Defensin amino acid sequence alignment.

<p>The amino acid sequences of the mature peptides of DgDEF1 and DgDEF2 are compared with the sequences of four mature defensin peptides of the A3 class, a defensin from <i>Arabidopsis halleri</i> (AhPDF1.4; GenBank accession no. AY961379.1), the Antifungal Protein 1 from <i>Raphanus sativus</i> seeds (RsAFP1) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072442#pone.0072442-Terras1" target="_blank">[55]</a>, a defensin from <i>D. merckii</i> (AMP1) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072442#pone.0072442-Osborn1" target="_blank">[53]</a> and the aluminum-induced tobacco protein (NtPit1) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072442#pone.0072442-Ezaki1" target="_blank">[52]</a>. Gaps to optimize the alignment were introduced using the program ClustalW (EMBL), and the editor GeneDoc was used to present the alignment <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072442#pone.0072442-Nicholas1" target="_blank">[89]</a>. Identical amino acids at conserved positions are labeled by inverse print, whereas positions without full amino acid conservation are shaded in gray. Asterisks mark the cysteine residues conserved in the defensins from plants other than <i>D. glomerata</i>. All negatively charged amino acids in the unique C-terminal domains of DgDEF1 and DgDEF1 are marked by bold print and underlined.</p

Validation of SAGE-type library comparison results and analysis of expression levels of genes encoding proteins involved in infection thread formation by quantitative real-time polymerase chain reaction (qPCR).

<p>Values for qPCR results represent means of three biological replicates.</p>*<p>Contigs were originally classified based on 454 sequencing results. The tendency (nodule-enhanced or root-enhanced expression with R>10 based on the evaluation of the SAGE-type libraries) is considered to be confirmed when the fold change ≥2 (for nodule-enhanced genes) and ≤−2 (for root-enhanced genes) and the difference is significant, p<0.05. Bold indicates p<0.05; bold underline indicates p<0.0019 (Bonferroni correction).</p>†<p>Due to R<10.</p

<i>D. glomerata</i> homologs of genes encoding components of the common symbiosis pathway or proteins involved in infection thread growth in legumes (legume data from [34], [36], [39], [40], [42], [43], [44], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88]).

<p>qPCRs were performed based on RNA from nodules and roots of non-inoculated plants. The last column refers to the expression in uninfected legume roots <i>vs</i>. mature legume nodules. If expression levels in roots and nodules differed by a factor of 2 or more, expression is described as nodule-enhanced or root-enhanced, respectively. If expression levels in both organs differed by a factor of 100 or more, expression is described as root- or nodule-specific, respectively. When more than one <i>D. glomerata</i> homolog of a legume gene is listed, the <i>D. glomerata</i> contig with the strongest homology between its implicated protein and the legume protein(s) is listed first. Homologies between the legume proteins and the <i>D. glomerata</i> proteins are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072442#pone.0072442.s005" target="_blank">Table S2</a>.</p><p>n.d. – not determined.</p

