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 (gVolante BUSCO stats: complete 85.79%, partial 4.6%, missing 9.61%). Here we report the results of the first analyses and the technical challenges we faced, especially in de novo assembly

The Draft Genome of Ruditapes philippinarum (the Manila clam)

<p>Bivalve molluscs are a highly successful and ancient Class, including over 20,000 known species, and they are an interesting group for evolutionary and biodiversity studies. Bivalves represent a good model for studying adaptation to anoxia/hypoxia, salinity, and temperature, and they are useful bioindicators for monitoring the concentration of pollutants and heavy metals 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; clams are first in production, followed by oysters, mussels, and scallops. A striking feature of bivalves—and the main reason behind this project—is the presence of an unusual mitochondrial inheritance system: the Doubly Uniparental Inheritance (DUI), so far detected in ~50 bivalve species, belonging to seven families. In DUI species, two mitochondrial genomes (mtDNAs) are present: one is transmitted through eggs (F-type, for female-inherited), the other through sperm (M-type, for male-inherited), and the amino acid p-distance between conspecific M and F genomes ranges from 10% to over 50%. DUI provides a unique and privileged point of view for studying several fundamental aspects of eukaryote biology. In DUI systems: i) males are naturally heteroplasmic, with two very divergent mtDNAs; ii) it is possible to follow germ line mitochondria during development (to study mitochondrial inheritance and bottleneck); iii) mitochondria are under selection for male functions (e.g.: spermatogenesis, sperm swimming); iv) there are two coexisting mitochondrial genomes in the same nuclear background (coevolution, conflicts). All these interesting biological features are in sharp contrast with the lack of genomic resources about bivalve molluscs.</p>Here we present the draft genome of the DUI species Ruditapes philippinarum (the Manila clam). DNA from a male individual was sequenced with x40 Illumina HiSeq and with x30 PacBio RSII. We have tried to assembly this dataset with all available hybrid or PacBio only assembly pipelines. The best results were obtained with PacBio reads assembled by Canu assembler with contig N50 76 kb, and 39.92% completed and 74.60% partial genes according to CEGMA. We annotated families of tandem and dispersed repeats, we found a new highly repeated dispersed element, and characterised the major families of satellite DNA. We report the results of the first analyses as well as the technical challenges we faced, especially during the phase of de novo assembly

Mitogenomic sequences support a north–south subspecies subdivision within <i>Solenodon paradoxus</i>

<p>Solenodons are insectivores found only in Hispaniola and Cuba, with a Mesozoic divergence date versus extant mainland mammals. Solenodons are the oldest lineage of living eutherian mammal for which a mitogenome sequence has not been reported. We determined complete mitogenome sequences for six Hispaniolan solenodons (<i>Solenodon paradoxus</i>) using next-generation sequencing. The solenodon mitogenomes were 16,454–16,457 bp long and carried the expected repertoire of genes. A mitogenomic phylogeny confirmed the basal position of solenodons relative to shrews and moles, with solenodon mitogenomes estimated to have diverged from those of other mammals ca. 78 Mya. Control region sequences of solenodons from the northern (<i>n</i> = 3) and southern (<i>n</i> = 5) Dominican Republic grouped separately in a network, with <i>F</i>_ST = 0.72 (<i>p</i> = 0.036) between north and south. This regional genetic divergence supports previous morphological and genetic reports recognizing northern (<i>S. p. paradoxus</i>) and southern (<i>S. p. woodi</i>) subspecies in need of separate conservation plans.</p

Additional file 3 of Genomic legacy of the African cheetah, Acinonyx jubatus

Supplemental datasheets. Datasheet S1. List of cheetah-specific de novo predicted genes with functional domains annotated by InterPro scan. Datasheet S2. List of gene families in eight mammal species identified by protein homology. Datasheet S3. Results of gene family expansion and contraction analysis. Datasheet S4. CAFE results from gene family contraction and expansion analysis. Datasheet S5. Results of gene selection analysis. Datasheet S6. Reproductive system genes with damaging mutations. Datasheet S7. Segmental duplication genes. Datasheet S8. List of reproductive genes with segregated high effect mutations and corresponding genotypes of cheetah. (XLSX 711 kb

Additional file 2 of Genomic legacy of the African cheetah, Acinonyx jubatus

Supplemental tables. Table S1. Sequenced cheetah reads for de novo genome assembly. Table S2. Re-sequenced cheetah reads for population analyses. Table S3. Estimated cheetah genome size. Table S4. Cheetah genome assembly information. Table S5. Reference-assisted assembly of cheetah chromosomes. Table S6. RepeatMasker results for transposable elements in carnivore genomes. Table S7. Total length of repeat regions in cheetah. Table S8. Tandem repeats in five carnivore genomes. Table S9. Complex tandem repeat families. Table S10. Protein-coding gene annotation. Table S11. Non-coding RNA annotation. Table S12. Nuclear mitochondrial genes. Table S13. Lengths of cheetah synteny blocks. Table S14. Cheetah rearrangements. Table S15. Called SNV statistics. Table S16. SNV effects by impact. Table S17. SNV effects by functional class. Table S18. SNV effects by genomic region. Table S19. SNV locations relative to genes. Table S20. SNV distribution in cheetah genome. Table S21. SNV distribution in tiger genomes. Table S22. SNV locations and effects in coding genes of Felidae genomes. Table S23. SNV counts in genes in domestic cat and tigers. Table S24. SNV counts in genes in cheetahs. Table S25. Nucleotide diversity in mitochondrial genomes of mammals. Table S26. Nucleotide diversity in MHC class I and II genes. Table S27. Demographic models and their log-likelihood values. Table S28. Population data by DaDi. Table S29. Reproductive system genes with identified function. Table S30. Filtration of cheetah reproduction system genes. Table S31. Nucleotide diversity of masked assemblies. Table S32. Statistics on autosomal segmental duplications. (PDF 127 kb

Fluorescence <i>in situ</i> hybridization revealed the localization of tandem repeats in centromeric/pericentromeric regions of the Asian seabass genome and characterization of B chromosomes.

