scholarly journals The gene-rich genome of the scallop Pecten maximus

GigaScience ◽  
2020 ◽  
Vol 9 (5) ◽  
Author(s):  
Nathan J Kenny ◽  
Shane A McCarthy ◽  
Olga Dudchenko ◽  
Katherine James ◽  
Emma Betteridge ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gene Annotation ◽  
Atlantic Coast ◽  
Shallow Waters ◽  
Pharmaceutical Companies ◽  
Marine Bivalve ◽  
Pecten Maximus ◽  
Assembly Sequence ◽  
Algal Toxins ◽  
Large Numbers

Abstract Background The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. Findings Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. Conclusions The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.

scholarly journals The Gene-Rich Genome of the Scallop Pecten maximus

2020 ◽  
Author(s):  
Nathan J Kenny ◽  
Shane A McCarthy ◽  
Olga Dudchenko ◽  
Katherine James ◽  
Emma Betteridge ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Atlantic Coast ◽  
Shallow Waters ◽  
Pharmaceutical Companies ◽  
Marine Bivalve ◽  
Pecten Maximus ◽  
Assembly Sequence ◽  
Algal Toxins ◽  
Large Numbers ◽  
Wide Range

AbstractBackgroundThe King Scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and its ubiquity means that it plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies and fisheries management.FindingsHere we report the genome sequencing of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10x Chromium and Hi-C data, and its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb, and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species.ConclusionsThe genome assembly of Pecten maximus and its annotated gene set provide a high-quality platform for a wide range of investigations, including studies on such disparate topics as shell biomineralization, pigmentation, vision and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known as a gene conferring resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.

Studies on the ecology of some temporary freshwater pools in Victoria with special reference to microcrustaceans

1977 ◽  
Vol 28 (4) ◽  
pp. 439 ◽  
Author(s):  
DW Morton ◽  
IAE Bayly
Keyword(s):  
High Probability ◽  
Calanoid Copepod ◽  
Shallow Waters ◽  
New Combinations ◽  
Common Occurrence ◽  
Chemical Parameters ◽  
Daphnia Carinata ◽  
Large Numbers ◽  
Three New Species ◽  
Ph Range

Fifty-three temporary freshwater pools (mean depth 23 cm) located mainly in eastern Victoria were studied from February to September 1973. Chemical parameters determined were pH (range 5.7-8.2, mean 6.9), conductivity (K18, range 55-5500, mean 340 �S/cm), dissolved oxygen (range 23-170, mean 72% saturation) and turbidity (range 2-310, mean 50 Formazin turbidity units). A total of 60 microcrustacean species was recorded. The Australasian endemic cladoceran, Saycia cooki (King), was of common occurrence from June through to August. The fact that it tends to reach peak numbers early in the life of a pool is probably related to the production of large numbers of ephippial eggs. In contrast, cladocera which produce only one or two ephippial eggs, such as Chydorus, Moina and Simocephalus, tend to appear later in succession. Simocephalus expinosus (benthic) and Daphnia carinata, s.l. (planktonic) had mutually exclusive distributions and are apparently unable to coexist in shallow waters. Endemic cyclopoid copepods encountered included three new species of Microcyclops, M. arnaudi (Sars), Acanthocyclops australis Sars, and Acanthocyclops, sp. nov. Like Saycia, Microcyclops varicans and Acanthocyclops bisetosus exhibited maximal numbers early in succession. Several new combinations of coexisting calanoid copepod species belonging to the genera Boeckella and Hemiboeckella are reported. Computer analysis showed that the following four groups of species had a high probability of co-occurrence: (1) Cypretta sp., Attheyella australica, Ilyodromus sp., Saycia cooki; (2) Cyprinotus leanus, Acanthocyclops bisetosus, Moina tenuicornis; (3) Boeckella major, B. pseudochelae, Cypris sp., Daphnia carinata, s.l. ; (4) Simocephalus exspinosus, Microcyclops varicans.

scholarly journals The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 258
Author(s):  
Konrad Lohse ◽  
Alexander Mackintosh ◽  
Roger Vila ◽  
◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Protein Coding ◽  
Individual Male ◽  
Protein Coding Genes ◽  
A Genome ◽  
Inachis Io

We present a genome assembly from an individual male Aglais io (also known as Inachis io and Nymphalis io) (the European peacock; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority (99.91%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 11,420 protein coding genes.

scholarly journals Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1359
Author(s):  
Esther Camacho ◽  
Sandra González-de la Fuente ◽  
Jose C. Solana ◽  
Alberto Rastrojo ◽  
Fernando Carrasco-Ramiro ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Leishmania Major ◽  
De Novo ◽  
Gene Annotation ◽  
Leishmania Species ◽  
De Novo Genome Assembly ◽  
Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

scholarly journals Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yaoxi He ◽  
Xin Luo ◽  
Bin Zhou ◽  
Ting Hu ◽  
Xiaoyu Meng ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Genome Assembly ◽  
De Novo ◽  
Gene Annotation ◽  
Large Body ◽  
Phenotypic Traits ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Chinese Rhesus Macaque ◽  
Long Read

