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The Mitochondrial Genome of Grateloupia taiwanensis
(Halymeniaceae, Rhodophyta) and Comparative
Mitochondrial Genomics of Red Algae
MICHAEL S. DEPRIEST
1,
*, DEBASHISH BHATTACHARYA
2
, AND
JUAN M. LO
´PEZ-BAUTISTA
1
1
The University of Alabama, Department of Biological Sciences, Box 870344, Tuscaloosa,
Alabama 35487; and
2
Rutgers University, Department of Ecology, Evolution and Natural Resources,
14 College Farm Road, New Brunswick, New Jersey 08901
Abstract. Although red algae are economically highly
valuable for their gelatinous cell wall compounds as well as
being integral parts of marine benthic habitats, very little
genome data are currently available. We present mitochon-
drial genome sequence data from the red alga Grateloupia
taiwanensis S.-M. Lin & H.-Y. Liang. Comprising 28,906
nucleotide positions, the mitochondrial genome contig con-
tains 25 protein-coding genes and 24 transfer RNA genes. It
is highly similar to other red algal genomes in gene content
as well as overall structure. An intron in the cox1 gene was
found to be shared by G. taiwanensis and Grateloupia
angusta (Okamura) S. Kawaguchi & H. W. Wang. We also
used whole-genome alignments to compare G. taiwanensis
to different groups of red algae, and these results are con-
sistent with the currently accepted phylogeny of Rhodo-
phyta.
Introduction
Red algae (division Rhodophyta) are a monophyletic
group of mostly multicellular photosynthetic eukaryotes.
They occur primarily in tropical to temperate marine habi-
tats, though freshwater and extremophilic species are
known. Currently around 7000 species of red algae have
been named, and the total number of red algal species on
Earth has been estimated at around 14,000 (Guiry, 2012).
Economically, red algae are the source for agar and carra-
geenan, industrially valuable hydrocolloids (Bixler and
Porse, 2011); ecologically, red algae serve as primary pro-
ducers as well as providing microhabitats and substrates for
other organisms.
On the tree of life, the red algae occupy a distinctive
position, serving as a link between primary and secondary
endosymbiosis. They bear plastids of primary endosymbi-
otic origin, having arisen after an ancient phagotrophic
eukaryote engulfed a cyanobacterium. Consequently they
are grouped with Viridiplantae (green algae and land plants)
and Glaucophyta (glaucophytes, a small unicellular group)
in the supergroup Plantae, all of which are characterized by
primary plastids. In addition, they are the source of the
secondary plastids found in the numerous “brown” algal
lineages, such as heterokonts, cryptophytes, and dinoflagel-
lates, although it is unclear exactly how the secondary
plastid of red algal origin was inherited among these groups
(Keeling, 2013). Red algae are a link between these primary
and secondary endosymbiotic lineages, which has allowed
for many gene transfer events between these groups (Qiu et
al., 2013). Thus, genomic methods have been used to test
various hypotheses regarding the inheritance of the “red”
secondary plastid (e.g., Baurain et al., 2010; Burki et al.,
2012), necessitating a large amount of sequence data for red
algae as well as for other groups.
Red algal genomic research is progressing rapidly with
increasing computational capacity and falling sequencing
costs. The first fully sequenced red algal genome, Cyanidio-
schyzon merolae P. De Luca, R. Taddei, & L. Varano
(Matsuzaki et al., 2004), was shown to be highly compact,
with unusually low numbers of introns, transfer RNA genes,
and ribosomal RNA genes compared to other eukaryotes.
Received 14 June 2014; accepted 28 August 2014.
* To whom correspondence should be addressed. E-mail: msdepriest@
crimson.ua.edu
Abbreviations: bp, base pair; DCJ, double-cut-and-join; LCB, locally
collinear block; ORF, open reading frame.
Reference: Biol. Bull. 227: 191–200. (October 2014)
© 2014 Marine Biological Laboratory
191
These findings reflect the specialized ecological niche of C.
merolae, a unicellular extremophile found in very hot and
acidic environments. Compact genomes were also found in
Porphyridium purpureum (Bory de Saint-Vincent) K. M.
Drew & R. Ross (Bhattacharya et al., 2013), Pyropia
yezoensis (Ueda) M. S. Hwang & H. G. Choi (Nakamura et
al., 2013), and Chondrus crispus Stackhouse (Colle´n et al.,
2013), suggesting that the common ancestor of red algae
lived in an extreme environment, which led to a reduction of
the genome that was subsequently inherited by its non-
extremophilic descendants.
