Graham et al Appendix 2

Graham et al Appendix

Mitochondrial DNA similarity between pairs of species of Alismatales.

<p>Mitochondrial DNA similarity between pairs of species of Alismatales.</p

Characteristics of mitogenomes of four representatives of the Alismatales.

<p>Characteristics of mitogenomes of four representatives of the Alismatales.</p

Intron content (<i>cis-</i> and <i>trans</i>-spliced) in mitogenomes of the Alismatales.

<p>Intron content (<i>cis-</i> and <i>trans</i>-spliced) in mitogenomes of the Alismatales.</p

Maps of mitogenomes of <i>Zostera marina</i> and <i>Stratiotes aloides</i>.

<p>For <i>Zostera</i> upper genes are transcribed forward; lower genes are transcribed reverse. For <i>Stratiotes</i> inner genes are transcribed clockwise; outer genes are transcribed counter-clockwise. Genes are color coded as indicated in the lower left corner. The names of <i>trans</i>-spliced genes are followed by exon numbers. Only genes assumed to be functional are shown. The figure was created using OGDRAW [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177606#pone.0177606.ref038" target="_blank">38</a>].</p

Loss and pseudogenization of mitochondrial ribosomal protein genes in Alismatales.

<p>Bars represent events of loss or pseudogenization. Black bars mark unique events of gene loss from the mitogenome. Red (pseudogenization) and blue (loss) bars mark homoplasious gene changes.</p

Distribution of mitochondrial ribosomal protein genes in Alismatales mitogenomes.

<p>Blank boxes indicate absence of a gene from the mitogenome. Dark grey boxes indicate presence of a gene assumed to be functional. Light grey boxes and <b>Ψ</b> indicates a pseudogene or fragment of gene in the mitogenome. <b>N</b> indicates presence of a gene annotated as of mitochondrial origin in the nuclear genome of <i>Zostera marina</i>. (<b>n</b>) indicates likely presence of a gene in the nuclear genome of <i>Zostera marina</i>, though not annotated as of mitochondrial origin. *<i>Zostera noltii</i> has the same mitochondrial genes, but the potential nuclear location of genes is unknown.</p

Colinear gene clusters in four representatives of the Alismatales.

<p>Colinear gene clusters in four representatives of the Alismatales.</p

baits-120-60

The probe sequences to target phytochrome, phototropin and neochrome genes, with a special focus on those of hornworts and ferns

alignments_and_trees

This zip file contains the alignments and trees, as well as a ReadMe file