Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina.
ABSTRACT Mitochondria are descendants of the endosymbiotic α-proteobacterium most likely engulfed by the ancestral eukaryotic cells, and the proto-mitochondrial genome should have been severely streamlined in terms of both genome size and gene repertoire. In addition, mitochondrial (mt) sequence data indicated that frequent intron gain/loss events contributed to shaping the modern mt genome organizations, resulting in the homologous introns being shared between two distantly related mt genomes. Unfortunately, the bulk of mt sequence data currently available are of phylogenetically restricted lineages, i.e., metazoans, fungi, and land plants, and are insufficient to elucidate the entire picture of intron evolution in mt genomes. In this work, we sequenced a 12 kbp-fragment of the mt genome of the katablepharid Leucocryptos marina. Among nine protein-coding genes included in the mt genome fragment, the genes encoding cytochrome b and cytochrome c oxidase subunit I (cob and cox1) were interrupted by group I introns. We further identified that the cob and cox1 introns host open reading frames for homing endonucleases (HEs) belonging to distantly related superfamilies. Phylogenetic analyses recovered an affinity between the HE in the Leucocryptos cob intron and two green algal HEs, and that between the HE in the Leucocryptos cox1 intron and a fungal HE, suggesting that the Leucocryptos cob and cox1 introns possess distinct evolutionary origins. Although the current intron (and intronic HE) data are insufficient to infer how the homologous introns were distributed to distantly related mt genomes, the results presented here successfully expanded the evolutionary dynamism of group I introns in mt genomes.
- SourceAvailable from: Ryoma Kamikawa[Show abstract] [Hide abstract]
ABSTRACT: Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5' and 3' termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a "free-standing," IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames.Mobile genetic elements. 01/2014; 4:e29384.
Separate Origins of Group I Introns in Two Mitochondrial
Genes of the Katablepharid Leucocryptos marina
Yuki Nishimura1., Ryoma Kamikawa1,2., Tetsuo Hashimoto1,2, Yuji Inagaki1,2*
1Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan, 2Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
Mitochondria are descendants of the endosymbiotic a-proteobacterium most likely engulfed by the ancestral eukaryotic
cells, and the proto-mitochondrial genome should have been severely streamlined in terms of both genome size and gene
repertoire. In addition, mitochondrial (mt) sequence data indicated that frequent intron gain/loss events contributed to
shaping the modern mt genome organizations, resulting in the homologous introns being shared between two distantly
related mt genomes. Unfortunately, the bulk of mt sequence data currently available are of phylogenetically restricted
lineages, i.e., metazoans, fungi, and land plants, and are insufficient to elucidate the entire picture of intron evolution in mt
genomes. In this work, we sequenced a 12 kbp-fragment of the mt genome of the katablepharid Leucocryptos marina.
Among nine protein-coding genes included in the mt genome fragment, the genes encoding cytochrome b and
cytochrome c oxidase subunit I (cob and cox1) were interrupted by group I introns. We further identified that the cob and
cox1 introns host open reading frames for homing endonucleases (HEs) belonging to distantly related superfamilies.
Phylogenetic analyses recovered an affinity between the HE in the Leucocryptos cob intron and two green algal HEs, and
that between the HE in the Leucocryptos cox1 intron and a fungal HE, suggesting that the Leucocryptos cob and cox1 introns
possess distinct evolutionary origins. Although the current intron (and intronic HE) data are insufficient to infer how the
homologous introns were distributed to distantly related mt genomes, the results presented here successfully expanded the
evolutionary dynamism of group I introns in mt genomes.
Citation: Nishimura Y, Kamikawa R, Hashimoto T, Inagaki Y (2012) Separate Origins of Group I Introns in Two Mitochondrial Genes of the Katablepharid
Leucocryptos marina. PLoS ONE 7(5): e37307. doi:10.1371/journal.pone.0037307
Editor: Stuart Alexander Ralph, University of Melbourne, Australia
Received February 1, 2012; Accepted April 18, 2012; Published May 11, 2012
Copyright: ? 2012 Nishimura 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: RK was a research fellow supported by the Japanese Society for the Promotion of Sciences (JSPS) for Young Scientists (no. 210528). This work was
supported by a JSPS grant awarded to YI (no. 21370031), and grants from the Ministry of Education, Culture, Sports, Science and Technology awarded to YI and
TH (nos. 23117006 and 23117005). 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 declared that no competing interests exist.
