The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae)

Abstract

The complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M.Lin & H.-Y.Liang (Halymeniaceae, Rhodophyta) is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis. The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in sequence and share significant synteny. In contrast, less synteny is shared between G. taiwanensis and the plastid genome representatives of Bangiophyceae and Cyanidiophyceae. Nevertheless, the gene content of all six red algal plastid genomes here studied is highly conserved, and a large core repertoire of plastid genes can be discerned in Rhodophyta.

Full text

The Plastid Genome of the Red Macroalga
Grateloupia
taiwanensis
(Halymeniaceae)
Michael S. DePriest
1
*, Debashish Bhattacharya
2
, Juan M. Lo
´
pez-Bautista
1
1 Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America, 2 Department of Ecology, Evolution, and Natural
Resources, Rutgers University, New Jersey, United States of America
Abstract
The complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M.Lin & H.-Y.Liang (Halymeniaceae,
Rhodophyta) is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA
sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis.
The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in
sequence and share significant synteny. In contrast, less synteny is shared between G. taiwanensis and the plastid genome
representatives of Bangiophyceae and Cyanidiophyceae. Nevertheless, the gene content of all six red algal plastid genomes
here studied is highly conserved, and a large core repertoire of plastid genes can be discerned in Rhodophyta.
Citation: DePriest MS, Bhattacharya D, Lo
´
pez-Bautista JM (2013) The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS
ONE 8(7): e68246. doi:10.1 371/journal.pone.0068246
Editor: Heroen Verbruggen, University of Melbourne, Australia
Received March 5, 2013; Accepted May 26, 2013; Published July 19, 2013
Copyright: ß 2013 DePriest et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The authors acknowledge support from NSF Red Algal Tree of Life (grant DEB 0937978), and from the College of Arts and Sciences and Research Office
of The University of Alabama. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have read the journal’s policy and have the following conflict: Co-author Dr. Debashish Bhattacharya is a PLOS ONE Editorial
Board member. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.
* E-mail: msdepriest@crimson.ua.edu
Introduction
The red algae (division Rhodophyta) comprise over 6,300
species [1] of mostly multicellular, marine, photosynthetic
organisms. Along with Viridiplantae (green algae and higher
plants) and Glaucophyta, Rhodophyta is one of the three lineages
of eukaryotes originating from primary endosymbiosis of an
ancient cyanobacterium, forming the supergroup Plantae sensu lato.
The monophyly of Plantae s.l. is well supported in several analyses
[2][3[4]. Subsequent secondary endosymbioses have occurred,
resulting in a great diversity of plastid-bearing eukaryotes
throughout the tree of life. The chlorarachniophytes and
euglenoids separately acquired green algal endosymbionts, where-
as the numerous ‘‘brown’’ lineages (including haptophytes,
cryptophytes, stramenopiles, and alveolates) acquired red algal
endosymbionts. It remains unclear, however, at which point (or
points) in evolutionary history the acquisition of those red algal
plastids took place, and several hypotheses have been suggested to
explain the pattern, which have been tested and supported to
varying degrees [5]. However, it is clear that additional data
collection and analysis are needed for both the hosts and
endosymbionts in this partnership, that is, for brown algal lineages
and the red algae from which their plastids originated.
Molecular phylogenetic analysis has divided the red algae into
seven classes [6][7]. This phylogeny is given in Figure 1. Almost all
red algal species – over 6,000– belong to the class Florideophy-
ceae, which is most closely related to the class Bangiophyceae
(,150 species [1]). These two classes have been grouped in the
subphylum Eurhodophytina. The most anciently diverged of the
classes, the Cyanidiophyceae, consists of very few species divided
into three genera of extremophilic unicellular algae known to
inhabit acidic hot springs. Five red algal plastid genomes have
been published thus far, including representatives of these three
classes: Gracilaria tenuistipitata var. liui Zhang & Xia (Florideophy-
ceae); Porphyra purpurea (Roth) C.Agardh and Pyropia yezoensis (Ueda)
M.S.Hwang & H.G.Choi (Bangiophyceae); and Cyanidium caldarium
(Tilden) Geitler and Cyanidioschyzon merolae P.De Luca, R.Taddei &
L.Varano strain 10D (Cyanidiophyceae). Because almost all
known red algal diversity is found in the Florideophyceae, the
plastid genome sequence of a single species (G. tenuistipitata var. liui)
is clearly insufficient information to understand the whole
spectrum of characteristics that are shared by florideophycean
plastids. A thorough understanding of present-day red algal
plastids, with sufficient coverage across the red algal tree of life,
can help demonstrate the characteristics of ancestral red algae and
their plastids, which would have been the source of the secondary
endosymbiotic plastids of the brown algal lineages.
