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

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.

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

2017 ◽  
Author(s):  
Fabrizio Ghiselli ◽  
Aleksey Komissarov ◽  
Liliana Milani ◽  
Joseph P Dunham ◽  
Sophie Breton ◽  
...  
Keyword(s):  
De Novo ◽  
Germ Line ◽  
Draft Genome ◽  
Ruditapes Philippinarum ◽  
Manila Clam ◽  
Uniparental Inheritance ◽  
Mitochondrial Inheritance ◽  
Doubly Uniparental Inheritance ◽  
Illumina Hiseq ◽  
Inheritance System

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.

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

2017 ◽  
Author(s):  
Fabrizio Ghiselli ◽  
Aleksey Komissarov ◽  
Liliana Milani ◽  
Joseph P Dunham ◽  
Sophie Breton ◽  
...  
Keyword(s):  
De Novo ◽  
Germ Line ◽  
Draft Genome ◽  
Ruditapes Philippinarum ◽  
Manila Clam ◽  
Uniparental Inheritance ◽  
Mitochondrial Inheritance ◽  
Doubly Uniparental Inheritance ◽  
Illumina Hiseq ◽  
Inheritance System

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.

A proposed method for analyzing molecular signatures to detect hermaphroditism in freshwater mussels: a case study using the Eastern Floater (Pyganodon cataracta)

2021 ◽  
Author(s):  
Donald T. Stewart ◽  
Chloe M. Stephenson ◽  
Ljiljana M. Stanton ◽  
Emily E. Chase ◽  
Brent M. Robicheau ◽  
...  
Keyword(s):  
Freshwater Mussels ◽  
Uniparental Inheritance ◽  
Molecular Signatures ◽  
Doubly Uniparental Inheritance ◽  
Hydrophobic Properties ◽  
Mt Dna ◽  
Reading Frame ◽  
Mt Genome ◽  
Primary Nucleotide Sequence

Many freshwater mussels (Order Unionida) have an unusual system of doubly uniparental inheritance (DUI) of mitochondrial (mt) DNA. In species with DUI, males possess a female-transmitted (F-type) mt genome and a male-transmitted (M-type) mt genome. These genomes contain non-canonical open reading frame (orf) genes referred to as f-orf and m-orf, present in F and M mt genomes, respectively. These genes have been implicated in sexual development in Unionida. When gonochoric species become hermaphroditic, which has happened several times in Unionida, they lose their M-type mt genome, and f-orf genes evolve dramatically. Resulting F-ORF proteins are highly divergent in terms of primary nucleotide sequence, inferred amino acids, and hydrophobic properties; these genes (and proteins) are referred to as hermaphroditic orfs or h-orfs (and H-ORFs). We investigated patterns of hydrophobicity divergence for H-ORF proteins in hermaphrodites versus F-ORF proteins in closely related gonochoric species against cytochrome c oxidase subunit 1 (cox1) divergences. This approach was used to assess whether cryptic hermaphrodites can be detected. Although we did not detect evidence for the recent transition of any populations of Eastern Floaters, Pyganodon cataracta (Say, 1817) to hermaphroditism, our analyses demonstrate that molecular signatures in mtDNA can be used to detect hermaphroditism in freshwater mussels.

scholarly journals The draft nuclear genome assembly of Eucalyptus pauciflora: new approaches to comparing de novo assemblies

2019 ◽  
Author(s):  
Weiwen Wang ◽  
Ashutosh Das ◽  
David Kainer ◽  
Miriam Schalamun ◽  
Alejandro Morales-Suarez ◽  
...  
Keyword(s):  
Error Rate ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Nuclear Genome ◽  
Single Species ◽  
Test Case ◽  
High Coverage ◽  
Validation Set

