ATCCCTGTCGGCAACCATC / ATGTCCAGTGCAACCGCAG
ZmHDZ4 / CTGCTCCGCGCCAAGTT / TCCCTCAGCCTCTCGCTTAG
ZmHDZ5 / GAGGGCCCCATGGACCA / GTGCAGGAGTTGGTCCATACC
ZmHDZ6 / GGCCCAGTTCATGCACCA / ACCTGCTCCTCCGTGAACC
ZmHDZ7 / AACTGAGAAACTGCAAACGAAAGA / CAGAGCTTGTCTCCTTCCAAGAC
ZmHDZ8 / GATGATGGTTACGGCGTGG / GCACCTGCTCGGAGCTCA
ZmHDZ9 / CCCGGAGTGGATGATGGAG / CGAACATGGACTCGAGAGACTT
ZmHDZ10 / GGAATGCGTGCGGAATG / GCCGAACGCCATCATCTC
ZmHDZ11 / GATCATGAGCATCAAGAACAGCAT / GCGAGGGGCATTGAGAAGA
ZmHDZ12 / ACGGAGTGGATGATGCATGG / GAACATGGACTCCAGCGACTT
ZmHDZ13 / ACAACAAGAAGCTACAGGCAGAGA / TCTCTGACGTTGAGGTTGATGAG
ZmHDZ14 / CTCGTCTCCCCCCGTTTTC / CAGGCCTTGTACGAGTCGAAT
ZmHDZ15 / GTTCTCGACGGTGACGCA / CTGTTGTAGGCGTACTCGGTCA
ZmHDZ16 / GCGTCGCCCTACCCTTACTC / ACGTCAAGAAGGAGGTGAAACC
ZmHDZ17 / CGGCTCCTGCTTTTCCAA / TCATCTGTGACCGGCACTTG
ZmUbi-2 / TGGTTGTGGCTTCGTTGGTT / GCTGCAGAAGAGTTTTGGGTACA

Table S2 Distribution of the conserved domains and motifs in maize HD-Zip proteins.

Gene Name / Gene Identifier / HD domain / Leucine zipper motif / START domain / MEKHLA domain
ZmHDZ1 / GRMZM2G021339 / √ / √
ZmHDZ2 / GRMZM2G122076 / √ / √
ZmHDZ3 / GRMZM2G003304 / √ / √
ZmHDZ4 / GRMZM2G351330 / √ / √
ZmHDZ5 / GRMZM2G178741 / √ / √
ZmHDZ6 / GRMZM2G117164 / √ / √
ZmHDZ7 / GRMZM2G002915 / √ / √
ZmHDZ8 / GRMZM2G056600 / √ / √
ZmHDZ9 / GRMZM2G041462 / √ / √
ZmHDZ10 / GRMZM2G041127 / √ / √
ZmHDZ11 / GRMZM2G139963 / √ / √
ZmHDZ12 / GRMZM2G034113 / √ / √
ZmHDZ13 / GRMZM2G097349 / √ / √
ZmHDZ14 / GRMZM2G132367 / √ / √
ZmHDZ15 / GRMZM2G005624 / √ / √
ZmHDZ16 / GRMZM2G119999 / √ / √
ZmHDZ17 / AC233899.1_FGP004 / √ / √
ZmHDZ18 / GRMZM2G126239 / √ / √
ZmHDZ19 / GRMZM2G134260 / √ / √
ZmHDZ20 / GRMZM2G366130 / √ / √
ZmHDZ21 / GRMZM2G068672 / √ / √
ZmHDZ22 / GRMZM2G307400 / √ / √
ZmHDZ23 / GRMZM2G307397 / √ / √
ZmHDZ24 / GRMZM2G166041 / √ / √
ZmHDZ25 / GRMZM2G148074 / √ / √
ZmHDZ26 / GRMZM2G142962 / √ / √
ZmHDZ27 / GRMZM2G047715 / √ / √
ZmHDZ28 / GRMZM2G477415 / √ / √
ZmHDZ29 / GRMZM2G106276 / √ / √
ZmHDZ30 / GRMZM2G105834 / √ / √
ZmHDZ31 / GRMZM2G478937 / √ / √
ZmHDZ32 / GRMZM2G131476 / √ / √
ZmHDZ33 / GRMZM2G127537 / √ / √
ZmHDZ34 / GRMZM2G044752 / √ / √
ZmHDZ35 / GRMZM2G126808 / √ / √
ZmHDZ36 / AC187157.4_FGP005 / √ / √ / √ / √
ZmHDZ37 / GRMZM2G003509 / √ / √ / √ / √
ZmHDZ38 / GRMZM2G109987 / √ / √ / √ / √
ZmHDZ39 / GRMZM2G178102 / √ / √ / √ / √
ZmHDZ40 / GRMZM2G469551 / √ / √ / √ / √
ZmHDZ41 / AC235534.1_FGP007 / √ / √ / √
ZmHDZ42 / GRMZM2G001289 / √ / √ / √
ZmHDZ43 / GRMZM2G004334 / √ / √ / √
ZmHDZ44 / GRMZM2G004957 / √ / √ / √
ZmHDZ45 / GRMZM2G026643 / √ / √ / √
ZmHDZ46 / GRMZM2G109252 / √ / √ / √
ZmHDZ47 / GRMZM2G116658 / √ / √ / √
ZmHDZ48 / GRMZM2G118063 / √ / √ / √
ZmHDZ49 / GRMZM2G122897 / √ / √ / √
ZmHDZ50 / GRMZM2G123140 / √ / √ / √
ZmHDZ51 / GRMZM2G126646 / √ / √ / √
ZmHDZ52 / GRMZM2G130442 / √ / √ / √
ZmHDZ53 / GRMZM2G145690 / √ / √ / √
ZmHDZ54 / GRMZM2G386276 / √ / √ / √
ZmHDZ55 / GRMZM2G438260 / √ / √ / √