* E-mail: firstname.lastname@example.org
. These authors contributed equally to this work.
Group I (gI) introns are a major class of introns found in
bacterial genomes, mitochondrial and plastid genomes, and
eukaryotic nuclear genomes  as well as genomes of viruses/
phages . In eukaryotes, gI introns in the nuclear genomes are
exclusively inserted in ribosomal RNA (rRNA) genes, whereas the
introns reside in genes encoding both structural RNAs and
proteins in organellar genomes . The typical secondary
structure of gI introns consists of approximately 10 double helical
elements designated as P1–P10 . These helical elements are
further organized into three domains at the tertiary structural
level, which are important for efficient splicing of this class of
introns . Many gI introns host open reading frames (ORFs) for
homing endonucleases (HEs) , which may facilitate intron
invasion into the intron-less alleles within a population of the same
species, as well as those in different species [7,8,9]. Intron-encoded
(intronic) HEs are divided into four types, such as LAGLIDADG,
GIY-YIG, His-Cys box, and NHN families, on the basis of highly
conserved motifs .
Mitochondrial (mt) gene/genome data are potentially informa-
tive for inspecting the evolution of gI introns hosting HEs, as a
number of gI introns has been identified in mt genomes .
Nevertheless, the mt intron data currently available are largely
knowledge regarding the evolution of gI introns is highly likely
groups mentioned above have been more intensively sequenced
completed mt genomes are of metazoans, and 97 and 61 mt
metazoan mt genomes listed in NCBI Entrez Genome database
(http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome), as of
January 2012. Thus, we can shed light on novel aspects in the
from the lineages of which mt gene sequences have not been
Katablepharida is a group of heterotrophic unicellular eukary-
otes whose members widely distribute in aquatic environments
. Phylogenetic analyses of small and large subunit rRNA genes
strongly suggested that katablepharids are closely related to
cryptomonads and goniomonads . In this study, we report
two gI introns hosting LAGLIDADG-type HEs in the katable-
pharid Leucocryptos marina mt genome, and explored the evolution-
ary histories of these introns by combining their putative
PLoS ONE | www.plosone.org1May 2012 | Volume 7 | Issue 5 | e37307
secondary structures, the intron positions, and the phylogenetic
affinities of the intronic HEs.
Results and Discussion
Group I introns in Leucocryptos mt genome
We determined an approximately 12 kbp-long region of the
Leucocryptos mt genome including NADH dehydrogenase subunit
11 (nad11), NADH dehydrogenase subunit 1 (nad1), NADH
dehydrogenase subunit 6 (nad6), ATP synthase F0 subunit 6
(atp6), NADH dehydrogenase subunit 7 (nad7), cytochrome c
oxidase subunit 2 (cox2), cytochrome c oxidase subunit 3 (cox3),
cytochrome b (cob), and cytochrome c oxidase subunit 1 (cox1) genes
in this order (Fig. 1; Note that the 39 terminus of cox1 and the 59
terminus of nad11 are not available in this mt genome fragment).
The intergenic spacer regions are short, ranging from 4–65 bp in
length. Neither transfer RNA nor ribosomal RNA gene was found
in the mt genome fragment determined in the current study. By
the comparison between the cDNA and genomic sequences, two
introns in this region, one in the cob gene and the other in the cox1
gene, were detected (highlighted as triangles in Fig. 1). No sign of
RNA editing was found so far.
The two introns in the cob and cox1 genes are likely of group I, as
these sequences can be folded into typical secondary structures of
gI introns comprising 11–12 double helical domains (P1–P10;
Figs. 2A & 2B). In our BlastN survey, the putative core region of
the cob intron showed sequence similarity to those of group ID
introns [e.g., the one lying in the Chaetosphaeridium globsum cob gene
(GenBank accession no. AF494279.1) with an E-value=10213].