Abstract We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), rheMacS increases sequence contiguity 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp). We improve gene annotation by generating more than two million full-length transcripts from ten different tissues by long-read RNA sequencing. We sequence resolve 53,916 structural variants (96% novel) and identify 17,000 ape-specific structural variants (ASSVs) based on comparison to ape genomes. Many ASSVs map within ChIP-seq predicted enhancer regions where apes and macaque show diverged enhancer activity and gene expression. We further characterize a subset that may contribute to ape- or great-ape-specific phenotypic traits, including taillessness, brain volume expansion, improved manual dexterity, and large body size. The rheMacS genome assembly serves as an ideal reference for future biomedical and evolutionary studies.

Anonyx sarsi: a major unrecognized scavenger and predator in the intertidal zone

1999 ◽  
Vol 79 (6) ◽  
pp. 1127-1128 ◽  
Author(s):  
A. Ingólfsson ◽  
I. Agnarsson
Keyword(s):  
Intertidal Zone ◽  
Shallow Waters ◽  
Large Numbers ◽  
Baited Traps ◽  
Important Predator

Anonyx sarsi (Crustacea: Amphipoda) is a widely distributed scavenger and predator in shallow waters of northern seas. It was caught, often in large numbers, in baited traps in the intertidal in Iceland, especially during mid-winter. Although hitherto only sporadically recorded from the intertidal, the species is undoubtedly among the most important carrion feeders there, and probably an important predator as well.

scholarly journals The genome sequence of the Glanville fritillary, Melitaea cinxia (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 266
Author(s):  
Roger Vila ◽  
Alex Hayward ◽  
Konrad Lohse ◽  
Charlotte Wright ◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Melitaea Cinxia ◽  
Protein Coding ◽  
Individual Male ◽  
Protein Coding Genes ◽  
A Genome

We present a genome assembly from an individual male Melitaea cinxia (the Glanville fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 499 megabases in span. The complete assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 13,666 protein coding genes.

scholarly journals A De Novo Genome Assembly, Gene Annotation, And Expression Atlas For The Monarch Butterfly Danaus plexippus

2020 ◽  
Author(s):  
José M. Ranz ◽  
Pablo M. González ◽  
Bryan D. Clifton ◽  
Nestor O. Nazario ◽  
Pablo L. Hernández-Cervantes ◽  
...  
Keyword(s):  
Life Cycle ◽  
Genome Assembly ◽  
Noncoding Rna ◽  
De Novo ◽  
Gene Annotation ◽  
Life Stage ◽  
Monarch Butterfly ◽  
Major Advance ◽  
De Novo Genome Assembly ◽  
Expression Atlas

ABSTRACTThe monarch butterfly epitomizes insect biodiversity decline. Understanding the genetic basis of the adaptation of the monarch to a changing environment requires genomic and transcriptomic resources that better reflect its genetic diversity while being informative about gene functionality during life cycle. We report a reference-quality genome assembly from an individual resident at a nonmigratory colony in Mexico, and a new gene annotation and expression atlas for 14,865 genes, including 492 unreported long noncoding RNA (lncRNA) genes, based on RNA-seq data from 14 larval and pupal stages, plus adult morphological sections. Two thirds of the genes show significant expression changes associated with a life stage or section, with lncRNAs being more finely regulated during adulthood than protein-coding genes, and male-biased expression being four times more common than female-biased. The two portions of the heterochromosome Z display distinct patterns of differential expression between the sexes, reflecting that dosage compensation is either absent or incomplete –depending on the sample– in the ancestral but not in the novel portion of the Z. This study represents a major advance in the genomic and transcriptome resources available for D. plexippus while providing the first systematic analysis of its transcriptional program across most of its life cycle.

scholarly journals The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775)

2021 ◽  
Vol 6 ◽  
pp. 304
Author(s):  
Alex Hayward ◽  
Roger Vila ◽  
Dominik R. Laetsch ◽  
Konrad Lohse ◽  
Tobias Baril ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Protein Coding ◽  
Individual Female ◽  
Protein Coding Genes ◽  
A Genome

We present a genome assembly from an individual female Melitaea athalia (also known as Mellicta athalia; the heath fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 610 megabases in span. In total, 99.98% of the assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 12,824 protein coding genes.

scholarly journals Transcript- and annotation-guided genome assembly of the European starling

2021 ◽  
Author(s):  
Katarina C. Stuart ◽  
Richard J. Edwards ◽  
Yuanyuan Cheng ◽  
Wesley C. Warren ◽  
David W. Burt ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gene Annotation ◽  
European Starling ◽  
Genomic Research ◽  
Important Species ◽  
Base Calling ◽  
Sequencing Technologies ◽  
Long Read ◽  
Full Length Transcript ◽  
Species Specific

AbstractThe European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (94.6% BUSCO completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, SAAGA) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counter-intuitive behaviour in traditional BUSCO metrics, and present BUSCOMP, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, S. vulgaris vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.

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