Table S3 Genomic syntenic blocks in the maize genome. The gene colinearity data were collected from the Plant Genome Duplication Database (PGDD, http://chibba.agtec.uga.edu/duplication). The physical initiation position of each homologous HD-Zip gene and the resident genomic block on the individual chromosomes (chrom_Zm) are labeled as “Zm_start and Zm_block_start”. The ending positions are labeled as “Zm_end and Zm_block_end”.

block_1 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr1 / GRMZM2G003509 / 173247814 / 173257862 / 166731472 / 173257862
Locus 2 / chr3 / GRMZM2G178102 / 123281942 / 123288759 / 114893019 / 123288759
block_2 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr1 / GRMZM2G139963 / 14957965 / 14960921 / 14405531 / 20218493
Locus 2 / chr9 / GRMZM2G178741 / 151525953 / 151528343 / 151739975 / 149575220
block_3 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr1 / GRMZM2G097349 / 243185151 / 243187447 / 242209875 / 243277640
Locus 2 / chr9 / GRMZM2G178741 / 151525953 / 151528343 / 151739975 / 151518716
block_4 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr2 / GRMZM2G041127 / 188712314 / 188714917 / 181481264 / 191505927
Locus 2 / chr7 / GRMZM2G056600 / 129296234 / 129298384 / 115132369 / 134737413
block_5 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr2 / GRMZM2G034113 / 195705583 / 195707271 / 195696769 / 199099102
Locus 2 / chr7 / GRMZM2G041462 / 142432248 / 142434060 / 142418819 / 145338551
block_6 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr2 / GRMZM2G001289 / 8289450 / 8295263 / 8289450 / 11762535
Locus 2 / chr10 / GRMZM2G118063 / 58000726 / 58009253 / 58000726 / 68739253
block_7 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr2 / GRMZM2G001289 / 8289450 / 8295263 / 925414 / 12209656
Locus 2 / chr10 / GRMZM2G122897 / 142813273 / 142817535 / 148042902 / 140389775
block_8 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr4 / GRMZM2G126646 / 177612036 / 177616331 / 168769110 / 181906080
Locus 2 / chr5 / GRMZM2G145690 / 211123234 / 211127092 / 217056143 / 207707495
block_9 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr5 / GRMZM2G117164 / 190526953 / 190528628 / 188894598 / 200533509
Locus 2 / chr2 / GRMZM2G351330 / 22220873 / 22222180 / 24097702 / 12008624
block_10 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr6 / GRMZM2G004334 / 109244071 / 109247202 / 108478031 / 110008265
Locus 2 / chr5 / GRMZM2G145690 / 211123234 / 211127092 / 211773221 / 210356112
block_11 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr6 / GRMZM2G068672 / 70173601 / 70175049 / 60352538 / 71395904
Locus 2 / chr9 / GRMZM2G134260 / 20839231 / 20841005 / 25722859 / 20599326
block_12 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr7 / GRMZM2G127537 / 123539134 / 123541042 / 123539134 / 127761580
Locus 2 / chr1 / GRMZM2G142962 / 198225939 / 198227907 / 198225939 / 200664592
block_13 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr7 / GRMZM2G127537 / 123539134 / 123541042 / 123539134 / 125357466
Locus 2 / chr2 / GRMZM2G366130 / 186502150 / 186503354 / 186502150 / 185617611
block_14 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr9 / GRMZM2G105834 / 145045937 / 145048121 / 139766916 / 147598598
Locus 2 / chr1 / GRMZM2G126808 / 29542836 / 29544587 / 41105576 / 25428035
block_15 / chrom_Zm / Zm / Zm_start / Zm_end / Zm_block_start / Zm_block_end
Locus 1 / chr10 / GRMZM2G118063 / 58000726 / 58009253 / 58000726 / 66329339
Locus 2 / chr4 / GRMZM2G130442 / 29009093 / 29014800 / 29009093 / 26404136

