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. 2015 Mar 17;16(1):204. doi: 10.1186/s12864-015-1418-3

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© Leliaert and Lopez-Bautista; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Alignments between the chloroplast genomes of Bryopsis plumosa , B. hypnoides , and Tydemania expeditiones . The Mauve algorithm [81] was used to align the cpDNAs between B. plumosa and B. hypnoides (A), and between B. plumosa and T. expeditiones (B). Corresponding colored boxes are locally collinear blocks (LCBs), which represent homologous regions of sequences that do not contain any major rearrangements. Inside each block a sequence identity similarity profile is shown. Inverted LCBs are presented as blocks below the center line. Annotations are shown above and below the LCBs: protein coding genes as white boxes, tRNA genes in green, rRNA genes in red and short repeats in pink. Lowered position of a box indicates inverted orientation. The asterisk indicates the large tRNA region in B. hypnoides.