Expression analysis of <i>BrnsLtp</i> genes by UniGene (Transcripts Per Million, TPM).

a<p><b>UN, unigene number; ^bB, bud; ^cF, flower; ^dL, leaf; ^eR, root; ^fS, seed; ^gSi, silique; ^hWP, whole plant; ⁱUT, unspecified tissue; “√” and “–” represent “exist” and “not exist”, respectively. Underlined indicated specific expression.</b></p

Multiple sequence alignment of the putative mature BrnsLtp proteins.

<p>The conserved cysteine residues are marked against a dark blue background. The names of different types of BrnsLtps are indicated with different color backgrounds. And the accession number of each gene was showed in the parentheses. Consensus residues Thr/Ser-X1-X2-Asp-Arg/Lys and Pro-Tyr-X-Ile-Ser are marked by rectangles. Tryptophan residues (W) are indicated with yellow circles.</p

Putative <i>nsLtp</i> genes identified in the genome of <i>B. rapa</i>.

a<p><b>ECM, eight-cysteine motif;</b><b>^bSP, signal peptide; ^cAA, number of amino acids; ^dMP, mature protein; ^eMM, molecular mass in Dalton; ^fpI, isoelectric point (cysteine residues were not taken into account in the pI caculation). A cluster of tandem duplication repeats was indicated by an asterisk after the gene names. The values in ECM allowing direct identification of the nsLtp type are indicated in bold italic.</b></p

Phylogenetic tree of BrnsLtps.

<p>The amino acids of the ECMs were used for Neighbor-Joining phylogenetic tree construction using the MEGA 5.05 software. The ten types of nsLtps and another five AtnsLtps are indicated with circles or triangles of different colors. And the accession number of each gene is showed in the parentheses nearby the corresponding gene name.</p

Alignments of the coding sequences and the deduced protein sequences of selected <i>BrnsLtp</i> genes in <i>B. rapa</i>.

<p>(A) Alignment of the <i>BrnsLtpII.2</i> and <i>BrnsLtpII.12</i> coding sequences. (B) Alignment of the BrnsLtpII.2 and BrnsLtpII.12 protein sequences. (C) Alignment of the <i>BrnsLtpI.5/6/10/11/13</i> coding sequences. (D) Alignment of the BrnsLtpI.5/6/10/11/13 protein sequences. Nucleic acid bases or amino acid residues in positions conserved in 100, 75, and 50% of all sequences are shaded in dark blue, purple, and light blue, respectively. The asterisks in (B) and (D) indicate the cysteine residues of the deduced protein backbones.</p

Gene structure of the <i>BrnsLtps</i> and <i>AtLtps</i>.

<p>Only those genes with introns (26 <i>AtLtps</i> and 19 <i>BrnsLtps</i>) are showed. The accession number of each gene is displayed in red font inside the parentheses. Intron phases are analysed based on the exon information. Phase 0 is designated introns between exons, phase 1 is designated introns between the first and the second nucleotide in a codon, and phase 2 is designated introns between the second and the third nucleotide in a codon <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084556#pone.0084556-Long1" target="_blank">[55]</a>.</p

Identification of homologous <i>nsLtp</i> genes between <i>A. thaliana</i> and three subgenomes in <i>B. rapa</i>.

a<p><b>CCB, conserved collinear block; ^bLF, the least fractionated blocks of B. </b><b><i>rapa</i></b><b>; ^cMF1, the medium fractionated blocks of B. </b><b><i>rapa</i></b><b>; ^dMF2, the most fractionated blocks of B. </b><b><i>rapa</i></b><b>.</b></p

Alignments of the precursor protein sequences of nsLtps with known functions and their homologous in <i>B. rapa</i>.

<p>Alignments of the precursor protein sequences of nsLtps with known functions and their homologous in <i>B. rapa</i>.</p

Schematic representation of the selected CREs in the <i>AtLTP1</i> and <i>BrnsLtpI.3</i> promoters.

<p>Schematic representation of the selected CREs in the <i>AtLTP1</i> and <i>BrnsLtpI.3</i> promoters.</p

Genomic localization of the <i>BrnsLtp</i> genes on the chromosomes of <i>B. rapa</i>.

<p>Chromosome numbers are indicated above each chromosome. The number of <i>BrnsLtp</i> genes distributed on each <i>B. rapa</i> chromosome is indicated by an Arabic numeral in the bracket, which is under the relative chromosome number. And the accession number of each gene was showed in the parentheses underneath the corresponding gene name. The <i>BrnsLtp</i> genes present on duplicated chromosomal segments are connected by blue lines between the two relevant chromosomes. Tandem duplicated genes are marked on a yellow background. The conserved collinear blocks on each chromosome are labeled A to X and are color-coded according to inferred ancestral chromosomes following an established convention.</p