Limits...
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.


The complete mitochondrial genomes of Melibe leonina (A) and Tritonia diomedea (B).Both mitochondrial genomes were found to code for the expected 22 transfer RNA, 13 protein-coding genes, and a short and large ribosomal subunit. The 13 protein-coding gene order was found to be identical to all other opisthobranchs.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4440745&req=5

pone.0127519.g001: The complete mitochondrial genomes of Melibe leonina (A) and Tritonia diomedea (B).Both mitochondrial genomes were found to code for the expected 22 transfer RNA, 13 protein-coding genes, and a short and large ribosomal subunit. The 13 protein-coding gene order was found to be identical to all other opisthobranchs.

Mentions: The resulting M. leonina de novo assembly contained 225,098 contiguous sequences with an N50 of 1384 base pairs (bp) and greater than 100X average coverage. The overall nuclear genome size was 272 Mbp. The complete mitochondrial genome of M. leonina was located on a single contiguous sequence that was 14,513 bp in length (Fig 1A; KP764764). The average coverage of the contiguous sequence was 3036X with a total read count of 610,149. A region located at nucleotides 8560–8756 (198 bp) of the M. leonina mitochondrial genome had significantly higher coverage. This region peaked at a depth of about 8,500 reads and was located in a region containing a long stretch of non-coding nucleotides high in adenine and thymine content and a small portion of the Gln tRNA.


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)

The complete mitochondrial genomes of Melibe leonina (A) and Tritonia diomedea (B).Both mitochondrial genomes were found to code for the expected 22 transfer RNA, 13 protein-coding genes, and a short and large ribosomal subunit. The 13 protein-coding gene order was found to be identical to all other opisthobranchs.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0127519.g001: The complete mitochondrial genomes of Melibe leonina (A) and Tritonia diomedea (B).Both mitochondrial genomes were found to code for the expected 22 transfer RNA, 13 protein-coding genes, and a short and large ribosomal subunit. The 13 protein-coding gene order was found to be identical to all other opisthobranchs.
Mentions: The resulting M. leonina de novo assembly contained 225,098 contiguous sequences with an N50 of 1384 base pairs (bp) and greater than 100X average coverage. The overall nuclear genome size was 272 Mbp. The complete mitochondrial genome of M. leonina was located on a single contiguous sequence that was 14,513 bp in length (Fig 1A; KP764764). The average coverage of the contiguous sequence was 3036X with a total read count of 610,149. A region located at nucleotides 8560–8756 (198 bp) of the M. leonina mitochondrial genome had significantly higher coverage. This region peaked at a depth of about 8,500 reads and was located in a region containing a long stretch of non-coding nucleotides high in adenine and thymine content and a small portion of the Gln tRNA.

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.