On the other hand, the putative core region of the cox1 intron
appeared to share sequence similarity to those of group IA1
introns [e.g., the one lying in the Scenedesmus obliqus large subunit of
rRNA gene (GenBank accession number AF204057.1) with an E-
value=261026]. The two gI introns are also distinguishable from
one another by the two following points: (i) The cox1 intron have
two extra double helical domains, P7.1 and P9.1 (shaded in
Fig. 2A), which are absent in the cob intron; (ii) An ORF occupies
the loop region between P1 and P10 in the cob intron, while an
ORF places in the loop region between P1 and P2 in the cox1
intron (Figs. 2A & 2B)
The ORFs hosted in the cob intron and cox1 intron likely encode
217 amino acid (aa) residue-long and 267 aa residue-long
polypeptides, respectively. The two intronic ORFs likely encode
LAGLIDADG-type HEs, but no significant similarity was detected
between their putative aa sequences by a BlastP search (bl2seq)
with the default settings. Henceforth here, we designate the HE
hosted in the cob intron as HELm-cob, while that hosted in the cox1
intron as HELm-cox1. HELm-coband HELm-cox1appeared to belong to
distant superfamilies, LAGLIDADG_2 (pfam031611) and LA-
GLIDADG_1 (pfam00961), respectively.
Origin of the Leucocryptos cob intron
We aligned the aa sequences of 30 members of LAGLI-
DADG_2 superfamily including HELm-cob, and subjected to the
maximum-likelihood (ML) and Bayesian phylogenetic analyses. In
the unrooted phylogeny of this ‘LAGLIDADG_2’ alignment,
HELm-coband two HEs encoded in the cob introns of two green
algae, Nephroselmis olivacea and Chlorokybus atmophyticus, grouped
together with a BP of 98% and a Bayesian posterior probability
(BPP) of 1.00 (surrounded by dotted line in Fig. 3A), suggesting
that the cob introns harboring the Leucocryptos and green algal HEs
evolved from a single ancestral intron. The ancestral intron most
likely (i) lied at phase-0 position of the codon corresponding to
Gln138 in the Saccharomyces cerevisiae cob gene (GenBank accession
number NC_001224), and (ii) hosted a HE belonging to
LAGLIDADG_2 superfamily in the loop region between P1 and
P2 as shown in Fig. S1A. Unfortunately, it is difficult to retrieve
deeper insights for the origin of Leucocryptos cob intron by intron
positions, as the HEs hosted by the introns lying in the
homologous positions were sporadically distributed in the
LAGLIDADG_2 phylogeny (Fig. 3A).
Origin of the Leucocryptos cox1 intron
We prepared a ‘LAGLIDADG_1’ alignment comprising the aa
sequences of HELm-cox1and 24 members of LAGLIDADG_1
superfamily. The unrooted LAGLIDADG_1 phylogeny united
HELm-cox1and the HE hosted in the forth out of 15 cox1 introns in
the fungus Rhizophydium sp. with a BP of 71% and a BPP of 0.96
(surrounded by dotted line in Fig. 3B). Although the statistical
support for this clade was inconclusive, the introns hosting the two
HEs described above exclusively share the homing position—
phase-0 position of the codon corresponding to Thr93 in the S.
cerevisiae cox1 gene (GenBank accession number NC_001224).
Thus, Leucocryptos cox1 intron and the forth intron in Rhizophydium
cox1 gene likely derived from a single ancestral intron, which lied
at phase-0 position of the codon corresponding to Thr93 in the S.
cerevisiae cox1 gene, and hosted a LAGLIDADG_1-type HE in the
loop region between P1 and P10 (see Fig. S1B). Of note,
independent from the Leucocryptos cox1 intron, cox1 introns in
multiple land plant species appeared to share the ancestries with
the fungal introns [13,14]. Thus, fungal mt genomes might hold
keys to elucidate the evolution in mt introns as a whole.