The florideophycean genus Grateloupia C. Agardh contains
around 90 species [1] of benthic macroalgae that are distributed in
warm temperate to tropical waters worldwide. Some species of
Grateloupia are known invasive species. Grateloupia taiwanensis S.-
M.Lin & H.-Y. Liang was first described in 2008 by Lin et al. [8]
but it has since been recorded in the Gulf of Mexico [9].The genus
is currently being split into several genera based on combined
molecular and morphological analysis [10], and it is possible that
G. taiwanensis will be placed into a new genus.
Grateloupia belongs to the order Halymeniales, whereas Gracilaria
tenuistipitata var. liui is in the order Gracilariales. Both orders are
classified in the subclass Rhodymeniophycidae, but their phylo-
genetic relationships within the subclass are unresolved, due to
consistent ambiguity in the phylogenetic position of Gracilariales
[11][12][13]. Comparisons between the plastid genomes of
Gracilaria tenuistipitata and Grateloupia taiwanensis will establish a
PLOS ONE | www.plosone.org 1 July 2013 | Volume 8 | Issue 7 | e68246

Figure 1. Phylogeny of Rhodophyta, adapted from Yoon
et al.
[6]. Numbers of species are from AlgaeBase [1].
doi:10.1371/journal.pone.0068246.g001
Figure 2. The
Grateloupia taiwanensis
plastid genome. Colors indicate different gene classifications, as listed in Table 2.
doi:10.1371/journal.pone.0068246.g002
Grateloupia taiwanensis Plastid Genome
PLOS ONE | www.plosone.org 2 July 2013 | Volume 8 | Issue 7 | e68246

basis for contrasting the common characteristics of the plastid in
Florideophyceae with those of the other classes, as well as
comparing the plastids of Rhodymeniophycidae with the other
subclasses of Florideophyceae, which have yet to be published.
Materials and Methods
An individual of Grateloupia taiwanensis from Orange Beach, AL,
USA, which was collected in a previous study [9] was selected for
genome sequencing. DNA was extracted from the field-collected
sample using the QIAGEN DNEasy Plant Mini Kit (QIAGEN,
Valencia, CA, USA) following the manufacturer’s instructions.
The sequencing library was prepared using the Nextera DNA
Sample Prep Kit (Illumina, San Diego, CA, USA) per the
manufacturer’s protocol and sequenced on one-half lane of an
Illumina Genome Analyzer IIX using the TruSeq SBS Kit v5
(Illumina) in a 1506150 bp paired-end run. The data were
adapter- and quality-trimmed (error threshold = 0.05, n ambigu-
ities = 2) using CLC Genomics Workbench (CLC Bio, Aarhus,
Denmark) prior to de-novo assembly with same (automatic bubble
size, minimum contig length = 100 bp). The raw reads were then
mapped to the assembly contigs (similarity = 90%, length fraction
= 75%), and regions with no evidence of short-read data were
removed. The resulting assembly included one large contig
191,270 bp in size, which was determined to be the plastid
genome by several criteria: (1) BLAST searches [14] of commonly
known plastid genes against the entire assembly produced hits on
this contig with significant e-values (e#10
220
); (2) a genome size of
191,270 bp is congruent with the sizes of other red algal plastid
genomes, which range from 150 to 191 kbp [15]; (3) because each
cell contains many plastids and therefore many copies of the
plastid genome, it follows that cpDNA will be relatively over-
represented in the short sequence reads.
The G. taiwanensis plastid genome was imported to Geneious
(Geneious version 5.1.7; available from http://www.geneious.
com/) and set to circular topology. Using the Geneious ORF
Finder and the standard genetic code, the start codons ATG and
GTG, and a minimum length of 90 bp, the genome contained 768
ORFs. Preliminary annotation was performed using DOGMA
[16] with an e-value cutoff of 10
220
for BLAST hits. After
alignments for each gene, these were checked manually and the
corresponding ORF in the genome sequence was annotated. The
remaining ORFs were translated using the standard genetic code
and submitted to phmmer (http://hmmer.janelia.org/), searching
against the UniProtKB database (http://www.uniprot.org). After
including the additional start codon TTG, any ORFs occurring
outside any annotation were searched for functional domains using
the InterProScan Geneious plugin version 1.0.5 [17]. Annotations
for those ORFs with putative functional domains were included in
the genome.