Table S4 The predicted Selaginella and Physcomitrella HD-Zip proteins used in this study. Sequences were downloaded from the Plant Transcription Factor Database, v.3.0 (http://planttfdb.cbi.edu.cn). The class of each HD-Zip protein is based on the phylogenetic analysis against the Arabidopsis, Vitis, rice and maize proteins.

Species / Original ID / Protein length (a.a.) / Class
Selaginella / 18196 / 104 / HD-Zip I
Selaginella / 19476 / 87 / HD-Zip I
Selaginella / 81609 / 127 / HD-Zip I
Selaginella / 18217 / 87 / HD-Zip I
Selaginella / 6792 / 140 / HD-Zip II
Selaginella / 139631 / 185 / HD-Zip II
Selaginella / 77000 / 821 / HD-Zip III
Selaginella / 270225 / 855 / HD-Zip III
Selaginella / 270954 / 840 / HD-Zip III
Physcomitrella / Pp1s4_70V6 / 341 / HD-Zip I
Physcomitrella / Pp1s7_280V6 / 386 / HD-Zip I
Physcomitrella / Pp1s28_46V6 / 419 / HD-Zip I
Physcomitrella / Pp1s28_54V6 / 365 / HD-Zip I
Physcomitrella / Pp1s31_96V6 / 298 / HD-Zip I
Physcomitrella / Pp1s34_317V6 / 369 / HD-Zip I
Physcomitrella / Pp1s34_327V6 / 357 / HD-Zip I
Physcomitrella / Pp1s65_42V6 / 350 / HD-Zip I
Physcomitrella / Pp1s65_52V6 / 344 / HD-Zip I
Physcomitrella / Pp1s77_184V6 / 343 / HD-Zip I
Physcomitrella / Pp1s96_191V6 / 332 / HD-Zip I
Physcomitrella / Pp1s108_47V6 / 345 / HD-Zip I
Physcomitrella / Pp1s143_73V6 / 332 / HD-Zip I
Physcomitrella / Pp1s154_145V6 / 339 / HD-Zip I
Physcomitrella / Pp1s325_51V6 / 326 / HD-Zip I
Physcomitrella / Pp1s431_27V6 / 345 / HD-Zip I
Physcomitrella / Pp1s31_269V6 / 328 / HD-Zip II
Physcomitrella / Pp1s31_272V6 / 330 / HD-Zip II
Physcomitrella / Pp1s42_217V6 / 326 / HD-Zip II
Physcomitrella / Pp1s42_219V6 / 326 / HD-Zip II
Physcomitrella / Pp1s15_11V6 / 858 / HD-ZipIII
Physcomitrella / Pp1s55_99V6 / 880 / HD-Zip III
Physcomitrella / Pp1s67_107V6 / 1010 / HD-Zip III
Physcomitrella / Pp1s70_192V6 / 871 / HD-Zip III
Physcomitrella / Pp1s188_95V6 / 875 / HD-Zip III
Physcomitrella / Pp1s59_146V6 / 809 / HD-Zip IV
Physcomitrella / Pp1s84_236V6 / 794 / HD-Zip IV
Physcomitrella / Pp1s173_90V6 / 799 / HD-Zip IV
Physcomitrella / Pp1s209_10V6 / 799 / HD-Zip IV

Table S5 RNA-seq mRNA abundance for maize HD-Zip genes in roots (Rt), coleoptiles (Cp), stem (St), internode (In), cob (Co), leaves (Le), shoot (Sh), tassel (Ta), silk (Si), husk (Hu), embryo (Em), pericarp (Pe) and seeds (Se) of field-grown maize. Values are expressed as the average number of fragments per kilobase of transcript per million fragments mapped (FPKM).