In addition, many red algal organellar genomes have been
published in recent years. These genomes are functional
remnants of the original bacterial endosymbionts, retaining
only a few genes related to cellular respiration or photosyn-
thesis in a single circular chromosome. Genes that were not
retained were either transferred to the nucleus via endosym-
biotic gene transfer or simply lost (Timmis et al., 2004). The
remaining mitochondrial and plastid genes are useful for
studying organellar function as well as for phylogenetic
analysis. Since next-generation sequencing technologies
have become more accessible, many red algal genomics
researchers have used these techniques to generate sequence
data for organellar genomes (e.g., Hwang et al., 2013;
Campbell et al., 2014; S. Y. Kim et al., 2014). However,
relative to the total number of red algae, few mitochondrial
and plastid genomes have been sequenced, with many large
taxonomic groups unrepresented.
At present, the phylogeny of Rhodophyta is unresolved at
deep nodes. Molecular systematics studies of red algae,
using single or several phylogenetic markers, have not pro-
duced an unambiguous topology, and the branching pattern
is unclear at the class and ordinal levels, despite numerous
studies dealing with this issue (Freshwater et al., 1994;
Ragan et al., 1994; Oliveira and Bhattacharya, 2000; Saun-
ders and Hommersand, 2004; Yoon et al., 2006; Le Gall and
Saunders, 2007). The paucity of sequence data available for
red algae is a major limiting factor for resolving the phy-
logeny, both in taxon sampling and character (i.e., marker)
sampling. Next-generation sequencing technologies can
generate very large amounts of sequence data in a short
time, making them highly valuable in improving phylo-
genetic resolution for Rhodophyta.
The current study presents mitochondrial genome se-
quence data from Grateloupia taiwanensis S.-M. Lin &
H.-Y. Liang, a mesophilic, multicellular benthic red alga
that grows on rocks in the shallow subtidal zone and has a
disjunct distribution. It was first described in the Pacific (Lin
et al., 2008), but it was later identified as a non-native
species in the Gulf of Mexico, closely related to the aggres-
sive invasive species Grateloupia turuturu Yamada
(DePriest and Lo´pez-Bautista, 2012). More generally, the
genus Grateloupia is used as food and in pharmaceutical
research, making Grateloupia an interesting target for fu-
ture study. The plastid genome of G. taiwanensis was pub-
lished by DePriest et al. (2013), who demonstrated patterns
of gene retention and genome structure among red algal
plastids. Similar methods are used in the current study to
examine the mitochondrial genome of G. taiwanensis, syn-
thesizing data from a selection of the 17 mitochondrial
genomes previously available for red algae.
Materials and Methods
Sample collection and DNA extraction
The Grateloupia taiwanensis specimen used in this study
was collected in April 2011 from a jetty in Orange Beach,
Alabama (30°16⬘27.6⬙N 87°33⬘34.0⬙W). A large portion of the
thallus (approximately 60 cm
2
) was removed and preserved in
silica gel for DNA extraction, and the remainder was vouch-
ered on a herbarium sheet and deposited in The University of
Alabama Herbarium. DNA was extracted from the silica-
preserved sample using the QIAGEN DNEasy Plant mini kit
(QIAGEN, Valencia, CA). To maximize DNA yield, the large
Table 1
Characteristics of red algal mitochondrial genomes used in this study
Grateloupia
taiwanensis
Grateloupia
angusta
Chondrus
crispus
Gelidium
vagum
Gracilaria
salicornia
Rhodymenia
pseudopalmata
Sporolithon
durum
Pyropia
haitanensis
Cyanidioschyzon
merolae
Size (bp) 28,906 27,943 25,836 24,901 25,272 26,166 26,202 37,023 32,211
G⫹C (%) 31.4 30.2 28.9 30.4 28.4 29.5 28.4 30.7 27.2
Protein-coding
genes
26 26 26 23 25 24 24 23 34
tRNAs 24 19 23 18 20 21 19 24 25
GenBank
Accession
KM999231 KC875853 NC_001677 KC875754 KF824534 KC875752 KF186230 JQ736808 NC_000887
Reference This study S. Y. Kim
et al. (2014)
Leblanc et al.
(1995)
Yang et al.
(2014)
Campbell
et al. (2014)
K. M. Kim
et al. (2014)
K. M. Kim
et al. (2013)
Mao et al.