To determine tRNA sequences, the plastid genome was
submitted to the tRNAscan-SE version 1.2.1 server [18][19].
The genome was searched with default settings using the ‘‘Mito/
Chloroplast’’ model. To determine rRNA sequences, a set of
known plastid rRNA sequences was extracted from the Gracilaria
tenuistipitata var. liui genome and used as a query sequence to
search the G. taiwanensis genome using BLAST. A search for
tmRNA sequences was performed using BRUCE v1.0 [20]. The
genome was visualized using GenomeVx [21] and edited using
Adobe Illustrator CS2 (http://www.adobe.com/products/
illustrator.html).
The five published red algal plastid genomes, with annotations,
were downloaded from GenBank. Gene names were checked with
the preferred name in UniProtKB and revised in order to make
the most accurate comparisons between genomes. In situations
where one gene had multiple names, if all were orthologous
Table 1. Characteristics of red algal plastid genomes analyzed in this study.
Florideophyceae Bangiophyceae Cyanidiophyceae
Grateloupia
taiwanensis
Gracilaria tenuistipitata
var.
liui
Porphyra
purpurea
Pyropia
yezoensis
Cyanidioschyzon
merolae
strain 10D
Cyanidium caldarium
General characteristics
Size (bp) 191,270 183,883 191,028 191,952 149,987 164,921
G+C (%) 30.6 29.2 33.0 33.1 37.6 32.7
Intergenic space (%) 18.1 15.5 15.3 15.9 9.3 10.5
Protein-coding genes
Number of protein-coding genes 234 204 207 207 193 199
Unique gene annotations 35 13 0 0 4 15
Number of ribosomal proteins 47 47 47 46 46 45
Start codon usage (%)
ATG 87.6 89.7 91.8 92.3 97.9 98.5
GTG 6.0 2.0 5.8 5.3 2.1 1.0
TTG 6.4 7.8 2.4 1.4 – 0.5
others – 0.5 – 1.0 – –
RNAs
Number of tRNAs 29 29 37 38 31 30
Number of rRNA operons 1 1 2 2 1 1
GenBank accession KC894740 AY673996 PPU38804 AP006715 AB002583 AF022186
Intergenic space is defined as any portion of the genome that does not bear a gene or RNA annotation.
doi:10.1371/journal.pone.0068246.t001
Grateloupia taiwanensis Plastid Genome
PLOS ONE | www.plosone.org 3 July 2013 | Volume 8 | Issue 7 | e68246

according to BLAST (e #10
210
) against UniProtKB, the name
used by the majority of species was used. Names of known and
putative protein-coding genes (i.e., excluding tRNAs or rRNAs)
were extracted from the genomes, and the sets were compared
using VENNTURE [22]. Genes found to be missing from a
certain species or group of species were checked using BLAST in
order to ensure that this gene is not present. For structure and
arrangement comparisons, the genomes were aligned using the
Table 2. List of genes in the Grateloupia taiwanensis plastid genome (233 total).
