scholarly journals DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING

2021 ◽  
Author(s):  
James L Dimond ◽  
Nhung Nguyen ◽  
Steven B Roberts
Keyword(s):  
Draft Genome ◽  
Genomic Region ◽  
Nanopore Sequencing ◽  
Sea Anemones ◽  
Cpg Dinucleotides ◽  
Algal Symbiosis ◽  
Anthopleura Elegantissima ◽  
Base Modifications ◽  
Pass Through ◽  
Methylation Profiling

Abstract Symbiosis with protists is common among cnidarians such as corals and sea anemones, and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolishwhich detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.

scholarly journals DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING

2021 ◽  
Author(s):  
James L. Dimond ◽  
Nhung Nguyen ◽  
Steven B. Roberts
Keyword(s):  
Draft Genome ◽  
Genomic Region ◽  
Nanopore Sequencing ◽  
Sea Anemones ◽  
Cpg Dinucleotides ◽  
Algal Symbiosis ◽  
Anthopleura Elegantissima ◽  
Base Modifications ◽  
Pass Through ◽  
Methylation Profiling

ABSTRACTSymbiosis with protists is common among cnidarians such as corals and sea anemones, and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.

The Spermatozoon of Actinia Equina L. Var. Mesembryanthemum

1980 ◽  
Vol 60 (1) ◽  
pp. 193-204 ◽  
Author(s):  
A. U. Larkman ◽  
M. A. Carter
Keyword(s):  
Fine Structure ◽  
Sexual Reproduction ◽  
Recent Work ◽  
Developmental Stages ◽  
Early Stage ◽  
Genetic Material ◽  
Sea Anemones ◽  
Free Living ◽  
Pass Through ◽  
Parent Female

Actinia equina var. mesembryanthemum, the beadlet anemone (Stephenson, 1935), is a very common and widely distributed littoral anthozoan, whose sexual reproduction shows several interesting characteristics. Adult sea anemones of both sexes brood planulae and more advanced developmental stages within the gastrovascular cavity, although earlier embryonic stages are rarely found brooded in this way. Chia & Rostron (1970) suggest that embryos are expelled from the parent female anemone at an early stage and pass through a free-living phase before re-entering anemones of either sex for brooding. However, recent work (Cain, 1974) suggests that juvenile anemones are genetically related to the adult anemones in which they are brooded, and also the distribution of genetic material during sexual reproduction appears to be abnormal (Carter & Thorp, 1979). In an attempt to achieve a better understanding of the unusual sexual reproduction of this species, an ultrastructural investigation of gametogenesis was undertaken. This paper describes the fine structure of the spermatozoon within the testis.

scholarly journals De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration

2020 ◽  
Vol 10 (10) ◽  
pp. 3541-3548
Author(s):  
Simon Yung Wa Sin ◽  
Lily Lu ◽  
Scott V. Edwards
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Genomic Region ◽  
Plumage Coloration ◽  
Sexual Dichromatism ◽  
Effective Population ◽  
Cardinalis Cardinalis ◽  
Northern Cardinal ◽  
Genomic Studies

Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype–phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly-contiguous assembly for C. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene in C. cardinalis. Transcription factor binding motifs discovered in the unique insertion region in C. cardinalis suggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000–250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome of C. cardinalis provides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.

scholarly journals A Draft Genome of the Ginger Species Alpinia nigra and New Insights into the Genetic Basis of Flexistyly

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1297
Author(s):  
Surabhi Ranavat ◽  
Hannes Becher ◽  
Mark F. Newman ◽  
Vinita Gowda ◽  
Alex D. Twyford
Keyword(s):  
Genetic Basis ◽  
De Novo ◽  
Draft Genome ◽  
Spatial Separation ◽  
Genomic Region ◽  
Alpinia Nigra ◽  
Floral Phenotype ◽  
Temporal And Spatial ◽  
Candidate Regions ◽  
High Depth

Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a de novo assembly of the genome of Alpinia nigra using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high FST values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype.

scholarly journals Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

2021 ◽  
Author(s):  
Ulrich Technau ◽  
Sophia Robb ◽  
Grigory Genikhovich ◽  
Juan Montenegro ◽  
Witney Fropf ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Draft Genome ◽  
Gene Clusters ◽  
Sea Anemone ◽  
Gene Repertoire ◽  
Sea Anemones ◽  
Animal Evolution ◽  
Topologically Associated Domains ◽  
Genome Assemblies ◽  
Chromosome Level

Abstract Draft genome sequences of non-bilaterian species have provided important insights into the evolution of the metazoan gene repertoire. However, there is little information about the evolution of gene clusters, genome architectures and karyotypes during animal evolution. Here we report chromosome-level genome assemblies of two related anthozoan cnidarians, the sea anemones, Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence of the chromosomes between the two species. We show that, in contrast to Bilateria, Hox and NK clusters of investigated cnidarians are disintegrated, indicating that microsynteny conservation is largely lost. In line with that, we find no evidence for topologically associated domains, suggesting fundamental difference in long-range gene regulation compared to vertebrates. However, both sea anemone genomes show remarkable chromosomal conservation with other cnidarians, several bilaterians and the sponge Ephydatia muelleri, allowing us to reconstruct the putative cnidarian and metazoan chromosomes, consisting of 19 and 16 ancestral linkage groups, respectively. These data suggest that large parts of the ancestral metazoan genome have been retained in chromosomes of some extant lineages, yet, higher order gene regulation may have evolved only after the cnidarian-bilaterian split.

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