(2012)
Ohta et al.
(1998)
192 M. S. DEPRIEST ET AL.
sample was separated into eight pieces, and DNA was ex-
tracted from each piece individually. DNA samples were then
pooled for genome sequencing.
Whole-genome sequencing
Whole genomic DNA from G. taiwanensis was se-
quenced in the laboratory of Debashish Bhattacharya (Rut-
gers University, New Jersey). The procedure for whole-
genome sequencing of this sample was described in
DePriest et al. (2013): The sequencing library was prepared
using the Nextera DNA Sample Prep kit (Illumina, San
Diego, CA) 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 150 ⫻150-bp
paired-end run. The data were adapter- and quality-trimmed
(error threshold ⫽0.05, nambiguities ⫽2) using CLC
Genomics Workbench (CLC Bio, Aarhus, Denmark) prior
to de-novo assembly with the same software (automatic
bubble size, minimum contig length ⫽100 bp). The raw
reads were then mapped to the assembly contigs (similar-
ity ⫽90%, length fraction ⫽75%), and regions with no
evidence of short-read data were removed.
Identification of mitochondrial genome
The assembly contained about 62.7 Mbp separated into
130,269 contigs. The N50 statistic, defined as the sequence
length for which 50% of the total base pairs in the assembly
are contained in contigs at least as long, was 4703 bp.
Figure 1. The mitochondrial genome of Grateloupia taiwanensis, drawn by OGDRAW software (Bock
et al., 2007). The gap between trnS(GCT) and trnR(TCT) indicates the ends of the linear contig.
193GRATELOUPIA TAIWANENSIS MITOGENOME
Despite the somewhat poor assembly results, one contig of
length 28,906 was identified as the mitochondrial genome,
on the basis of several criteria. First, when the assembly was
queried for known red algal mitochondrial genes using
BLAST (Altschul et al., 1997), the resulting significant hits
(eⱕ10
⫺20
) were found in this contig. Second, the size of
the contig (28,906 bp) is similar to the lengths of other red
algal mitochondrial genomes (Table 1). Third, multicellular
red algae are known to have large numbers of mitochondria
per cell (Garbary and Pei, 2006) and, therefore, many copies
of the mitochondrial genome per cell, causing relative en-
richment of the mitochondrial genome in the extracted
DNA. Thus it is reasonable that the mitochondrial genome
resolved as a single contig after assembly.
Annotation of genes
The goal of annotation is to indicate the start and stop
positions of genes, including protein-coding genes, tRNAs,
and rRNAs, in the mitochondrial genome. These data will
be compared between taxa in the analysis. The mitochon-
drial genome contig was then isolated from the assembly,
imported to Geneious R7 (Geneious, 2014), and set to
represent a circular topology for visualization and genome
comparison purposes only. To detect open reading frames
(ORFs), the Geneious ORF Finder was used. For the genetic
code, the Mold/Protozoan Mitochondrial option was se-
lected; this codon translation scheme has been shown in red
algae of the classes Florideophyceae and Bangiophyceae
(Boyen et al., 1994; Leblanc et al., 1995; Burger et al.,
1999), but not Cyanidiophyceae (Ohta et al., 1998). Only
one codon is different between the Standard genetic code
and the Mold/Protozoan Mitochondrial code: in the Stan-
dard code, the codon UGA is a “stop” codon, but in the
Mold/Protozoan Mitochondrial code, UGA codes for the
amino acid tryptophan.
To determine which ORFs likely represented actual mito-
chondrial genes, the G. taiwanensis mitochondrial genome
was aligned with that of Grateloupia angusta (Okamura)
S. Kawaguchi & H. W. Wang (S. Y. Kim et al., 2014), using
the Mauve genome alignment ver. 2.3.1 (Darling et al.,
2004) plugin in Geneious with the progressiveMauve algo-
rithm (Darling et al., 2010) and default settings. Protein-
coding gene annotations in G. angusta that corresponded to
an ORF in G. taiwanensis were annotated on the G. taiwan-
ensis mitochondrial genome. These annotations were con-
firmed with a BLAST search against the UniProtKB se-
quence database (UniProt, 2014), with eⱕ10
⫺10
as the
cutoff for a positive identification.