Classification Number Genes
Genetic systems
Maintenance 2 dnaB
rne
RNA polymerase 5 rpoA rpoB rpoC1 rpoC2 rpoZ
Transcription factors 4 ntcA ompR
rbcR ycf29
Translation 4 infB infC tsf tufA
Ribosomal proteins
Large subunit 28 rpl1 rpl2 rpl3 rpl4 rpl5 rpl6
rpl9 rpl11
rpl12 rpl13 rpl14 rpl16 rpl18 rpl19 rpl20 rpl21
rpl22 rpl23 rpl24 rpl27 rpl28 rpl29 rpl31 rpl32
rpl33 rpl34 rpl35 rpl36
Small subunit 19 rps1 rps2 rps3 rps4 rps5 rps6 rps7 rps8
rps9 rps10 rps11 rps12 rps13 rps14 rps16 rps17
rps18 rps19 rps20
tRNA processing 1
tilS
Protein quality control 4 clpC dnaK ftsH groEL
Photosystems
Phycobilisomes 12 apcA apcB apcD apcE apcF cpcA cpcB cpcG
cpcS
cpeA cpeB nblA
Photosystem I 13 psaA psaB psaC psaD psaE psaF psaI psaJ
psaK psaL psaM ycf3 ycf4
Photosystem II 19 psbA psbB psbC psbD psbE psbF psbH psbI
psbJ psbK psbL psbN psbT psbV psbX psbY
psbZ psb28 ycf12
Cytochrome complex 11
ccs1 ccsA petA petB petD petF petG petJ
petL petM petN
Redox system 7 acsF bas1 dsbD
ftrB grx pbsA trxA acsF
ATP synthesis
ATP synthase 8 atpA atpB atpD atpE atpF atpG atpH atpI
Metabolism
Carbohydrates 6 cfxQ odpA odpB
pgmA rbcL rbcS cfxQ odpA
Lipids 5 accA accB accD acp P
fabH accA accB accD
Nucleotides 2 carA
upp
Amino acids 8 argB gltB lab ilvH
syfB syh trpA trpG
Cofactors 4 chlI moeB preA thiG chlI moeB preA thiG
Transport
Transport 9 cemA secA secG secY ycf16 ycf24 ycf38 ycf43
ycf63
Unknown
Conserved ORFs 28 ORF58 ORF65 ORF83 ORF621 ycf17 ycf19 ycf20
ycf21
ycf22 ycf26 ycf33
ycf34 ycf35 ycf36 ycf37 ycf39
ycf40 ycf45
ycf46 ycf52 ycf53 ycf54 ycf55 ycf56
ycf60 ycf65 ycf80
ycf92
Unique ORFs 34 Gtai_orf01, Gtai_orf02, …, Gtai_orf34
Genes in bold are shared among all red algal plastids (140 total). Genes underlined are shared among Eurhodophytina (21 total). Genes italicized are shared among
Florideophyceae (5 total). Categories for classification follow Ohta et al. [30].
doi:10.1371/journal.pone.0068246.t002
Grateloupia taiwanensis Plastid Genome
PLOS ONE | www.plosone.org 4 July 2013 | Volume 8 | Issue 7 | e68246

Mauve Genome Alignment version 2.2.0 [23] Geneious plugin
using the progressiveMauve algorithm [24] and default settings.
To aid in visualization, we designated the beginning of the rbcL
marker as position 1 in each genome.
Results
The Grateloupia taiwanensis plastid genome
The 191,270 bp plastid genome (Figure 2) includes 233 ORFs
identified as protein-coding genes, of which 35 are found only in
G. taiwanensis and not in the other red algae examined in this study.
Additionally, it contains 29 tRNA sequences, 3 rRNA sequences,
and 1 tmRNA sequence (Table 1). The rRNA operon is not
repeated. The tmRNA sequence appears to be homologous to the
ssrA tmRNA of Gracilaria tenuistipitata var. liui. The GC-content of
the G. taiwanensis plastid genome is 30 1). The proportion of
intergenic space in G. taiwanensis was 18.1%, which is comparable
to the other Eurhodophytina and higher than the Cyanidiophy-
ceae (Table 1). The sequence was deposited in GenBank (accession
number KC894740).
Gene content
All of the plastid genomes considered in this study share a set of
140 protein-coding genes, and an additional 21 genes are shared
Figure 3. Mauve genome alignments of linearized plastid
genomes, with
G. taiwanensis
set as reference. Corresponding
colored boxes indicate locally collinear blocks (LCBs), which represent
homologous gene clusters. LCBs below the horizontal line in the second
genome indicate reversals. Heights of vertical bars within LCBs indicate
relative sequence conservation at that position. A: G. taiwanensis and
Gracilaria tenuistipitata;B:G. taiwanensis and Porphyra purpurea;C:G.
taiwanensis and Pyropia yezoensis;D:G. taiwanensis and Cyanidioschy-
zon merolae;E:G. taiwanensis and Cyanidium caldarium.
doi:10.1371/journal.pone.0068246.g003
Table 3. tRNA sequences present in red algal plastid genomes.