Table_1_All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants.XLSX

Recent advances in plant developmental genetics together with rapid accumulation of transcriptomic data on plants from divergent lineages provide an exciting opportunity to explore the evolution of plant morphology. To understand leaf origin in sporophytes of land plants, we have combined the available molecular and structural data on development of leaves with different morphologies in different plant lineages: clubmosses, spikemosses, leptosporangiate ferns, ophioglossioid ferns, marattioid ferns, whisk ferns, horsetails, and conifers. Specifically, we address the peculiarities of proximo-distal, ad/abaxial, and lateral development; presence/absence of mesophyll differentiation into palisade and spongy parenchyma; and type of leaf vascular bundles (collateral and bicollateral). Furthermore, taxon-specific and morphology-specific features of leaf development are considered in the context of the organization of shoot apical meristems (SAMs)—monoplex, simplex, or duplex—that produce leaf primordia. The data available imply that cellular patterns of leaf initiation correlate strongly with the structure of the SAMs but not with further leaf development or morphology. The later stages of leaf development are neither correlated with SAM structure nor with taxonomy. Occurrence and, if available, patterns of expression of homologs of the angiosperm genes responsible for the development of adaxial (ARP and C3HDZ) and abaxial (YABBY and KANADI) leaf domains, or establishment of the leaf marginal meristem (WOX) are discussed. We show that there is no correlation in the set of homologs of TFs that regulate abaxial and adaxial leaf domain development between leaves containing only spongy and no palisade mesophyll (of spikemosses, clubmosses, whisk ferns, horsetails, and most conifers), and leaves differentiated into palisade and spongy mesophyll (of leptosporangiate ferns, Ginkgo, Gnetum, and angiosperms). Expression of three out of four regulators of leaf development in primordia of both leaves and sporangia—C3HDZ in spikemosses and whisk ferns, YABBY in clubmosses and KANADI in spikemosses and horsetails—indicates that a sporangium developmental program could have been co-opted as a “precursor program” for the origin of microphylls and euphylls. Additionally, expression of leaf development regulators in SAMs of spikemosses (ARP, C3HDZ, and KANADI), clubmosses (YABBY), leptosporangiate ferns (C3HDZ), and horsetails (C3HDZ and KANADI) indicates that at least some mechanisms of SAM regulation were co-opted as well in the pre-program of leaf precursors.</p

Presentation_1_All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants.pdf

Recent advances in plant developmental genetics together with rapid accumulation of transcriptomic data on plants from divergent lineages provide an exciting opportunity to explore the evolution of plant morphology. To understand leaf origin in sporophytes of land plants, we have combined the available molecular and structural data on development of leaves with different morphologies in different plant lineages: clubmosses, spikemosses, leptosporangiate ferns, ophioglossioid ferns, marattioid ferns, whisk ferns, horsetails, and conifers. Specifically, we address the peculiarities of proximo-distal, ad/abaxial, and lateral development; presence/absence of mesophyll differentiation into palisade and spongy parenchyma; and type of leaf vascular bundles (collateral and bicollateral). Furthermore, taxon-specific and morphology-specific features of leaf development are considered in the context of the organization of shoot apical meristems (SAMs)—monoplex, simplex, or duplex—that produce leaf primordia. The data available imply that cellular patterns of leaf initiation correlate strongly with the structure of the SAMs but not with further leaf development or morphology. The later stages of leaf development are neither correlated with SAM structure nor with taxonomy. Occurrence and, if available, patterns of expression of homologs of the angiosperm genes responsible for the development of adaxial (ARP and C3HDZ) and abaxial (YABBY and KANADI) leaf domains, or establishment of the leaf marginal meristem (WOX) are discussed. We show that there is no correlation in the set of homologs of TFs that regulate abaxial and adaxial leaf domain development between leaves containing only spongy and no palisade mesophyll (of spikemosses, clubmosses, whisk ferns, horsetails, and most conifers), and leaves differentiated into palisade and spongy mesophyll (of leptosporangiate ferns, Ginkgo, Gnetum, and angiosperms). Expression of three out of four regulators of leaf development in primordia of both leaves and sporangia—C3HDZ in spikemosses and whisk ferns, YABBY in clubmosses and KANADI in spikemosses and horsetails—indicates that a sporangium developmental program could have been co-opted as a “precursor program” for the origin of microphylls and euphylls. Additionally, expression of leaf development regulators in SAMs of spikemosses (ARP, C3HDZ, and KANADI), clubmosses (YABBY), leptosporangiate ferns (C3HDZ), and horsetails (C3HDZ and KANADI) indicates that at least some mechanisms of SAM regulation were co-opted as well in the pre-program of leaf precursors.</p

