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Tree Genetics & Genomes

, 11:126 | Cite as

The complete peach dehydrin family: characterization of three recently recognized genes

  • Carole Leavel BassettEmail author
  • Kirsten M. Fisher
  • Robert E. FarrellJr.
Original Article
Part of the following topical collections:
  1. Genome Biology

Abstract

Three genes encoding dehydrins have been previously described from peach. In the course of searching the peach genome, three additional members of this stress-associated family were recognized, PpDhn4-6. PpDhn1 and 6 have no introns, whereas the remaining four genes have a single intron located near the 3′ end of the serine (S) tract. PpDHN2 was the only dehydrin with a predicted basic pI; pI predictions for the other dehydrins ranged from about 5.3 to about 6.3. None of the peach dehydrins have tryptophan residues, but, in contrast to most dehydrins, three (PpDHN1, 3, and 4) have one or more cysteine residues. Phylogenetic analysis indicated a close relationship between PpDhn1 and 6 and PpDhn3 and 4. Expression analysis under low temperature and dehydration confirmed that PpDhn2 is the major responder to drought, while both PpDhn1 and 6 respond exclusively to cold. Comparison of the first 500 base pairs upstream of the translation start site revealed the presence of cis-elements associated with low temperature and drought/osmotic/salt and hormone response regulation.

Keywords

Abiotic stress Gene expression Promoter comparison Woody plants 

Notes

Acknowledgments

We appreciate the expert technical assistance of Ms. Jing Ma in the expression studies. This work was supported in its entirety by the USDA, the Agricultural Research Service, CRIS project 8080-21000-022-00D.

Data archiving statement

The genes described herein can be found at the National Center for Biotechnology Information or the Genome Database for Rosaceae as follows: PpDhn 4: GenBank Accession No. XM_007200796, GDR Locus No. ppa026861m; PpDhn5: GenBank Accession No. XM_007201751, GDR Locus No. ppa010975m; and PpDhn6: GenBank Accession No. XM_007202386, GDR Locus No. ppa009997m. Promoter regions can be found under GenBank Accession numbers as follows: PpDhn1: AY819770, PpDhn2: AY819770, PpDhn3: EU286278; use 500 bases upstream of GDR scaffold_8:16894027…16894705 (− strand) for PpDhn4; scaffold_8:11638043…11641172 (− strand) for PpDhn5; and scaffold_7:17137970…17139156 (+ strand) for PpDhn6.

GenBank accession numbers for the grape dehydrin sequences are as follows: XM03631828 (VvDHN1a), XM022285883 (VvDHN2), CAN73166 (VvDHN3), and XM002285369 (VvDHN4). Arabidopsis dehydrin GenBank gene ID numbers for the polypeptides identified by gene name are as follows: At3g50980 (Xero1), At3g50970 (Xero2), At5g66400 (Rab18), At1g20450 (ERD10), At1g76180 (ERD14), and At1g20440 (COR47).

Supplementary material

11295_2015_923_MOESM1_ESM.docx (15 kb)
Fig. S1 The alignment was conducted using the T-Coffee program (Notredame et al. 2000; Di Tommaso et al. 2011). Additional alignment was done by hand to maximize matches to relevant sequence features, such as the Y domain, the S tract and the last K motif. Dashes indicate regions lacking in sequence matches; the K motif is underlined and the Y domain is highlighted in gray. Degenerate K motifs are indicated by a dotted underline. (DOCX 15 kb)
11295_2015_923_MOESM2_ESM.pdf (23 kb)
Fig. S2 Phylogenetic tree resulting from the maximum likelihood analysis of six peach dehydrins (−lnL 3669.353). Bootstrap support values > 50 % (100 replicates) are indicated above branches. (PDF 23 kb)
11295_2015_923_Fig9_ESM.jpg (1.2 mb)
Fig. S3

Intrinsic disorder profiles for PPDHN1 and 2. Amino acid sequences for the two predicted proteins were submitted to the DISOPRED server at PSIPRED (Ward et al. 2004). The graphic shows the DISOPRED3 disorder confidence levels relative to the amino acid positions as solid blue lines; solid orange lines represent confidence predictions on residuess involved in protein-protein interaction. The dashed line represents the threshold above which amino acids are regarded as disordered. (JPEG 1263 kb)

11295_2015_923_Fig10_ESM.jpg (1.3 mb)
Fig. S4

Intrinsic disorder profiles for PPDHN3 and 4. The legend is the same as that for Figure S3. (JPEG 1311 kb)

11295_2015_923_Fig11_ESM.jpg (1.2 mb)
Fig. S5

Intrinsic disorder profiles for PPDHN5. Two polypeptides are predicted beginning at different translation start sites. PPDHN5 begins at MAQIRDEYGN.... whereas PPDHN5B begins 22 residues 5' of the predicted PPDHN5 start site (MGLPFLISYFDRGLALFVKNTQ-MAQIRDEYGN...). (JPEG 1227 kb)

11295_2015_923_Fig12_ESM.jpg (886 kb)
Fig. S6

Intrinsic disorder profile for PPDHN6. The legend is the same as that for Figure S3. (JPEG 886 kb)

11295_2015_923_MOESM3_ESM.docx (15 kb)
Supplemental Table S1 (DOCX 14 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2015

Authors and Affiliations

  • Carole Leavel Bassett
    • 1
    Email author
  • Kirsten M. Fisher
    • 2
  • Robert E. FarrellJr.
    • 3
  1. 1.USDA, ARS, Appalachian Fruit Research Station (formerly)KeedysvilleUSA
  2. 2.Department of Biological SciencesCalifornia State University, Los AngelesLos AngelesUSA
  3. 3.Department of BiologyPennsylvania State University, YorkYorkUSA

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