The clan of HELm-cox1and the Rhizophydium HE was further
connected to the HE encoded in the first out of 16 cox1 intron of
the fungal Podospora anserina, and that encoded in a single cox1
intron of the mycetozoan Dictyostelium fasciculatam (BP of 70% and
BPP of 0.99; Fig. 3B). Both Podospora and Dictyostelium introns lie
between the first and second letters of the codon corresponding
Ala94 in the S. cerevisiae cox1 gene (phase-1), being in close
proximity to but apparently distinct from the homing position of
the Leucocryptos and Rhizophydium introns (see above). One
Figure 1. Primary structure of the partial mitochondrial genome of the katablepharid Leucocryptos marina. Protein-coding genes (and
their directions) are shown by arrows. Abbreviations; nad11, NADH dehydrogenase subunit 11; nad1, NADH dehydrogenase subunit 1; nad6, NADH
dehydrogenase subunit 6; atp6, ATP synthase F0 subunit 6; nad7, NADH dehydrogenase subunit 7; cox2, cytochrome c oxidase subunit 2; cox3,
cytochrome c oxidase subunit 3; cob, cytochrome b; cox1, cytochrome c oxidase subunit 1. Introns inserted in the cob and cox1 genes are shown as
triangles. The genes initially amplified by reverse transcriptase PCR are shown in orange, while those amplified from genomic DNA were in green. The
59 terminus of the nad11 gene and the 39 terminus of the cox1 gene were not determined in the current study (highlighted by dotted lines).
Mitochondrial Group I Introns of a Katablepharid
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possibility is that HELm-cox1and the Rhizophydium HE, and the
Podospora and Dictyostelium HEs have evolved from a single ancestral
HE and still recognize the identical nucleotide sequence (or very
similar sequences), but the cleavage position altered after the
separation of the two HE pairs. In any case, the evolutionary link
between the cox1 introns in Leucocryptos and Rhizophydium, and those
in Podospora and Dictyostelium can be assessed only after the
enzymatic properties of the HEs hosted in the four cox1 introns are
Intron evolution in Leucocryptos mt genome: ‘lateral
transfer’ versus ‘parallel loss’
Introns in organellar genomes are generally regarded as mobile
genetic elements powered by intronic HEs, as ‘trans-genomic’
intron invasion have been accumulated in the literature . In the
global eukaryotic phylogeny, katablepharids highly likely form a
clade with goniomonads and cryptomonads, but are closely related
to neither green algae nor fungi [12,15]. Thus, the evolutionarily
homologous introns resided in distantly related mt genomes
(Figs. 2A & 2B) can be rationalized by lateral transfer events.
Nevertheless, considering the cyclic model for gain and loss of
selfish genetic elements including gI introns , we cannot
exclude the alternative scenario which assumes that (i) the two
introns in cob and cox1 genes discussed above have been vertically
inherited from the common ancestor of katablepharids, green
algae and fungi, but (ii) secondary intron loss occurred in other
descendent lineages, as the HE sequences considered here unlikely
represent the true diversity of LAGLIDADG_2-type or LAGLI-
DADG_1-type HE superfamily. The origins of the two gI introns
found in Leucocryptos mt genome should be revisited after in-depth
surveying introns and intronic HEs in the mt genomes of
phylogenetically broad eukaryotic lineages, particularly those of
close relatives of katablepharids, such as goniomonads and
Materials and Methods
From cell culture to DNA sequencing
The katablepharid Leucocryptos marina NIES-1335 and the
haptophyte Chrysochromulina sp. NIES-1333 were purchased from
the National Institute for Environmental Study (NIES). Leucocryptos
was maintained in f/2 medium (http://mcc.nies.go.jp/02medium.
Figure 2. Putative secondary structures of the group I intron RNAs. A. Secondary structure of the Leucocryptos cob intron. Putative Watson–
Crick and wobble base pairs are shown by lines and open circles, respectively. Capital and small letters represent intron and exon nucleotides,
respectively. Double helical structures, which are characteristic to group I introns, are labeled as P1–P10. The open reading frame (ORF) for a
LAGLIDADG-type homing endonuclease (closed box; 217 amino acid residues) was found in the 718 nucleotide-long loop region between P1 and P2.