Image_4_All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants.JPEG

Recent advances in plant developmental genetics together with rapid accumulation of transcriptomic data on plants from divergent lineages provide an exciting opportunity to explore the evolution of plant morphology. To understand leaf origin in sporophytes of land plants, we have combined the available molecular and structural data on development of leaves with different morphologies in different plant lineages: clubmosses, spikemosses, leptosporangiate ferns, ophioglossioid ferns, marattioid ferns, whisk ferns, horsetails, and conifers. Specifically, we address the peculiarities of proximo-distal, ad/abaxial, and lateral development; presence/absence of mesophyll differentiation into palisade and spongy parenchyma; and type of leaf vascular bundles (collateral and bicollateral). Furthermore, taxon-specific and morphology-specific features of leaf development are considered in the context of the organization of shoot apical meristems (SAMs)—monoplex, simplex, or duplex—that produce leaf primordia. The data available imply that cellular patterns of leaf initiation correlate strongly with the structure of the SAMs but not with further leaf development or morphology. The later stages of leaf development are neither correlated with SAM structure nor with taxonomy. Occurrence and, if available, patterns of expression of homologs of the angiosperm genes responsible for the development of adaxial (ARP and C3HDZ) and abaxial (YABBY and KANADI) leaf domains, or establishment of the leaf marginal meristem (WOX) are discussed. We show that there is no correlation in the set of homologs of TFs that regulate abaxial and adaxial leaf domain development between leaves containing only spongy and no palisade mesophyll (of spikemosses, clubmosses, whisk ferns, horsetails, and most conifers), and leaves differentiated into palisade and spongy mesophyll (of leptosporangiate ferns, Ginkgo, Gnetum, and angiosperms). Expression of three out of four regulators of leaf development in primordia of both leaves and sporangia—C3HDZ in spikemosses and whisk ferns, YABBY in clubmosses and KANADI in spikemosses and horsetails—indicates that a sporangium developmental program could have been co-opted as a “precursor program” for the origin of microphylls and euphylls. Additionally, expression of leaf development regulators in SAMs of spikemosses (ARP, C3HDZ, and KANADI), clubmosses (YABBY), leptosporangiate ferns (C3HDZ), and horsetails (C3HDZ and KANADI) indicates that at least some mechanisms of SAM regulation were co-opted as well in the pre-program of leaf precursors.</p

Image_1_All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants.jpg

Recent advances in plant developmental genetics together with rapid accumulation of transcriptomic data on plants from divergent lineages provide an exciting opportunity to explore the evolution of plant morphology. To understand leaf origin in sporophytes of land plants, we have combined the available molecular and structural data on development of leaves with different morphologies in different plant lineages: clubmosses, spikemosses, leptosporangiate ferns, ophioglossioid ferns, marattioid ferns, whisk ferns, horsetails, and conifers. Specifically, we address the peculiarities of proximo-distal, ad/abaxial, and lateral development; presence/absence of mesophyll differentiation into palisade and spongy parenchyma; and type of leaf vascular bundles (collateral and bicollateral). Furthermore, taxon-specific and morphology-specific features of leaf development are considered in the context of the organization of shoot apical meristems (SAMs)—monoplex, simplex, or duplex—that produce leaf primordia. The data available imply that cellular patterns of leaf initiation correlate strongly with the structure of the SAMs but not with further leaf development or morphology. The later stages of leaf development are neither correlated with SAM structure nor with taxonomy. Occurrence and, if available, patterns of expression of homologs of the angiosperm genes responsible for the development of adaxial (ARP and C3HDZ) and abaxial (YABBY and KANADI) leaf domains, or establishment of the leaf marginal meristem (WOX) are discussed. We show that there is no correlation in the set of homologs of TFs that regulate abaxial and adaxial leaf domain development between leaves containing only spongy and no palisade mesophyll (of spikemosses, clubmosses, whisk ferns, horsetails, and most conifers), and leaves differentiated into palisade and spongy mesophyll (of leptosporangiate ferns, Ginkgo, Gnetum, and angiosperms). Expression of three out of four regulators of leaf development in primordia of both leaves and sporangia—C3HDZ in spikemosses and whisk ferns, YABBY in clubmosses and KANADI in spikemosses and horsetails—indicates that a sporangium developmental program could have been co-opted as a “precursor program” for the origin of microphylls and euphylls. Additionally, expression of leaf development regulators in SAMs of spikemosses (ARP, C3HDZ, and KANADI), clubmosses (YABBY), leptosporangiate ferns (C3HDZ), and horsetails (C3HDZ and KANADI) indicates that at least some mechanisms of SAM regulation were co-opted as well in the pre-program of leaf precursors.</p

