Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia

Plazzi, Federico; Puccio, Guglielmo; Passamonti, Marco

doi:10.1093/gbe/evw187

Cited by 55 publications

(97 citation statements)

References 176 publications

(248 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The size of the fully Sanger-sequenced mitochondrial genome of Ruditapes decussatus (reference female F4) is of 18,995 bp, and it includes 13 protein-coding genes, 22 tRNAs and 2 rRNAs. Our data support the presence of the atp8 gene in the mtDNA of Ruditapes decussatus; atp8 has been reported as missing in several bivalve species, however, more accurate searches often led to the identification of the gene, so, in most cases, the alleged lack of atp8 is likely ascribable to annotation inaccuracies due to the extreme variability and the small size of the gene ( Breton, Stewart & Hoeh, 2010 ; Breton et al, 2014 ; Plazzi, Puccio & Passamonti, 2016 ).…”

Section: Discussionsupporting

confidence: 83%

“…Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mtDNA variability and unusual features, such as: large mitochondrial genomes (up to ∼47Kb), high proportion of URs (i.e., number of base pairs annotated as URs over the total mtDNA length), novel protein coding genes with unknown function, frequent and extensive gene rearrangement, and differences in strand usage ( Gissi, Iannelli & Pesole, 2008 ; Breton et al, 2011 ; Ghiselli et al, 2013 ; Milani et al, 2014b ; Plazzi, Puccio & Passamonti, 2016 ). Moreover, mitochondrial genome size varies among bivalves because of gene duplications and losses ( Serb & Lydeard, 2003 ; Passamonti et al, 2011 ; Ghiselli et al, 2013 ), and sometimes genes are fragmented as in the case of ribosomal genes in oysters ( Milbury et al, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The complete mitochondrial genome of the grooved carpet shell,Ruditapes decussatus(Bivalvia, Veneridae)

Ghiselli

Milani

Iannello

et al. 2017

PeerJ

Self Cite

View full text Add to dashboard Cite

Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i) assembled Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of Ruditapes decussatus is a cause or an effect of the ongoing replacement of Ruditapes decussatus with the invasive Ruditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point.

show abstract

Section: Discussionsupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome of the grooved carpet shell,Ruditapes decussatus(Bivalvia, Veneridae)

Ghiselli

Milani

Iannello

et al. 2017

PeerJ

Self Cite

View full text Add to dashboard Cite

show abstract

“…The r8s method was used instead of BEAST because the former has been shown to be effective in recent studies (Carbonell-Caballero et al 2015; de Casas et al 2016; Feng et al 2016; Plazzi et al 2016) and the latter would require much more computational time with this large datasets here. The fossils used here were from a survey of literature and online resources on Paleobiology Database website (https://www.paleobiodb.org/; last accessed November 12, 2016) for the oldest fossil of the corresponding MRCA nodes.…”

Section: Methodsmentioning

confidence: 99%

Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication

et al. 2016

View full text Add to dashboard Cite

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.

show abstract

“…18 and references therein). It is currently represented by two orders, Trigoniida and Unionida (taxonomy from ref.…”

Section: Introductionmentioning

confidence: 99%

Evolution of sex-dependent mtDNA transmission in freshwater mussels (Bivalvia: Unionida)

Guerra

Plazzi

Stewart

et al. 2017

Sci Rep

Self Cite

View full text Add to dashboard Cite

Doubly uniparental inheritance (DUI) describes a mode of mtDNA transmission widespread in gonochoric freshwater mussels (Bivalvia: Palaeoheterodonta: Unionida). In this system, both femaleand male-transmitted mtDNAs, named F and M respectively, coexist in the same species. In unionids, DUI is strictly correlated to gonochorism and to the presence of the atypical open reading frames (ORFans) F-orf and M-orf, respectively inside F and M mtDNAs, which are hypothesized to participate in sex determination. However, DUI is not found in all three Unionida superfamilies (confirmed in Hyrioidea and Unionoidea but not in Etherioidea), raising the question of its origin in these bivalves. To reconstruct the co-evolution of DUI and of ORFans, we sequenced the mtDNAs of four unionids (two gonochoric with DUI, one gonochoric and one hermaphroditic without DUI) and of the related gonochoric species Neotrigonia margaritacea (Palaeoheterodonta: Trigoniida). Our analyses suggest that rearranged mtDNAs appeared early during unionid radiation, and that a duplicated and diverged atp8 gene evolved into the M-orf associated with the paternal transmission route in Hyrioidea and Unionoidea, but not in Etherioidea. We propose that novel mtDNA-encoded genes can deeply influence bivalve sex determining systems and the evolution of the mitogenomes in which they occur.

show abstract

Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia

Cited by 55 publications

References 176 publications

The complete mitochondrial genome of the grooved carpet shell,Ruditapes decussatus(Bivalvia, Veneridae)

The complete mitochondrial genome of the grooved carpet shell,Ruditapes decussatus(Bivalvia, Veneridae)

Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication

Evolution of sex-dependent mtDNA transmission in freshwater mussels (Bivalvia: Unionida)

Contact Info

Product

Resources

About