AbstractBackgroundSelecting the best genome assembly from a collection of draft assemblies for the same species remains a difficult task. Here, we combine new and existing approaches to help to address this, using the non-model plant Eucalyptus pauciflora (snow gum) as a test case. Eucalyptus pauciflora is a long-lived tree with high economic and ecological importance. Currently, little genomic information for Eucalyptus pauciflora is available.FindingsWe generated high coverage of long-(Nanopore, 174x) and short-(Illumina, 228x) read data from a single Eucalyptus pauciflora individual and compared assemblies from four assemblers with a variety of settings: Canu, Flye, Marvel, and MaSuRCA. A key component of our approach is to keep a randomly selected collection of ~10% of both long- and short-reads separate from the assemblies to use as a validation set with which to assess the assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in eight ways: contig N50, BUSCO scores, LAI scores, assembly ploidy, base-level error rate, computing genome assembly likelihoods, structural variation and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ~0.006 errors per base.ConclusionsWe report a draft genome of Eucalyptus pauciflora, which will be a valuable resource for further genomic studies of eucalypts. These approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies for a single species.

scholarly journals A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9114 ◽  
Author(s):  
Jiawei Wang ◽  
Weizhen Liu ◽  
Dongzi Zhu ◽  
Xiang Zhou ◽  
Po Hong ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Reference Genome ◽  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
High Quality ◽  
Eukaryotic Genes

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

scholarly journals Evaluating the utility of the female-specific mitochondrialf-orfgene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5007 ◽  
Author(s):  
Brent M. Robicheau ◽  
Emily E. Chase ◽  
Walter R. Hoeh ◽  
John L. Harris ◽  
Donald T. Stewart ◽  
...  
Keyword(s):  
Population Genetic ◽  
Freshwater Mussels ◽  
Mitochondrial Protein ◽  
Species Level ◽  
Uniparental Inheritance ◽  
Genome Sequences ◽  
Doubly Uniparental Inheritance ◽  
Protein Coding ◽  
Coding Regions ◽  
Female Specific

Freshwater mussels (order: Unionida) represent one of the most critically imperilled groups of animals; consequently, there exists a need to establish a variety of molecular markers for population genetics and systematic studies in this group. Recently, two novel mitochondrial protein-coding genes were described in unionoids with doubly uniparental inheritance of mtDNA. These genes are thef-orfin female-transmitted mtDNA and them-orfin male-transmitted mtDNA. In this study, whole F-type mitochondrial genome sequences of two morphologically similarLampsilisspp. were compared to identify the most divergent protein-coding regions, including thef-orfgene, and evaluate its utility for population genetic and phylogeographic studies in the subfamily Ambleminae. We also tested whether thef-orfgene is phylogenetically informative at the species level. Our preliminary results indicated that thef-orfgene could represent a viable molecular marker for population- and species-level studies in freshwater mussels.

scholarly journals Refinement of Draft Genome Assemblies of Pigeonpea (Cajanus cajan)

2020 ◽  
Author(s):  
Soma Marla ◽  
Pallavi Mishra ◽  
Ranjeet Maurya ◽  
Mohar Singh ◽  
D. P. Wankhede ◽  
...  
Keyword(s):  
Cajanus Cajan ◽  
De Novo ◽  
Draft Genome ◽  
Data Sets ◽  
Segmental Duplications ◽  
Genome Coverage ◽  
Plant Genomes ◽  
Original Genome ◽  
Specific Trait ◽  
Important Quality

AbstractGenome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in Next Generation sequencing. Of late multiple draft assemblies of plant genomes are reported in many organisms. The draft assemblies of Cajanus cajan are with different levels of genome completeness; contain large number of repeats, gaps and segmental duplications. Draft assemblies with portions of genome missing, are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and prediction of gene component as desired by crop researchers. Genome coverage i.e. number of sequenced raw reads mapped on to certain locations of the genome is an important quality indicator of completeness and assembly quality in draft assemblies. Present work was aimed at improvement of coverage in reported de novo sequenced draft genomes (GCA_000340665.1 and GCA_000230855.2) of Pigeonpea, a legume widely cultivated in India. The two assemblies comprised 72% and 75% of estimated coverage of genome respectively. We employed assembly reconciliation approach to compare draft assemblies and merged them to generate a high quality near complete assembly with enhanced contiguity. Finished assembly has reduced number of gaps than reported in draft assemblies and improved genome coverage of 82.4%. Quality of the finished assembly was evaluated using various quality metrics and for presence of specific trait related functional genes. Employed pair-end and mate-pair local library data sets enabled to resolve gaps, repeats and other sequence errors yielding lengthier scaffolds compared to two draft assemblies. We report prediction of putative host resistance genes from improved sequence against Fusarium wilt disease and evaluated them in both wet laboratory and field phenotypic conditions.