<p>Labeled painting B chromosomes and tandem repeat probes were hybridized to metaphase chromosomes. The chromosomal position of three tandem repeats (green): (A) Sat_LM- centromeres; (B) Lca_217 and Lca_38 (C) pericentromeric region. (D) B chromosome-derived probes, ChB5 (green) and ChB6 (red), reveal the presence of a B chromosome in the <i>L</i>. <i>calcarifer</i> karyotype, as indicated by arrowhead. Chromosomes were counterstained with DAPI (blue). Bar is 10 μm for all images. (E) Association of B chromosomes with the linkage groups. Each linkage group is represented in coloured blocks, and the shadings delineate the genome superscaffolds (after optical mapping) that were assigned to the given linkage group. Rearrangements of portions from the four linkage groups, namely LG5, LG9, LG17 and LG19, together with regions without linkage group assignment (U) comprised the B chromosome.</p

<i>Lates calcarifer</i> has the best metrics from among the assembled fish genomes till date.

<p>The <i>L</i>. <i>calcarifer</i> genome contig N50 and scaffold N50 values were compared to the following fish genomes: <i>Anguilla japonica</i>, <i>Astatotilapia burtoni</i>, <i>Astyanax mexicanus</i>, <i>Boleophthalmus pectinirostris</i>, <i>Ctenopharyngodon idellus</i>, <i>Cynoglossus semilaevis</i>, <i>Cyprinus carpio</i>, <i>Danio rerio</i>, <i>Dicentrarchus labrax</i>, <i>Electrophorus electricus</i>, <i>Esox lucius</i>, <i>Gadus morhua</i>, <i>Gasterosteus aculeatus</i>, <i>Larimichthys crocea</i>, <i>Latimeria chalumnae</i>, <i>Metriaclima zebra</i>, <i>Neolamprologus brichardi</i>, <i>Notothenia coriiceps</i>, <i>Oncorhynchus mykiss</i>, <i>Oreochromis niloticus</i>, <i>Oryzias latipes</i>, <i>Pundamilia nyererei</i>, <i>Periophthalmodon schlosseri</i>, <i>Periophthalmus magnuspinnatus</i>, <i>Salmo salar</i>, <i>Scartelaos histophorus</i>, <i>Takifugu flavidus</i>, <i>Takifugu rubripes</i>, <i>Tetraodon nigroviridis</i>, <i>Thunnus orientalis</i>, and <i>Xiphophorus maculatus</i> (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005954#pgen.1005954.s002" target="_blank">S1 Table</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005954#pgen.1005954.s003" target="_blank">S2 Fig</a> for more details).</p

Survey of the <i>L</i>. <i>calcarifer</i> genome assembly identified long stretches of TRs lacking in the short read-based assembly and a continuous assembled telomeric region identified at the end of LG3.

<p>(A) Stretches of TRs were virtually missing from the <i>L</i>. <i>calcarifer</i> short read assembly (SRA) generated using 80X Illumina reads scaffolded with ~11,000 BAC ends (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005954#pgen.1005954.s016" target="_blank">S1 Table</a>) whereas the long read assembly (LRA) had a good representation of TRs (upper panel) and the different repeats were more fragmented in the SRA <i>vis-à-vis</i> the LRA (lower panel). (B) Arrangement of telomere monomer sequence (TTAGGG) on a single assembled contig, (unitig_1659; ~0.5 Mb) placed at the terminal end of LG3 (region indicated in orange). Every occurrence of the monomer is indicated by green bars. A highly dense region of (TTAGGG)n was observed between 455.5–466.9 kb, containing the monomer repeated in tandem 1,655 times. The region upstream to this dense region had short dispersed stretches of (TTAGGG)n and contained eight predicted genes (indicated by blue boxes).</p

Scaffolding using optical map, genetic map and synteny with closely related fish genomes produced chromosome-level assembly of the Asian seabass genome.

<p>(A) Comparison of <i>L</i>. <i>calcarifer</i> to two closely related fish species (<i>G</i>. <i>aculeatus</i>, and <i>D</i>. <i>labrax</i>) at the genome-wide level. Colours used for depicting assembled chromosomes are random for each of the three genomes. Different colours in a single <i>L</i>. <i>calcarifer</i> linkage group are used to represent the inter-chromosomal rearrangements. Black arcs show collinear blocks that are intra-chromosomally rearranged between the species. (B) Genome assembly (middle panel) shown anchored to two (LG15 and LG18) of the twenty four <i>L</i>. <i>calcarifer</i> linkage groups while the right panel represents the scaffolded assembly (regions in grey depict the additional contigs brought together by scaffolding).</p

Annotation statistics of the Asian seabass genome.

<p>Annotation statistics of the Asian seabass genome.</p