Gene / Root / Coleoptile / Stem / Internode / Cob / Leaves / Shoot / Tassel / Silks / Husk / Embryo / Pericarp / Seed
ZmHDZ1 / 8.43 / 8.14 / 8.69 / 8.70 / 8.77 / 9.21 / 9.06 / 8.39 / 8.62 / 10.15 / 7.24 / 9.22 / 8.91
ZmHDZ2 / 12.65 / 13.46 / 11.86 / 12.60 / 12.30 / 12.86 / 12.35 / 11.80 / 12.69 / 12.67 / 11.97 / 12.28 / 11.71
ZmHDZ3 / 10.91 / 11.13 / 10.04 / 10.29 / 10.29 / 9.73 / 10.09 / 9.58 / 10.33 / 10.55 / 9.24 / 10.24 / 9.76
ZmHDZ4 / 6.71 / 6.03 / 5.85 / 6.66 / 6.16 / 10.82 / 6.17 / 6.43 / 6.65 / 8.04 / 6.21 / 7.04 / 6.68
ZmHDZ5 / 7.78 / 9.87 / 7.51 / 8.98 / 8.30 / 7.03 / 8.41 / 8.36 / 9.85 / 7.99 / 6.01 / 9.17 / 8.68
ZmHDZ6 / 7.93 / 7.14 / 6.60 / 7.78 / 7.33 / 7.09 / 7.14 / 7.20 / 6.53 / 9.41 / 6.54 / 9.18 / 8.56
ZmHDZ7 / 8.86 / 6.98 / 8.77 / 9.09 / 7.34 / 9.85 / 8.96 / 6.97 / 10.85 / 7.19 / 6.62 / 6.88 / 6.99
ZmHDZ8 / 10.68 / 10.94 / 10.79 / 11.08 / 12.28 / 11.89 / 11.40 / 12.07 / 11.87 / 12.40 / 9.97 / 11.66 / 11.88
ZmHDZ9 / 8.64 / 8.35 / 6.46 / 7.03 / 7.48 / 6.43 / 6.59 / 6.79 / 8.70 / 8.54 / 6.04 / 9.01 / 8.59
ZmHDZ10 / 9.97 / 10.41 / 9.26 / 9.24 / 10.14 / 10.21 / 9.71 / 9.90 / 11.63 / 10.45 / 8.92 / 9.74 / 9.35
ZmHDZ11 / 9.07 / 10.77 / 9.53 / 10.76 / 11.23 / 9.16 / 10.64 / 10.48 / 11.76 / 9.89 / 6.98 / 10.62 / 10.42
ZmHDZ12 / 9.39 / 9.69 / 8.15 / 7.31 / 8.64 / 7.70 / 7.80 / 8.14 / 10.95 / 12.38 / 6.18 / 9.76 / 10.18
ZmHDZ13 / 9.65 / 10.55 / 9.00 / 9.20 / 8.84 / 7.09 / 9.61 / 8.62 / 10.28 / 7.77 / 6.76 / 6.56 / 8.74
ZmHDZ14 / 8.81 / 8.88 / 9.29 / 9.30 / 10.35 / 8.14 / 9.80 / 9.54 / 10.59 / 8.80 / 8.02 / 8.82 / 9.19
ZmHDZ15 / 8.76 / 7.67 / 8.95 / 9.45 / 10.91 / 7.82 / 9.51 / 10.97 / 10.24 / 10.72 / 8.53 / 11.44 / 9.56
ZmHDZ16 / 10.08 / 9.10 / 9.87 / 8.77 / 6.94 / 9.25 / 8.73 / 7.13 / 9.88 / 6.21 / 6.50 / 6.36 / 6.08
ZmHDZ17 / - / - / - / - / - / - / - / - / - / - / - / - / -
ZmHDZ18 / 8.14 / 7.67 / 8.80 / 7.40 / 9.99 / 7.38 / 9.07 / 10.52 / 10.22 / 11.41 / 9.12 / 10.37 / 9.19
ZmHDZ19 / 10.70 / 10.43 / 10.24 / 9.85 / 11.34 / 10.23 / 9.53 / 11.16 / 12.84 / 11.74 / 7.14 / 10.67 / 11.22
ZmHDZ20 / 5.50 / 5.42 / 5.91 / 6.03 / 6.18 / 6.51 / 5.95 / 5.88 / 6.32 / 6.10 / 6.49 / 5.54 / 5.75
ZmHDZ21 / 6.36 / 7.03 / 6.13 / 6.81 / 6.67 / 6.18 / 5.96 / 6.21 / 10.42 / 6.33 / 5.97 / 6.25 / 6.47
ZmHDZ22 / 6.44 / 6.56 / 6.42 / 6.75 / 6.82 / 7.21 / 6.59 / 6.25 / 6.86 / 6.66 / 6.84 / 6.39 / 6.62
ZmHDZ23 / 9.69 / 10.09 / 9.71 / 10.91 / 10.00 / 10.78 / 9.72 / 9.75 / 10.13 / 10.53 / 10.10 / 10.12 / 9.88