The complete mitochondrial genome of the golden mussel Limnoperna fortunei and comparative mitogenomics of Mytilidae

Uliano-Silva, Marcela; Americo, Juliana Alves; Costa, Igor Rodrigues da; Schomaker-Bastos, Alex; Rebelo, Mauro de Freitas; Prosdocimi, Francisco

doi:10.1016/j.gene.2015.11.043

Cited by 31 publications

(34 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Thus, the hyperdiverse nature of this clade, associated to poor taxon sampling and a possible high rate of mitochondrial genome evolution may have contributed to produce inconclusive results in mitochondrial analyses. Also, even though some relationships were not elucidated by mitochondrial phylogenomics alone, the information provided by the mitogenome has been proven several times to be useful in the study of evolutionary relationships for several taxa, either confirming (Prosdocimi et al, 2012; Finstermeier et al, 2013) or refuting previous phylogenetic hypotheses (Kayal et al, 2015; Uliano-Silva et al, 2016). Therefore, we still recommend the use of mitochondrial data, preferably alongside other markers (i.e., nuclear genes), to increase phylogenetic signal and recapture phylogenies.…”

Section: Discussionmentioning

confidence: 99%

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

Vieira

Prosdocimi

2019

PeerJ

Self Cite

View full text Add to dashboard Cite

The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the “no budget mitogenomics” approach ideal for comprehensive molecular studies, especially for subsampled taxa.

show abstract

Section: Discussionmentioning

confidence: 99%

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

Vieira

Prosdocimi

2019

PeerJ

Self Cite

View full text Add to dashboard Cite

show abstract

“…Mollusca is a megadiverse phylum originated in the PreCambrian/Cambrian border, according to the fossil record 9 , during which organisms conquered a great variety of habitats, food habits and evolved a variety of body sizes 10 . Bivalve mollusks present one of the most variable mitogenomes described among metazoans with low conservation of genome size, gene arrangement, strand assignment, gene duplications and losses, nucleotide composition, and more 6 8 .…”

mentioning

confidence: 99%

Complete mitochondrial genomes of Trisidos kiyoni and Potiarca pilula: Varied mitochondrial genome size and highly rearranged gene order in Arcidae

Sun

Kong

et al. 2016

Sci Rep

View full text Add to dashboard Cite

We present the complete mitochondrial genomes (mitogenomes) of Trisidos kiyoni and Potiarca pilula, both important species from the family Arcidae (Arcoida: Arcacea). Typical bivalve mtDNA features were described, such as the relatively conserved gene number (36 and 37), a high A + T content (62.73% and 61.16%), the preference for A + T-rich codons, and the evidence of non-optimal codon usage. The mitogenomes of Arcidae species are exceptional for their extraordinarily large and variable sizes and substantial gene rearrangements. The mitogenome of T. kiyoni (19,614 bp) and P. pilula (28,470 bp) are the two smallest Arcidae mitogenomes. The compact mitogenomes are weakly associated with gene number and primarily reflect shrinkage of the non-coding regions. The varied size in Arcidae mitogenomes reflect a dynamic history of expansion. A significant positive correlation is observed between mitogenome size and the combined length of cox1-3, the lengths of Cytb, and the combined length of rRNAs (rrnS and rrnL) (P < 0.001). Both protein coding genes (PCGs) and tRNA rearrangements is observed in P. pilula and T. kiyoni mitogenomes. This analysis imply that the complicated gene rearrangement in mitochondrial genome could be considered as one of key characters in inferring higher-level phylogenetic relationship of Arcidae.

show abstract

“…Thus, the hyperdiverse nature of this clade, associated to poor taxon sampling and a possible high rate of mitochondrial genome evolution may have contributed to produce inconclusive results in mitochondrial analyses. Also, even though some relationships were not elucidated by mitochondrial phylogenomics alone, the information provided by the mitogenome has been proven several times to be useful in the study of evolutionary relationships for several taxa, either confirming (Prosdocimi et al, 2012;Finstermeier et al, 2013) or refuting previous phylogenetic hypotheses (Kayal et al, 2015;Uliano-Silva et al, 2016). So, we still recommend PeerJ reviewing PDF | (2018:10:32218:1:1:NEW 8 Dec 2018)…”

Section: Manuscript To Be Reviewedmentioning

confidence: 86%

Peer Review #2 of "Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data (v0.1)"

2019

View full text Add to dashboard Cite

The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the "no budget mitogenomics" approach ideal for comprehensive molecular studies, especially for

show abstract

The complete mitochondrial genome of the golden mussel Limnoperna fortunei and comparative mitogenomics of Mytilidae

Cited by 31 publications

References 28 publications

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

Complete mitochondrial genomes of Trisidos kiyoni and Potiarca pilula: Varied mitochondrial genome size and highly rearranged gene order in Arcidae

Peer Review #2 of "Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data (v0.1)"

Contact Info

Product

Resources

About