scholarly journals Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Davide Guerra ◽  
Manuel Lopes-Lima ◽  
Elsa Froufe ◽  
Han Ming Gan ◽  
Paz Ondina ◽  
...  
Keyword(s):  
Freshwater Mussels ◽  
Complete Mitochondrial Genome ◽  
Physiological Role ◽  
Freshwater Mussel ◽  
Single Species ◽  
Open Reading Frames ◽  
Uniparental Inheritance ◽  
Doubly Uniparental Inheritance ◽  
Sexual Systems ◽  
Mitogenome Sequence

Abstract Background Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly uniparental inheritance (DUI) of mitochondria. DUI is a system in which distinct female-transmitted and male-transmitted mitotypes coexist in a single species. In families Unionidae and Margaritiferidae, the transition from dioecy to hermaphroditism and the loss of DUI appear to be linked, and this event seems to affect the integrity of the ORFan genes. These observations led to the hypothesis that the ORFans have a role in DUI and/or sex determination. Complete mitochondrial genome sequences are however scarce for most families of freshwater mussels, therefore hindering a clear localization of DUI in the various lineages and a comprehensive understanding of the influence of the ORFans on DUI and sexual systems. Therefore, we sequenced and characterized eleven new mitogenomes from poorly sampled freshwater mussel families to gather information on the evolution and variability of the ORFan genes and their protein products. Results We obtained ten complete plus one almost complete mitogenome sequence from ten representative species (gonochoric and hermaphroditic) of families Margaritiferidae, Hyriidae, Mulleriidae, and Iridinidae. ORFan genes are present only in DUI species from Margaritiferidae and Hyriidae, while non-DUI species from Hyriidae, Iridinidae, and Mulleriidae lack them completely, independently of their sexual system. Comparisons among the proteins translated from the newly characterized ORFans and already known ones provide evidence of conserved structures, as well as family-specific features. Conclusions The ORFan proteins show a comparable organization of secondary structures among different families of freshwater mussels, which supports a conserved physiological role, but also have distinctive family-specific features. Given this latter observation and the fact that the ORFans can be either highly mutated or completely absent in species that secondarily lost DUI depending on their respective family, we hypothesize that some aspects of the connection among ORFans, sexual systems, and DUI may differ in the various lineages of unionids.

scholarly journals The draft genome sequence of Eucalyptus polybractea based on hybrid assembly with short- and long-reads reads

2021 ◽  
Author(s):  
Teng Li ◽  
David Kainer ◽  
William J Foley ◽  
Allen Rodrigo ◽  
Carsten Kuelheim
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Draft Genome ◽  
Hybrid Assembly ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Genome Coverage ◽  
Protein Coding Genes ◽  
Long Reads ◽  
Long Read

Eucalyptus polybractea is a small, multi-stemmed tree, which is widely cultivated in Australia for the production of Eucalyptus oil. We report the hybrid assembly of the E. polybractea genome utilizing both short- and long-read technology. We generated 44 Gb of Illumina HiSeq short reads and 8 Gb of Nanopore long reads, representing approximately 83 and 15 times genome coverage, respectively. The hybrid-assembled genome, after polishing, contained 24,864 scaffolds with an accumulated length of 523 Mb (N50 = 40.3 kb; BUSCO-calculated genome completeness of 94.3%). The genome contained 35,385 predicted protein-coding genes detected by combining homology-based and de novo approaches. We have provided the first assembled genome based on hybrid sequences from the highly diverse Eucalyptus subgenus Symphyomyrtus, and revealed the value of including long-reads from Nanopore technology for enhancing the contiguity of the assembled genome, as well as for improving its completeness. We anticipate that the E. polybractea genome will be an invaluable resource supporting a range of studies in genetics, population genomics and evolution of related species in Eucalyptus.

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