The draft genome of Ruditapes philippinarum (the Manila clam), a promising model system for mitochondrial biology

The Class Bivalvia is a highly successful and ancient group including 20,000+ known species. They represent a good model for studying adaptation (anoxia/hypoxia, salinity, temperature, ...), and they are useful bioindicators for monitoring the concentration of pollutants in the water. They also make up an important source of food all over the world, with a production corresponding to ~20% of the global aquaculture yield. A striking feature of bivalves is the presence of an unusual mitochondrial inheritance system: the Doubly Uniparental Inheritance (DUI), so far detected in ~100 bivalve species. In DUI species, two mitochondrial genomes (mtDNAs) are present: one is transmitted through eggs (F-type), the other through sperm (M-type); the amino acid p-distance between conspecific M and F genomes ranges from 10% to over 50%. DUI provides a unique point of view for studying mitochondrial biology. In DUI systems: i) males are naturally heteroplasmic, with very divergent mtDNAs; ii) it is possible to study mitochondrial inheritance and bottleneck by following germ line mitochondria during development; iii) mitochondria are under selection for male functions. Here we present the draft genome of the DUI species Ruditapes philippinarum (the Manila clam). DNA from a male individual was sequenced with 40x Illumina HiSeq and 30x PacBio RSII. The best de novo assembly was obtained with Canu assembler, with contig N50=76kb (86% complete, 5% fragmented, and 9% missing metazoan orthologs according to BUSCO). Here we report the results of the first analyses and the technical challenges we faced, especially with the de novo assembly.

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De Novo Assembly of the Manila Clam Ruditapes philippinarum Transcriptome Provides New Insights into Expression Bias, Mitochondrial Doubly Uniparental Inheritance and Sex Determination

Molecular Biology and Evolution ◽

10.1093/molbev/msr248 ◽

2011 ◽

Vol 29 (2) ◽

pp. 771-786 ◽

Cited By ~ 66

Author(s):

F. Ghiselli ◽

L. Milani ◽

P. L. Chang ◽

D. Hedgecock ◽

J. P. Davis ◽

...

Keyword(s):

Sex Determination ◽

De Novo Assembly ◽

De Novo ◽

Ruditapes Philippinarum ◽

Manila Clam ◽

Uniparental Inheritance ◽

Doubly Uniparental Inheritance ◽

Expression Bias

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Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach

10.1101/265157 ◽

2018 ◽

Author(s):

Sébastien Renaut ◽

Davide Guerra ◽

Walter R. Hoeh ◽

Donald T. Stewart ◽

Arthur E. Bogan ◽

...

Keyword(s):

De Novo ◽

Freshwater Mussels ◽

Draft Genome ◽

Uniparental Inheritance ◽

Ecological Value ◽

Doubly Uniparental Inheritance ◽

Total Size ◽

High Coverage ◽

Genome Coverage ◽

Eukaryotic Genes

AbstractFreshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecological value and unique “doubly uniparental inheritance” mode of mitochondrial DNA transmission of freshwater mussels. The genome described here was obtained by combining high coverage short reads (65X genome coverage of Illumina paired-end and 11X genome coverage of mate-pairs sequences) with low coverage Pacific Biosciences long reads (0.3X genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54Gb (366,926 scaffolds, N50 = 6.5Kb, with 2.3% of “N” nucleotides), representing 86% of the predicted genome size of 1.80Gb, while over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Given the repeated genetic bottlenecks of V. ellipsiformis populations as a result of glaciations events, heterozygosity was also found to be remarkably low (0.6%), in contrast to most other sequenced bivalve species. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.

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Doubly Uniparental Inheritance and beyond: The contribution of the Manila clam Ruditapes philippinarum

Journal of Zoological Systematics & Evolutionary Research ◽

10.1111/jzs.12371 ◽

2020 ◽

Vol 58 (2) ◽

pp. 529-540 ◽

Cited By ~ 4

Author(s):

Marco Passamonti ◽

Federico Plazzi

Keyword(s):

Ruditapes Philippinarum ◽

Manila Clam ◽

Uniparental Inheritance ◽

Doubly Uniparental Inheritance

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The inheritance of viable mitochondria

10.7287/peerj.preprints.3122 ◽

2017 ◽

Author(s):

Liliana Milani ◽

Fabrizio Ghiselli

Keyword(s):

Genetic Information ◽

Mitochondrial Membrane ◽

De Novo ◽

Germ Line ◽

Mitochondrial Genomes ◽

Uniparental Inheritance ◽

Oxygen Species ◽

Deleterious Mutations ◽

Mtdna Mutation ◽

Doubly Uniparental Inheritance

Mitochondria cannot be produced de novo by the cell, but are inherited across generations. Their peculiar genetics (multiple genomes per cell, no meiosis, replication independent from cell cycle, high mutation rate) and the possible exposition to Reactive Oxygen Species (ROS) are predicted to produce a fast accumulation of deleterious mutations, a phenomenon known as Müller’s ratchet. Nonetheless, mitochondrial genomes persist accurately over million years. How is a viable mitochondrial genetic information preserved? To answer this question we review the following relevant topics: 1) the sources of mtDNA mutation (replication and ROS); 2) the origin of mitochondrial membrane potential; 3) the activity of germ line mitochondria; 4) the mitochondrial bottleneck; 5) mtDNA drift and selection. Finally we discuss such topics in the light of an unusual biological system (Doubly Uniparental Inheritance of mitochondria, DUI), in which also sperm mtDNA is regularly transmitted to the progeny.