Data_Sheet_2_All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants.fasta

Recent advances in plant developmental genetics together with rapid accumulation of transcriptomic data on plants from divergent lineages provide an exciting opportunity to explore the evolution of plant morphology. To understand leaf origin in sporophytes of land plants, we have combined the available molecular and structural data on development of leaves with different morphologies in different plant lineages: clubmosses, spikemosses, leptosporangiate ferns, ophioglossioid ferns, marattioid ferns, whisk ferns, horsetails, and conifers. Specifically, we address the peculiarities of proximo-distal, ad/abaxial, and lateral development; presence/absence of mesophyll differentiation into palisade and spongy parenchyma; and type of leaf vascular bundles (collateral and bicollateral). Furthermore, taxon-specific and morphology-specific features of leaf development are considered in the context of the organization of shoot apical meristems (SAMs)—monoplex, simplex, or duplex—that produce leaf primordia. The data available imply that cellular patterns of leaf initiation correlate strongly with the structure of the SAMs but not with further leaf development or morphology. The later stages of leaf development are neither correlated with SAM structure nor with taxonomy. Occurrence and, if available, patterns of expression of homologs of the angiosperm genes responsible for the development of adaxial (ARP and C3HDZ) and abaxial (YABBY and KANADI) leaf domains, or establishment of the leaf marginal meristem (WOX) are discussed. We show that there is no correlation in the set of homologs of TFs that regulate abaxial and adaxial leaf domain development between leaves containing only spongy and no palisade mesophyll (of spikemosses, clubmosses, whisk ferns, horsetails, and most conifers), and leaves differentiated into palisade and spongy mesophyll (of leptosporangiate ferns, Ginkgo, Gnetum, and angiosperms). Expression of three out of four regulators of leaf development in primordia of both leaves and sporangia—C3HDZ in spikemosses and whisk ferns, YABBY in clubmosses and KANADI in spikemosses and horsetails—indicates that a sporangium developmental program could have been co-opted as a “precursor program” for the origin of microphylls and euphylls. Additionally, expression of leaf development regulators in SAMs of spikemosses (ARP, C3HDZ, and KANADI), clubmosses (YABBY), leptosporangiate ferns (C3HDZ), and horsetails (C3HDZ and KANADI) indicates that at least some mechanisms of SAM regulation were co-opted as well in the pre-program of leaf precursors.</p

