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The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny.

Sevigny JL, Kirouac LE, Thomas WK, Ramsdell JS, Lawlor KE, Sharifi O, Grewal S, Baysdorfer C, Curr K, Naimie AA, Okamoto K, Murray JA, Newcomb JM - PLoS ONE (2015)

Bottom Line: Both Bayesian and maximum likelihood analyses resulted in similar tree topologies.In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic.In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America.

ABSTRACT
The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group.

No MeSH data available.


Transfer RNA secondary structures for both M. leonina (A) and T. diomedea (B).G-U pair bonds are indicated by a slanted line. The two serine tRNAs had a truncated d arm, seen in other heterobranchs. In T. diomedea (B), the UCU anticodon for the serine 1 tRNA (highlighted in red) has not been reported in any other gastropod.
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pone.0127519.g002: Transfer RNA secondary structures for both M. leonina (A) and T. diomedea (B).G-U pair bonds are indicated by a slanted line. The two serine tRNAs had a truncated d arm, seen in other heterobranchs. In T. diomedea (B), the UCU anticodon for the serine 1 tRNA (highlighted in red) has not been reported in any other gastropod.

Mentions: Ion Torrent sequencing of the T. diomedea genome yielded 4,020,000 reads totaling 804Mbp. The mitochondrial assembly from this organism produced a single contig 14,540 bp in length (Fig 1B; KP764765) with coverage of 34X. The sequence was confirmed with dideoxy sequencing and a region of high coverage was identified in the same area as that for M. leonina. Additional analysis of this region in T. diomedea suggested that it was actually a complex non-coding repeat region, which likely explains the higher coverage of this region in the assembly for both species. The mitochondrial genomes of M. leonina and T. diomedea were 72% identical with only 3872 of the nucleotides variable and 471 gaps between the two. The overall base composition of the mitochondrial genome for both species was also found to favor adenine and thymine. For M. leonina, A+T content was found to be 64.3% (26.98% A, 37.28% T, 15.07% C, and 20.68% G) and in T. diomedea, the A+T content was 65.4% (27.80% A, 37.58% T, 14.58% C, and 20.04% G). The M. leonina and T. diomedea mitochondrial genomes coded for the expected thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal subunits (short and large) that have been seen in related species. The gene order of the thirteen protein-coding genes of M. leonina and T. diomedea was identical to that of all other opisthobranchs published in GenBank. When the linear representation of the mitochondrial DNA was split and rearranged, raw reads from the genomic assembly spanned the location of the split and thus confirmed the circularity of both sequences. The location and secondary structure of all twenty-two tRNAs for both species were successfully identified using Arwen v1.2 (Fig 2).


The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny.

Sevigny JL, Kirouac LE, Thomas WK, Ramsdell JS, Lawlor KE, Sharifi O, Grewal S, Baysdorfer C, Curr K, Naimie AA, Okamoto K, Murray JA, Newcomb JM - PLoS ONE (2015)

Transfer RNA secondary structures for both M. leonina (A) and T. diomedea (B).G-U pair bonds are indicated by a slanted line. The two serine tRNAs had a truncated d arm, seen in other heterobranchs. In T. diomedea (B), the UCU anticodon for the serine 1 tRNA (highlighted in red) has not been reported in any other gastropod.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4440745&req=5

pone.0127519.g002: Transfer RNA secondary structures for both M. leonina (A) and T. diomedea (B).G-U pair bonds are indicated by a slanted line. The two serine tRNAs had a truncated d arm, seen in other heterobranchs. In T. diomedea (B), the UCU anticodon for the serine 1 tRNA (highlighted in red) has not been reported in any other gastropod.
Mentions: Ion Torrent sequencing of the T. diomedea genome yielded 4,020,000 reads totaling 804Mbp. The mitochondrial assembly from this organism produced a single contig 14,540 bp in length (Fig 1B; KP764765) with coverage of 34X. The sequence was confirmed with dideoxy sequencing and a region of high coverage was identified in the same area as that for M. leonina. Additional analysis of this region in T. diomedea suggested that it was actually a complex non-coding repeat region, which likely explains the higher coverage of this region in the assembly for both species. The mitochondrial genomes of M. leonina and T. diomedea were 72% identical with only 3872 of the nucleotides variable and 471 gaps between the two. The overall base composition of the mitochondrial genome for both species was also found to favor adenine and thymine. For M. leonina, A+T content was found to be 64.3% (26.98% A, 37.28% T, 15.07% C, and 20.68% G) and in T. diomedea, the A+T content was 65.4% (27.80% A, 37.58% T, 14.58% C, and 20.04% G). The M. leonina and T. diomedea mitochondrial genomes coded for the expected thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal subunits (short and large) that have been seen in related species. The gene order of the thirteen protein-coding genes of M. leonina and T. diomedea was identical to that of all other opisthobranchs published in GenBank. When the linear representation of the mitochondrial DNA was split and rearranged, raw reads from the genomic assembly spanned the location of the split and thus confirmed the circularity of both sequences. The location and secondary structure of all twenty-two tRNAs for both species were successfully identified using Arwen v1.2 (Fig 2).

Bottom Line: Both Bayesian and maximum likelihood analyses resulted in similar tree topologies.In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic.In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America.

ABSTRACT
The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group.

No MeSH data available.