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The inheritance of viable mitochondria

10.7287/peerj.preprints.3122v1 ◽

2017 ◽

Author(s):

Liliana Milani ◽

Fabrizio Ghiselli

Keyword(s):

Genetic Information ◽

Mitochondrial Membrane ◽

De Novo ◽

Germ Line ◽

Mitochondrial Genomes ◽

Uniparental Inheritance ◽

Oxygen Species ◽

Deleterious Mutations ◽

Mtdna Mutation ◽

Doubly Uniparental Inheritance

Mitochondria cannot be produced de novo by the cell, but are inherited across generations. Their peculiar genetics (multiple genomes per cell, no meiosis, replication independent from cell cycle, high mutation rate) and the possible exposition to Reactive Oxygen Species (ROS) are predicted to produce a fast accumulation of deleterious mutations, a phenomenon known as Müller’s ratchet. Nonetheless, mitochondrial genomes persist accurately over million years. How is a viable mitochondrial genetic information preserved? To answer this question we review the following relevant topics: 1) the sources of mtDNA mutation (replication and ROS); 2) the origin of mitochondrial membrane potential; 3) the activity of germ line mitochondria; 4) the mitochondrial bottleneck; 5) mtDNA drift and selection. Finally we discuss such topics in the light of an unusual biological system (Doubly Uniparental Inheritance of mitochondria, DUI), in which also sperm mtDNA is regularly transmitted to the progeny.

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Draft genome of Bugula neritina, a colonial animal packing powerful symbionts and potential medicines

Scientific Data ◽

10.1038/s41597-020-00684-y ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Mikhail Rayko ◽

Aleksey Komissarov ◽

Jason C. Kwan ◽

Grace Lim-Fong ◽

Adelaide C. Rhodes ◽

...

Keyword(s):

De Novo ◽

Draft Genome ◽

Transcriptome Data ◽

Biomedical Sciences ◽

Bugula Neritina ◽

Genome Sequences ◽

Illumina Hiseq ◽

Draft Assembly ◽

Metazoan Genome ◽

Animal Phyla

Abstract Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum Bryozoa). Interest in this species spans ecology and biomedical sciences because B. neritina is the natural source of bioactive compounds called bryostatins. Here we present a draft assembly of the B. neritina genome obtained from PacBio and Illumina HiSeq data, as well as genes and proteins predicted de novo and verified using transcriptome data, along with the functional annotation. These sequences will permit a better understanding of host-symbiont interactions at the genomic level, and also contribute additional phylogenomic markers to evaluate Lophophorate or Lophotrochozoa phylogenetic relationships. The effort also fits well with plans to ultimately sequence all orders of the Metazoa.

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Sex-Linked Mitochondrial Behavior During Early Embryo Development in Ruditapes philippinarum (Bivalvia Veneridae) a Species with the Doubly Uniparental Inheritance (DUI) of Mitochondria

Journal of Experimental Zoology Part B Molecular and Developmental Evolution ◽

10.1002/jez.b.22004 ◽

2012 ◽

Vol 318 (3) ◽

pp. 182-189 ◽

Cited By ~ 27

Author(s):

LILIANA MILANI ◽

FABRIZIO GHISELLI ◽

MARCO PASSAMONTI

Keyword(s):

Embryo Development ◽

Early Embryo ◽

Ruditapes Philippinarum ◽

Uniparental Inheritance ◽

Doubly Uniparental Inheritance ◽

Early Embryo Development

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Draft genome of the Reindeer (Rangifer tarandus)

10.1101/154724 ◽

2017 ◽

Author(s):

Zhipeng Li ◽

Zeshan Lin ◽

Lei Chen ◽

Hengxing Ba ◽

Yongzhi Yang ◽

...

Keyword(s):

Rangifer Tarandus ◽

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Repetitive Sequences ◽

Draft Genome ◽

Divergence Time ◽

Capra Hircus ◽

High Quality ◽

Illumina Hiseq

AbstractBackgroundReindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovids’ milk. A high quality reference genome of this specie will assist efforts to elucidate these and other important features in the reindeer.FindingsWe obtained 723.2 Gb (Gigabase) of raw reads by an Illumina Hiseq 4000 platform, and a 2.64 Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21,555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1,339 snRNA and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus, and ancestors of Bos taurus and Capra hircus, is estimated to be 29.55 million years ago (Mya).ConclusionsOur results provide the first high-quality reference genome for the reindeer, and a valuable resource for studying evolution, domestication and other unusual characteristics of the reindeer.

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