trnA (GGC)
trnA (TGC)
trnC (GCA)
trnD (GTC)
trnE (TTC)
trnF (GAA)
trnG (GCC)
trnG (TCC)
trnH (GTG)
trnI(GAT)
trnK (TTT)
trnL(CAA)
trnL(GAG)
trnL(TAA)
trnL(TAG)
trnM(CAT)
trnN(GTT)
trnP(TGG)
trnQ(TTG)
trnR(ACG)
trnR(CCG)
trnR(CCT)
trnR(TCT)
trnS(CGA)
trnS(GCT)
trnS(GGA)
trnS(TGA)
trnT(GGT)
trnT(TGT)
trnV(GAC)
trnV(TAC)
trnW(CCA)
trnY(GTA)
Cyanidiumcaldarium 11111111111111311111 1 1 111111 1
Cyanidioschyzonmerolae 1111111111111131111 1 11111111 1
Porphyrapurpurea 12111111121111131111111111111111 1
Pyropiayezoensis 12111111121111231111111111111111 1
Gracilariatenuistipitatavar. liui 11111111111 11211111 1 1 111111 1
Grateloupiataiwanensis 11111111111 11211111 1 1 111111 1
Anticodon sequence is given in 39–59 direction.
doi:10.1371/journal.pone.0068246.t003
Grateloupia taiwanensis Plastid Genome
PLOS ONE | www.plosone.org 5 July 2013 | Volume 8 | Issue 7 | e68246

among the Eurhodophytina (Table 2). Five additional genes are
shared only between G. taiwanensis and G. tenuistipitata var. liui.In
total, 167 of the protein-coding genes found in the plastid of G.
taiwanensis are shared with G.tenuistipitata var. liui. Of the 35
putative genes found only in G. taiwanensis, one is a gene for
glutaredoxin (grx). This grx gene is 104 aa in length and is most
similar to that of the cyanobacterium Arthrospira platensis (UniProt
blastx, match length 107 aa, 78.0% positives, e = 8.0610
238
). The
remaining 34 genes are unique ORFs with functional domains
indicated by InterProScan (see Table S1 for annotations). G.
taiwanensis and G. tenuistipitata var. liui share the same 29 plastid
tRNA genes (Table 3). Porphyra purpurea and Pyropia yezoensis contain
more tRNA genes than the others, with 37 and 38, respectively;
two tRNA genes – trnI(GAT) and trnA(TGC) – occur inside the
repeated rRNA operon. In terms of tRNA gene content, the
Florideophyceae and Cyanidiophyceae are more similar to each
other than to the Bangiophyceae.
Plastid genome rearrangements
Pairwise Mauve genome alignments for G. taiwanensis along with
each other five plastid genomes used in this study are given in
Figure 3. We calculated the double-cut-and-join (DCJ) genome
distance, indicative of the number of rearrangements that have
taken place between two genomes. The alignment of G. taiwanensis
and Gracilaria tenuistipitata var. liui shows a DCJ distance of 3; G.
taiwanensis and Porphyra purpurea,4;G. taiwanensis and Pyropia
yezoensis,8;G. taiwanensis and Cyanidioschyzon merolae, 20; G.
taiwanensis and Cyanidium caldarium, 21.
Discussion
The plastid genome of G. taiwanensis is similar to that of G.
tenuistipitata var. liui in terms of size, GC%, gene content, and
overall structure. However, there are several notable differences;
G. taiwanensis contains 67 putative protein-coding genes not present
in G. tenuistipitata var. liui, including 32 previously named genes and
34 novel ORFs. When additional plastid genome sequences for
Florideophyceae become available, it is possible that many of these
novel ORFs will be found in other red algae.
The results of the current study are generally consistent with the
phylogeny of Rhodophyta proposed by Yoon et al. [7]. Unlike in
Porphyra purpurea and Porphyra yezoensis, in which the rRNA operon
is repeated directly, G. taiwanensis has only one rRNA operon. This
is consistent with the hypothesis of Hagopian et al. [25] that the
repeated rRNA operon was lost separately in the Cyanidiophyceae
and the Florideophyceae. A similar pattern arose in the tRNA
genes in Cyanidiophyceae and Florideophyceae. The reason for
this is unclear, but because it is commonly accepted that the
Cyanidiophyceae is the sister group to the rest of the red algae, we
suggest that this is an example of convergent gene loss.