To find tRNA sequences, the mitochondrial genome se-
quence was submitted to the tRNAscan-SE ver. 1.21 server
(Lowe and Eddy, 1997; Schattner et al., 2005). The tRNA
annotations were then annotated on the genome. To locate
ribosomal RNA sequences, rRNA sequences were extracted
Table 2
Comparison of named protein-coding genes in red algal mitochondria; presence indicated by a dot; absence by a dash
atp6 atp8 atp9
ccmA
(yejW)
ccmF
(yejR)
cob
(cytB) cox1 cox2 cox3 nad1 nad2 nad3 nad4 nad4l nad5 nad6 rpl16 rpl20 rps3 rps4 rps8 rps11 rps12 rps14
sdh2
(sdhB)
sdh3
(sdhC)
sdh4
(sdhD) secY yejU yejV ymf16 ymf39
Grateloupia
taiwanensis
●●● ––● ●●●●●●● ● ●●● ●●–– ●●–●●●●–– – ●
Grateloupia
angusta
●●● ––● ●●●●●●● ● ●●● ●●–– ●●–●●●●–– – ●
Chondrus crispus ●●● ––● ●●●●●●● ● ●●● ●●–– ●●–●●●––– ●●
Gelidium vagum ●●● ––● ●●●●●●● ● ●● ● –●–– ●●–●● ●●–– – ●
Gracilaria
salicornia
●●● ––● ●●●●●●● ● ●●● ●●–– ●●–●●●●–– – ●
Rhodymenia
pseudopalmata
●●● ––● ●●●●●●● ● ●●● –●–– ●●–●●●●–– – –
Sporolithon
durum
●●● ––● ●●●●●●● ● ●●● –●–– ●–●●●●–– – ●
Pyropia
haitanensis
●●● ––● ●●●●●●● ● ●●● –●–– ●●–●●●––– ●●
Cyanidioschyzon
merolae
●●● ● ● ● ●●●●●●● ● ●● ● ●●●●● ● ● ● ● ● –●● –●
194 M. S. DEPRIEST ET AL.
from the G. angusta mitochondrial genome and queried
against the G. taiwanensis genome using BLAST; after
finding the location of each gene, it was annotated.
Comparison with other mitochondrial genomes
Selected red algal mitochondrial genomes for comparison
of gene content were downloaded from NCBI GenBank
(https://www.ncbi.nlm.nih.gov/genbank/). Lists of gene an-
notations in Geneious were copied and compared manually.
Names of apparently unmatched genes were checked by
searching UniProt for the gene name and using the preferred
name only, in order to avoid using multiple names for each
species. Uncharacterized ORFs were not included.
Mauve genome alignment
Mauve genome alignments are useful because they show
conserved regions and rearrangements in the genome be-
tween taxa. For this analysis, several Mauve alignments
were performed using default settings, with several selected
combinations of red algae, based on their taxonomic rela-
tionships: (1) G. taiwanensis and G. angusta; (2) G. tai-
wanensis and various Rhodymeniophycidae—Chondrus
crispus,Gelidium vagum Okamura, Gracilaria salicornia
(C. Agardh) E. Y. Dawson, and Rhodymenia pseudopal-
mata (J. V. Lamouroux) P. C. Silva; (3) G. taiwanensis and
Sporolithon durum (Foslie) R. A. Townsend & Woelker-
ling, subclass Corallinophycidae;(4) G. taiwanensis and
Pyropia haitanensis (T. J. Chang & B. F. Zheng) N. Kikuchi
& M. Miyata,class Bangiophyceae; and (5) G. taiwanensis
and Cyanidioschyzon merolae, class Cyanidiophyceae. To
aid in visualization, the cox1 gene, a commonly used phylo-
genetic and barcoding marker, was designated as position 1
of each circular genome, as Mauve requires sequences to be
linearized. Images of Mauve alignments were exported
from Geneious in PNG format and edited for publication.
Results
General characteristics and gene content
The mitochondrial genome contig is 28,906-bp long and
has a GC content of 31.4%. It includes 25 protein-coding
genes, 24 tRNAs, and 2 rRNA subunits (Fig. 1). The Grate-
loupia taiwanensis mitochondrial genome is most similar to
that of G. angusta and Chondrus crispus in these aspects
(Table 1). Two introns were found in genes in the G.
taiwanensis genome: one in cox1 and one in trnI(GAT). A
set of 20 named protein-coding genes (that is, excluding
uncharacterized open reading frames [ORFs]) is shared
across all species in the analysis (Table 2). When consid-
ering only named genes, G. taiwanensis,G. angusta, and
Gracilaria salicornia are identical in gene content, contain-
ing the 20 “core” genes in addition to rpl20, rps11, secY,
and ymf39. With minor differences, species of the subphy-
lum Eurhodophytina (containing Florideophyceae and
Bangiophyceae) are mostly alike in mitochondrial gene
content. The mitochondrial genome of Cyanidioschyzon
merolae, however, contains 30 genes, including 6 that are
not present in any of the Eurhodophytina.