B. Secondary structure of the Leucocryptos cox1 intron. The details of this figure are same as described in A, except the ORF for a LAGLIDADG-type
homing endonuclease (closed box; 267 amino acid residues) was found in the 827 nucleotide-long loop region between P1 and P10. P9.1 and P7.1,
which are absent in the Leucocryptos cob intron, are shaded.
Mitochondrial Group I Introns of a Katablepharid
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Mitochondrial Group I Introns of a Katablepharid
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html#f2) with Chrysochromulina as a prey at 20uC under 14:10
hours of light:dark cycles.
We harvested the Leucocryptos cells containing a small amount of
the Chrysochromulina (prey) cells, and this sample was then subjected
to DNA and RNA extractions by using Plant DNA Isolation
Reagent (TaKaRa) and RNeasy Plant Mini Kit (QIAGEN),
respectively. Total RNA was used for random hexamer-primed
cDNA synthesis by Superscript II reverse transcriptase (Invitro-
gen). The experiments mentioned above were conducted by
following the manufactures’ instructions. The cDNA and total
DNA were used as the templates for polymerase chain reactions
(PCR) aiming at the amplification of gene transcripts and genome
We initially amplified six mt gene transcripts by reverse
transcriptase PCR (RT-PCR) with the primer sets shown in
Table 1—cob, cox1, cox3, nad1, nad7, and nad11. PCR products
were cloned into pGEM-TEasy vector (Promega). For each gene
transcript, we completely sequenced eight clones and confirmed
no sequence heterogeneity among clones, except the cob and cox3
transcripts. The cob and cox3 samples appeared to consist of two
distinctive types of amplicons, one with and the other without in-
frame TGA codons (data not shown; no in-frame TGA codon was
found in the cox1, nad1, nad7, or nad11 sample). We regarded the
amplicons with in-frame TGA codons as the mt gene transcripts
from the haptophyte (Chrysochromulina) prey cells for two reasons:
Firstly, our preliminary phylogenetic analyses indicated that the
two amplicons were distantly related to each other, and only the
one with in-frame TGA codons displayed an intimate affinity to
the haptophyte homologues (Figs. S2A & B). Secondly, the genus
Chrysochromulina belongs to one of the two classes in Haptophyta,
Prymnesiophyceae, whose mt genomes assign TGA, one of the
three termination codons in the standard genetic code, to
tryptophan [17,18]. On the basis of the phylogenetic results and
feature in codon usage, we concluded that the cob and cox3
transcripts with in-frame TGA codons were most likely originated
from the haptophyte prey cells, and were not considered in the
We then amplified the mt genome fragments corresponding to
the six transcripts with no in-frame TGA codon with exact-match
primers (not shown). We also amplified the intergenic spacer
regions between nad11 and nad1, nad1 and nad7, nad7 and cox3, cox3
and cob, and cob and cox1 with outwarded exact match primers
designed based on the six mt gene transcripts initially determined
(see above) as performed in previous works [19,20]. As the result of
the PCR with outward primers, three genes (nad6, atp6, and cox2)
were additionally found. Cloning and sequencing were performed
as described above. The partial mt genome sequence was
deposited to DNA Data Bank of Japan (GenBank/EMBL/DDBJ
accession no. AB693966).
Prediction of intron secondary structures
Each of cob and cox1 genes in the Leucocryptos mt genome
appeared to possess a single gI intron with a HE (see Results and
Discussion). Both 59 and 39 splice sites were determined by
comparing the cDNA and genomic sequences. Intron secondary
structures were predicted using MFOLD , followed by manual
modification by referring the general structures of gI introns
presented in GOBASE .