As expected, our analyses show that pairs of plastid genomes of
red algae found in the same taxonomic class demonstrate the most
structural and functional similarity (Cyanidioschyzon/Cyanidium,
Porphyra/Pyropia, and Grateloupia/Gracilaria), which decreases with-
the degree of relatedness. The presence of 140 ‘‘core’’ plastid genes
reflects high conservation in the plastids of red algae, compared to
green algal plastids, which show much more variability in genome
size, GC%, and other attributes [26]. Despite their similar sizes,
red algal plastid genomes contain many more genes than green
algal genomes, and the genes are packed tightly together with
much less intergenic sequence. Thus far, G. taiwanensis shows the
most intergenic sequence of any red algal plastid (18.1%), but this
value is relatively low compared to those of green algal plastids.
As more and more genomes are annotated and published,
comparative genomics of primary and secondary plastids will
provide new insights into the pattern and process of endosymbi-
osis, especially in those lineages with red-derived plastids. The
genes shared among all red algal plastids are likely to be essential
for plastid function in Rhodophyta and offer a useful starting point
for future annotation of plastid genomes. Several previous studies
focused on red-derived plastids [27][28][29] have shown the
potential of plastid genome research in answering unresolved
questions in the history of these lineages. For these reasons, red
algal plastid genomes remain a highly interesting subject for
research. Forthcoming sequence data will advance our under-
standing of the evolution of the red algal plastid.
Supporting Information
Table S1 Novel ORFs found in the G. taiwanensis
plastid genome.
(DOCX)
Acknowledgments
The authors would like express gratitude to Dana C. Price (Rutgers
University) for technical assistance.
Author Contributions
Conceived and designed the experiments: MSD JLB. Performed the
experiments: MSD. Analyzed the data: MSD. Contributed reagents/
materials/analysis tools: MSD DB JLB. Wrote the paper: MSD.
References
1. Guiry MD, Guiry GM (2013) AlgaeBase. World-wide electronic publication,
National University of Ireland, Galway. Available: http://www.algaebase.org.
2. Rodrı
´
guez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, et al.
(2005) Monophyly of primary photosynthetic eukaryotes: green plants, red algae,
and glaucophytes. Curr Biol 15: 1325–1330.
3. Reyes-Prieto A, Bhattacharya D (2007) Phylogeny of Calvin cycle enzymes
supports Plantae monophyly. Mol Phylogenet Evol 45: 384–391.
4. Price DC, Chan CX, Yoon HS, Yang EC, Qui H, et al. (2012) Cyanophora
paradoxa genome elucidates origin of photosynthesis in algae and plants. Science
335: 843–847.
5. Gross J, Bhattacharya D, Pelletreau KN, Rumpho ME, Reyes-Prieto A (2012)
Secondary and tertiary endosymbiosis and kleptoplasty. In Genomics of
Chloroplasts and Mitochondria, Advances in Photosynthesis and Respiration
vol. 35, R. Bock and V. Knoop, eds. Springer.
6. Yoon HS, Zuccarello GC, Bhattacharya D (2010) Evolutionary history and
taxonomy of red algae. In Red Algae in the Genomic Age, Cellular Origin, Life
in Extreme Habitats and Astrobiology vol. 13, J. Seckbach and D.J. Chapman,
eds. Springer.
7. Yoon HS, Mu¨ ller KM, Sheath RG, Ott FD, Bhattacharya D (2006) Defining the
major lineages of red algae (Rhodophyta). J Phycol 42: 482–492.
8. Lin SM, Liang HY, Hommersand M (2008) Two types of auxiliary cell ampullae
in Grateloupia (Halymeniaceae, Rhodophyta), including G. taiwanensis sp. nov. and
G. orientalis sp. nov. from Taiwan based on rbcL gene sequence analysis and
cystocarp development. J Phycol 44: 196–214.
9. DePriest MS, Lo´pez-Bautista JM (2012) Sequencing of the rbcL marker reveals
the non-native red alga Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) in
Alabama. Gulf of Mexico Science 2012 (1–2): 7–13.
10. Gargiulo GM, Morabito M, Manghisi A (2013) A re-assessment of reproductive
anatomy and postfertilization development in the systematics of Grateloupia
(Halymeniales, Rhodophyta). Cryptogamie Algol 34(1): 3–35.
11. Harper JT, Saunders GW (2001) Molecular systematics of the Florideophyceae
(Rhodophyta) using nuclear large and small subunit rDNA sequence data.