Genomic structure and rearrangements
The genomes of G. taiwanensis and G. angusta are highly
similar with no rearrangements (Fig. 2); full bars represent
higher similarity between the two genomes, and lower or
absence of bars represents lower or absent similiarity be-
tween the G. taiwanensis and G. angusta mitocondrial ge-
nomes. Sequence similarity is consistent throughout, but a
region of reduced similarity can be observed roughly be-
tween positions 1800 and 3000 in the alignment (all base
pair positions given in this section refer to positions in the
alignment, rather than positions in either genome). This
region corresponds to the intron found in the cox1 gene.
Figure 2. Mauve genome alignment of Grateloupia taiwanensis and Grateloupia angusta.
195GRATELOUPIA TAIWANENSIS MITOGENOME
From positions 21,108 to 21,859, G. taiwanensis was
found to have a region including three additional tRNA
genes—trnY(GTA), trnR(TCT), and trnS(GCT); this
region absent in G. angusta also includes the gap created
when the contig was circularized for representational
purposes.
When compared to other members of subclass Rhody-
meniophycidae (Fig. 3), G. taiwanensis again appears
highly similar. The group II intron shared by G. taiwanensis
and G. angusta in cox1 is now represented by a large gap,
as this intron is not present in Chondrus crispus, Gelidium
vagum, Gracilaria salicornia, or Rhodymenia pseudopal-
mata. The three tRNA genes found in G. taiwanensis but
missing from G. angusta are also missing from these four
Rhodymeniophycidae species. A small region from bases
24,454 to 24,491 in Gelidium vagum (18,420 to 18,454
reverse in Gracilaria salicornia) may be an alignment ar-
tifact and is unlikely to represent homology, as this region
Figure 3. Mauve genome alignment of Grateloupia taiwanensis and Rhodymeniophycidae species.
196 M. S. DEPRIEST ET AL.
occurs inside different genes between the two species. Ex-
cluding this tiny block, the Mauve alignment resulted in
three locally collinear blocks (LCBs) shared across all five
species, but no evidence of rearrangements was found.
Sporolithon durum, belonging to a different subclass
(Corallinophycidae), is still highly similar to G. taiwanensis
(Fig. 4). The group II cox1 intron and the three additional
tRNA genes of G. taiwanensis are absent in S. durum as
well.At position 21,163 in G. taiwanensis, a gap corre-
sponding to the G. taiwanensis orf172 is evident; this gene
is not present in S. durum, which has a different annotation,
orf-Sdur34, immediately after this gap, at its position
21,621. These two ORFs do not appear to be homologous.
Several rearrangements are evident between G. taiwan-
ensis and Pyropia haitanensis (class Bangiophyceae) (Fig.
5). The alignment recognized four LCBs, with three large-
scale rearrangements, indicated by the double-cut-and-join
(DCJ) distance value of 3. The cox1 gene contains many
introns in P. haitanensis, indicated by gaps in the alignment
inside this gene, which is located in the LCB at position 1.
Two intronic ORFs are found within the P. haitanensis cox1
gene, but it is unclear whether either of these ORFs corre-
spond to the one found in G. taiwanensis. A small LCB
located at position 32,540 in P. haitanensis (21,111 in G.
taiwanensis) contains two of the three tRNA genes—
trnR(TCT) and trnY(GTA)—previously found in G. taiwan-
ensis but none of the other Florideophyceae species. A
region of genes from positions ⬃30,500 to the end of the P.
haitanensis genome, excluding the aforementioned small
LCB, is located outside any LCB. These genes are present
in G. taiwanensis, but they are contained in the larger LCBs.
This may indicate genome rearrangements of a small
scale—that is, of single genes.
Between G. taiwanensis and Cyanidioschyzon merolae
Figure 4. Mauve genome alignment of Grateloupia taiwanensis and Sporolithon durum.
Figure 5. Mauve genome alignment of Grateloupia taiwanensis and Pyropia haitanensis.