Data_Sheet_5_All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants.PDF

Recent advances in plant developmental genetics together with rapid accumulation of transcriptomic data on plants from divergent lineages provide an exciting opportunity to explore the evolution of plant morphology. To understand leaf origin in sporophytes of land plants, we have combined the available molecular and structural data on development of leaves with different morphologies in different plant lineages: clubmosses, spikemosses, leptosporangiate ferns, ophioglossioid ferns, marattioid ferns, whisk ferns, horsetails, and conifers. Specifically, we address the peculiarities of proximo-distal, ad/abaxial, and lateral development; presence/absence of mesophyll differentiation into palisade and spongy parenchyma; and type of leaf vascular bundles (collateral and bicollateral). Furthermore, taxon-specific and morphology-specific features of leaf development are considered in the context of the organization of shoot apical meristems (SAMs)—monoplex, simplex, or duplex—that produce leaf primordia. The data available imply that cellular patterns of leaf initiation correlate strongly with the structure of the SAMs but not with further leaf development or morphology. The later stages of leaf development are neither correlated with SAM structure nor with taxonomy. Occurrence and, if available, patterns of expression of homologs of the angiosperm genes responsible for the development of adaxial (ARP and C3HDZ) and abaxial (YABBY and KANADI) leaf domains, or establishment of the leaf marginal meristem (WOX) are discussed. We show that there is no correlation in the set of homologs of TFs that regulate abaxial and adaxial leaf domain development between leaves containing only spongy and no palisade mesophyll (of spikemosses, clubmosses, whisk ferns, horsetails, and most conifers), and leaves differentiated into palisade and spongy mesophyll (of leptosporangiate ferns, Ginkgo, Gnetum, and angiosperms). Expression of three out of four regulators of leaf development in primordia of both leaves and sporangia—C3HDZ in spikemosses and whisk ferns, YABBY in clubmosses and KANADI in spikemosses and horsetails—indicates that a sporangium developmental program could have been co-opted as a “precursor program” for the origin of microphylls and euphylls. Additionally, expression of leaf development regulators in SAMs of spikemosses (ARP, C3HDZ, and KANADI), clubmosses (YABBY), leptosporangiate ferns (C3HDZ), and horsetails (C3HDZ and KANADI) indicates that at least some mechanisms of SAM regulation were co-opted as well in the pre-program of leaf precursors.</p

Data_Sheet_4_All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants.FASTA

Recent advances in plant developmental genetics together with rapid accumulation of transcriptomic data on plants from divergent lineages provide an exciting opportunity to explore the evolution of plant morphology. To understand leaf origin in sporophytes of land plants, we have combined the available molecular and structural data on development of leaves with different morphologies in different plant lineages: clubmosses, spikemosses, leptosporangiate ferns, ophioglossioid ferns, marattioid ferns, whisk ferns, horsetails, and conifers. Specifically, we address the peculiarities of proximo-distal, ad/abaxial, and lateral development; presence/absence of mesophyll differentiation into palisade and spongy parenchyma; and type of leaf vascular bundles (collateral and bicollateral). Furthermore, taxon-specific and morphology-specific features of leaf development are considered in the context of the organization of shoot apical meristems (SAMs)—monoplex, simplex, or duplex—that produce leaf primordia. The data available imply that cellular patterns of leaf initiation correlate strongly with the structure of the SAMs but not with further leaf development or morphology. The later stages of leaf development are neither correlated with SAM structure nor with taxonomy. Occurrence and, if available, patterns of expression of homologs of the angiosperm genes responsible for the development of adaxial (ARP and C3HDZ) and abaxial (YABBY and KANADI) leaf domains, or establishment of the leaf marginal meristem (WOX) are discussed. We show that there is no correlation in the set of homologs of TFs that regulate abaxial and adaxial leaf domain development between leaves containing only spongy and no palisade mesophyll (of spikemosses, clubmosses, whisk ferns, horsetails, and most conifers), and leaves differentiated into palisade and spongy mesophyll (of leptosporangiate ferns, Ginkgo, Gnetum, and angiosperms). Expression of three out of four regulators of leaf development in primordia of both leaves and sporangia—C3HDZ in spikemosses and whisk ferns, YABBY in clubmosses and KANADI in spikemosses and horsetails—indicates that a sporangium developmental program could have been co-opted as a “precursor program” for the origin of microphylls and euphylls. Additionally, expression of leaf development regulators in SAMs of spikemosses (ARP, C3HDZ, and KANADI), clubmosses (YABBY), leptosporangiate ferns (C3HDZ), and horsetails (C3HDZ and KANADI) indicates that at least some mechanisms of SAM regulation were co-opted as well in the pre-program of leaf precursors.</p