J Phycol 37: 1073–1082.
12. Withall RD, Saunders GW (2006) Combining small and large subunit ribosomal
DNA genes to resolve relationships among orders of the Rhodymeniophycidae
(Rhodophyta): recognition of the Acrosymphytales ord. nov. and Sebdeniales
ord. nov. Eur J Phycol 41(4): 379–384.
13. Le Gall L, Saunders GW (2007) A nuclear phylogeny of the Florideophyceae
(Rhodophyta) inferred from combined EF2, small subunit and large subunit
Grateloupia taiwanensis Plastid Genome
PLOS ONE | www.plosone.org 6 July 2013 | Volume 8 | Issue 7 | e68246

ribosomal DNA: establishing the new red algal subclass Corallinophycidae. Mol
Phylogenet Evol 43: 1118–1130.
14. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped
BLAST and PSI-BLAST: a new generation of protein database search
programs. Nuc Acids Res 25: 3389–3402.
15. Lo´pez-Bautista JM (2010) Red algal genomics: a synopsis. In Red Algae in the
Genomic Age, Cellular Origin, Life in Extreme Habitats and Astrobiology vol.
13, J. Seckbach and D.J. Chapman, eds. Springer.
16. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar
genomes with DOGMA. Bioinformatics 20(17): 3252–3255.
17. Zdobnov EM, Apweiler R (2001) InterProScan – an integration platform for the
signature-recognition methods in InterPro. Bioinformatics 17(9): 847–848.
18. Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and
snoGPS web servers for the detection of tRNAs and snoRNAs. Nuc Acids Res
33: W686–W689.
19. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of
transfer RNA genes in genomic sequence. Nuc Acids Res 25: 955–964.
20. Laslett D, Canback B, Andersson S (2002) BRUCE: a program for the detection
of transfer-messenger RNA genes in nucleotide sequences. Nuc Acids Res 30:
3449–3453.
21. Conant GC, Wolfe KH (2007) GenomeVx: simple web-based creation of
editable circular chromosome maps. Bioinformatics 24: 861–862.
22. Martin B, Chadwick W, Yi T, Park SS, Lu D, et al. (2012) VENNTURE – a
novel Venn diagram investigational tool for multiple pharmacological dataset
analysis. PLOS ONE 7(5): e36911.
23. Darling AE, Mau B, Blatter FR, Perna NT (2004) Mauve: multiple alignment of
conserved genomic sequence with rearrangements. Genome Res 14: 1394–1403.
24. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome
alignment with gene gain, loss, and rearrangement. PLOS ONE 5(6): e11147.
25. Hagopian J, Reis M, Kitakima J, Bhattacharya D, de Oliveira MC (2004)
Comparative analysis of the complete chloroplast genome of the red alga
Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts
and their relationship to other chloroplasts. J Mol Evol 59: 464–477.
26. Lang BF, Nedelcu AM (2012) Plastid genomes of algae. In Genomics of
Chloroplasts and Mitochondria, Advances in Photosynthesis and Respiration
vol. 35, R. Bock and V. Knoop, eds. Springer.
27. Petersen J, Teich R, Brinkmann H, Cerff R (2006) A ‘‘green’’ phosphoribu-
lokinase in complex algae with red plastids: evidence for a single secondary
endosymbiosis leading to haptophytes, cryptophytes, heterokonts, and dinofla-
gellates. J Mol Evol 62: 143–157.
28. Cattolico RA, Jacobs MA, Zhou Y, Chang J, Duplessis M, et al. (2008)
Chloroplast genome sequencing of Heterosigma akashiwo CCMP452 (West
Atlantic) and NIES293 (West Pacific) strains. BMC Genomics 9: 211.
29. Le Courgille´ G, Pearson G, Valente M, Viegas C, Gschloessl B, et al. (2009).
Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus:
further insights on the evolution of red-algal derived plastids. BMC Evol Biol 9:
253.
30. Ohta N, Matsuzaki M, Misumi O, Miyagishima S, Nozaki H, et al. (2003)
Complete sequence and analysis of the plastid genome of the unicellular red alga
Cyanidioschyzon merolae. DNA Res 10: 67–77.
Grateloupia taiwanensis Plastid Genome
PLOS ONE | www.plosone.org 7 July 2013 | Volume 8 | Issue 7 | e68246