197GRATELOUPIA TAIWANENSIS MITOGENOME
(class Cyanidiophyceae), the same number of rearrange-
ments are apparent (Fig. 6), again with a DCJ distance of 3,
but with five LCBs. The cox1 intron of G. taiwanensis is not
present in C. merolae. A large gap region between positions
⬃9,500 and ⬃20,000 in C. merolae includes several genes
that are not present in G. taiwanensis.
Discussion
The mitochondrial genome of Grateloupia taiwanensis is
typical of red algae, especially Florideophyceae, in overall
structure and characteristics. Red algal mitochondria seem
to vary less in their genomes than in their plastids; however,
these genomes are very different in size, with plastid ge-
nomes about five times larger than mitochondrial genomes.
Larger genomes with more genes would hypothetically have
more possibilities for gene losses and genome rearrange-
ments, but a definitive conclusion on this topic cannot be
drawn from these results.
On the other hand, the mitochondrial genome of Cyanidio-
schyzon merolae is very different from that of the other taxa
in our analysis, being largest in size (32,211 bp) and con-
taining the most protein-coding genes (34). It may seem
counter-intuitive that an extremophilic organism with a
highly reduced nuclear genome retains a relatively large
mitochondrial genome. But this supports the hypothesis that
the common ancestor of Rhodophyta was itself an extremo-
phile, occurring in acidic hot springs as do present-day
Cyanidiophyceae. Cyanidioschyzon merolae may possess
many characteristics of this ancestor, including several mito-
chondrial genes that are not present in other groups of red
algae, as over time these genes have been either lost or
transferred out of the mitochondrion. However, of the seven
classes of red algae, only three (Cyanidiophyceae, Bangio-
phyceae, and Florideophyceae) currently have mitochon-
drial genomes available, and the unrepresented classes are
all phylogenetically placed between Cyanidiophyceae and
the others. Additional sequencing is necessary so that pat-
terns of gene retention may be further investigated.
Besides several additional tRNA genes found in Grate-
loupia taiwanensis, the mitochondrial genome of G. taiwan-
ensis is highly similar to that of Grateloupia angusta, which
would be expected of species belonging to the same genus.
It should be noted, though, that Grateloupia is a genus
undergoing extensive taxonomic revision. Gargiulo et al.
(2013) split Grateloupia s.l. into several genera, on the basis
of both morphological and sequence data. This includes
several resurrected taxa and some new genera, which the
authors intend to describe in a forthcoming paper. Grate-
loupia taiwanensis was not included in their analysis, but
considering previous phylogenetic analyses (Lin et al.,
2008; DePriest and Lo´pez-Bautista, 2012), G. taiwanensis
appears to belong to a clade that Gargiulo et al. (2013)
suggest should become a new genus based on Grateloupia
subpectinata Holmes. Grateloupia angusta does not belong
to this clade, instead belonging to a clade corresponding to
the genus Pachymeniopsis Y. Yamada ex S. Kawabata
(Gargiulo et al., 2013). Therefore, although we refer to two
species of Grateloupia in the current study, it is most likely
that neither one actually belongs to Grateloupia s.s. In this
case, the unique cox1 intron shared by these two species
would have a wider taxonomic distribution than simply one
genus, possibly present in the entire family or order.
We have demonstrated a simple set of methods for in-
vestigating a new organellar genome, from sequencing and
annotation to large-scale comparisons among species. With
the increasing popularity and efficiency of next-generation
sequencing, many red algal organellar genomes have re-
cently been quickly published in short papers simply to
Figure 6. Mauve genome alignment of Grateloupia taiwanensis and Cyanidioschyzon merolae.
198 M. S. DEPRIEST ET AL.
make the data available. However, we have shown that a
more in-depth characterization of a new organellar genome
can produce scientifically interesting results, such as the
differences in gene content between Grateloupia taiwanen-
sis and Grateloupia angusta, with simple methods based on
next-generation sequencing technology and publicly avail-
able software. Future genome sequencing efforts in red
algae should focus on unsampled taxonomic groups so that
the full potential of red algal organellar genomes can be
revealed and allow for a better understanding of deeper
phylogenomic relationships among red algal groups.
Acknowledgments
This study was funded by the National Science Founda-
tion (ATOL/DEB 0937978 and ATOL/DEB 1036495) to
JLB. Additional funding was provided by the Dean of the
College of Arts & Sciences, the Office of Research, the
Graduate School, and the Department of Biological Sci-
ences at The University of Alabama. MSD would also like
to express his gratitude to the 2013 E. O. Wilson Biodiver-
sity Fellowship.
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