Additional file 2 of Chromosome constitution and genetic relationships of Morus spp. revealed by genomic in situ hybridization

Additional file 2: Supplementary Table 1. List of the mulberry accessions used in this study

ML phylogenetic tree for Methyltransf_2 domains in COMT proteins.

<p>The phylogenetic tree derived by the ML method with bootstrap analysis (1000 replicates) from alignment of amino acid sequences of Methyltransferase domains predicted in COMT proteins from <i>Arabidopsis</i>, <i>B</i>. <i>rapa</i>, <i>B</i>. <i>oleracea</i>, <i>B</i>. <i>napus</i>, and outgroup using MEGA 6.0 program.</p

Cloning and Phylogenetic Analysis of <i>Brassica napus</i> L. <i>Caffeic Acid O-Methyltransferase 1</i> Gene Family and Its Expression Pattern under Drought Stress

<div><p>For many plants, regulating lignin content and composition to improve lodging resistance is a crucial issue. Caffeic acid O-methyltransferase (COMT) is a lignin monomer-specific enzyme that controls S subunit synthesis in plant vascular cell walls. Here, we identified 12 <i>BnCOMT1</i> gene homologues, namely <i>BnCOMT1-1</i> to <i>BnCOMT1-12</i>. Ten of 12 genes were composed of four highly conserved exons and three weakly conserved introns. The length of intron I, in particular, showed enormous diversification. Intron I of homologous <i>BnCOMT1</i> genes showed high identity with counterpart genes in <i>Brassica rapa</i> and <i>Brassica oleracea</i>, and intron I from positional close genes in the same chromosome were relatively highly conserved. A phylogenetic analysis suggested that <i>COMT</i> genes experience considerable diversification and conservation in <i>Brassicaceae</i> species, and some <i>COMT1</i> genes are unique in the <i>Brassica</i> genus. Our expression studies indicated that <i>BnCOMT1</i> genes were differentially expressed in different tissues, with <i>BnCOMT1-4</i>, <i>BnCOMT1-5</i>, <i>BnCOMT1-8</i>, and <i>BnCOMT1-10</i> exhibiting stem specificity. These four <i>BnCOMT1</i> genes were expressed at all developmental periods (the bud, early flowering, late flowering and mature stages) and their expression level peaked in the early flowering stage in the stem. Drought stress augmented and accelerated lignin accumulation in high-lignin plants but delayed it in low-lignin plants. The expression levels of <i>BnCOMT1s</i> were generally reduced in water deficit condition. The desynchrony of the accumulation processes of total lignin and <i>BnCOMT1</i>s transcripts in most growth stages indicated that <i>BnCOMT1s</i> could be responsible for the synthesis of a specific subunit of lignin or that they participate in other pathways such as the melatonin biosynthesis pathway.</p></div

ML phylogenetic tree for intron I in Brassicaceae COMT1 genes.

<p>The phylogenetic tree derived by the ML method with bootstrap analysis (1000 replicates) from alignment of gene sequences of intron I from three <i>Brassicaceae</i> species using MEGA 6.0 program.</p

Tissue specific expression characteristics of <i>BnCOMT1s</i>.

<p>The tissue-specific expression levels of 10 of twelve <i>BnCOMT1</i> genes (except <i>BnCOMT1-1</i> and <i>BnCOMT1-7</i>) in eight different tissues (root, stem, leaf, bud, flower, 15D, 30D and 45D) were checked by real-time qRT-PCR.</p

Sequence identity of intron I for <i>BnCOMT1s</i>.

<p>Data on the upper right present the sequence identity regardless of the unmatched regions possibly emerged in either end of two aligned intron sequences, and data on the bottom left present the sequence identity of full-length intron sequences.</p

Protein sequence identity and similarity of BnCOMT1s.

<p>Data on the upper right present the sequence identity, and data on the bottom left present the sequence similarity.</p

Total lignin content and spatial expression characteristics of stem specific <i>BnCOMT1s</i> under drought stress.

<p>H1, H2 were high-lignin content materials and L1, L2 were low materials. The grey color represents the drought treatment and blue represents the natural condition. BS, ES, LS, and MS were respectively short for budding stage, early flowering stage, late flowering stage and mature stage.</p