Phylogenetic analyses of intronic HEs
The HE encoded in the Leucocryptos cob intron (HELm-cob) was
aligned with 29 HEs belonging to the LAGLIDADG_2 super-
family, which showed significant similarity to HELm-cobin TBlastN
search against the GenBank nr database (E-values,10210). We
carefully assessed the alignments from the Blast search, and
excluded redundant sequences and the sequences which produced
very short alignments with HELm-cob. After manual refinement
followed by the exclusion of ambiguously aligned positions, 183 aa
positions were remained in the final ‘LAGLIDADG_2’ alignment.
Pairwise aa identities and similarities ranged from 30 to 98%, and
from 48 to 98%, respectively (Fig. S3A). The HE sequence hosted
in the Chlorokybus atmophyticus cob intron showed the highest aa
identity (47%) to HELm-cob, while the ones hosted in the Millerozyma
farinose and Chlorogonium elongatum cob genes showed the lowest aa
identity (34%) to HELm-cob(see the upper triangular in Fig. S3A).
The HE sequence hosted in the Chlorokybus atmophyticus cob intron
showed the highest aa similarity (65%) to the HELm-cob, while the
one hosted in the Chlamydomonas incerta cob genes showed the lowest
Figure 3. Maximum-likelihood (ML) phylogenetic analyses of homing endonuclease (HE) sequences. A. Unrooted ML phylogeny
inferred from the LAGLIDADG_2 alignment containing 183 amino acid positions. Thirty HEs belonging to LAGLIDADGE_2 superfamily were subjected
to the ML and Bayesian methods. The HEs hosted in cob introns are shown in dark blue. The details of the homing positions of the HE-hosting cob
introns (phase and codon) are given on the right side of the tree. Codon numbers are based on the Saccharomyces cerevisiae cob gene (GenBank
accession number NC_001224). Only ML bootstrap values equal to or greater than 50% are shown. The resultant tree inferred from Bayesian analysis
was essentially identical to that from the ML analysis (data not shown). The branches supported by Bayesian posterior probabilities (BPPs) equal to or
greater than 0.95 were highlighted by thick lines. The GenBank accession numbers of the HE sequences used in this tree are given in brackets. B.
Unrooted ML phylogeny inferred from the LAGLIDADG_1 alignment containing 191 amino acid positions. Twenty five HEs belonging to
LAGLIDADGE_1 superfamily were subjected to the ML and Bayesian methods. The HEs hosted in cox1 introns are shown in dark red. The details of the
homing positions of the HE-hosting cox1 introns (phase and codon) are given on the right side of the tree. Codon numbers are based on the S.
cerevisiae cox1 gene (GenBank accession number NC_001224). We are unsure the precise position of the intron identified in the Flammulina velutipues
cox1 gene, as only HE sequence has been deposited in the GenBank database (labeled with a question mark). Other details are same as described in
Table 1. Degenerate primers used for reverse-transcription
Genes NamesDirectionsSequences (59 – 39)
cox1 Hcox1F forwardACNAAYCAYAARGAYATHGG
cox3 Hcox3F forwardCCNTTYCAYTTRGTNGAYCC
nad1 Hnad1F forwardCGNGGNCCNAAYGTNGTNGG
Mitochondrial Group I Introns of a Katablepharid
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aa similarity (49%) to HELm-cob(see the lower triangular in Fig.
The same procedure described above was repeated to prepare a
‘LAGLIDADG_1’ alignment including the HE encoded in the
Leucocryptos cox1 intron (HELm-cox1) and 24 HEs belonging to the
LAGLIDADG_1 superfamily, which can form global alignments
with HELm-cox1with TBlastN E-values,10210. The final LAGLI-
DADG_1 alignment contains 191 unambiguously-aligned aa
positions. Pairwise aa identities and similarities ranged from 14
to 95%, and from 34 to 97%, respectively (Fig. S3B). The HE
sequence hosted in the Rhizophydium sp. cox1 intron showed the
highest aa identity (44%) to HELm-cox1, while the one hosted in the
Flammulina velutipes cox1 gene showed the lowest aa identity (20%)
to HELm-cox1(see the upper triangular in Fig. S3B). The HE
sequence hosted in the Podospora anserina cox1 intron showed the
highest aa similarity (62%) to HELm-cox1, while the ones hosted in
the Blastomyces dermatitidis cox1 gene and Allomyces macrogynus cob
gene showed the lowest aa similarity (41%) to HELm-cob(see the
lower triangular in Fig. S3B). The GanBank accession numbers of
the HE sequences considered in the two alignments, and the
precise positions of the introns hosting these HEs are shown in
Figs. 3A and B.
The two HE alignments were separately subjected to ML
analysis. The LG model  incorporating empirical aa frequen-
cies and among-site rate variation approximated by a discrete
gamma (C) distribution with four categories (LG+C+F model) was
selected as the most appropriate model for the aa substitutions in
the LAGLIDADG_1 alignment by the program Aminosan 
under the Akaike information criterion. Similarly, the VT model
 incorporating empirical aa frequencies and among-site rate
variation approximated by a discrete C distribution with four
categories (VT+C+F model) was selected as the most appropriate
model for the aa substitutions in the LAGLIDADG_2 alignment.
The ML analyses were performed using RAxML 7.2.1  with
the selected model described above. The ML tree was heuristically
searched from 10 distinct parsimony trees. In RAxML bootstrap
analyses (100 replicates), the heuristic tree search was performed
from a single parsimony tree per replicate.
The two HE alignments were also analyzed by Bayesian method
with the LG+C model using PhyloBayes v.3.2 . As VT model
is not available in PhyloBayes, we applied the LG+C model to the
LAGLIDADG_2 alignment. Two independent Markov chain
Monte Carlo chains (MCMC) were run for 72,000–78,000 points.
The first 100 points were discarded as ‘burn-in’ on the basis of the
log-likelihood plots (data not shown). For each analysis, we
compared the frequencies of all bipartitions observed in the two
independent MCMC runs in detail, and confirmed the conver-
gence between the two runs by the ‘maxdiff’ value being smaller
than that recommended in the manual of the program (i.e.,
maxdiff,0.1; data not shown). Subsequently, the consensus trees
with branch lengths and BPP were calculated from the rest of the
intron RNAs. A. Schematic structures of Leucocryptos, Chlorokybus,
and Nephroselmis cob introns. LAGLIDADG_2-type homing
endonucleases are encoded in the region between P1 and P2 in
the three introns (shown as closed boxes). B. Schematic structures
of Leucocryptos and Rhizophydium cox1 introns. Both introns harbor
LAGLIDADG_1-type homing endonucleases in the region
between P1 and P10 (shown as closed boxes).
Putative secondary structures of group I
COB and COX3 amino acid (aa) alignments. A. The ML
phylogeny inferred from the COB alignment comprises 31 taxa
with 368 unambiguously aligned aa positions B. The ML
phylogeny inferred from the COX3 alignment comprising 26
taxa with 218 unambiguously aligned aa positions. Leucocryptos
marina and Chrysochromulina sp. are highlighted by arrowheads. The
haptophyte clade is shaded. Only ML bootstrap values equal to or
greater than 50% are shown. Methods: The two aa alignments
were separately analyzed with the ML method with the LG+C+F
model by using RAxML ver. 7.2.1. The details of the ML and ML
bootstrap analyses were same as described in Materials and
Methods/Phylogenetic analyses of intronic HEs.
Maximum-likelihood (ML) analyses of the
Pairwise aa identity matrix of the 30 endonuclease (HE) sequences
in the LAGLIDADG_2 alignment. We also recoded 20 aa
characters in the HE sequences to six Dayhoff classes, and then
made the identity matrix presented below diagonal. B. Pairwise aa
identity matrix of the 25 HE sequences in the LAGLIDADG_1
alignment. We also provide the pairwise ‘Dayhoff-class’ identity
matrix below diagonal. For each sequence, the GenBank accession
no. is shown in brackets.
Amino acid (aa) sequence homology. A.
We thank S. Ishikawa (University of Tsukuba, Japan) for his advice on
Conceived and designed the experiments: YN RK TH YI. Performed the
experiments: YN RK. Analyzed the data: YN RK YI. Wrote the paper:
YN RK TH YI.
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