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.

scholarly journals Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

2020 ◽  
Author(s):  
Bob Zimmermann ◽  
Sofia M.C. Robb ◽  
Grigory Genikhovich ◽  
Whitney J. Fropf ◽  
Lukas Weilguny ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Sister Group ◽  
Sea Anemone ◽  
Cambrian Explosion ◽  
Sea Anemones ◽  
Chromosome Conformation ◽  
Topologically Associated Domains ◽  
Long Read ◽  
Evolving Model ◽  
Conserved Noncoding Elements

AbstractCnidaria (sea anemones, jellyfish, corals and hydra) form a close sister group to Bilateria. Within this clade, the sea anemone Nematostella vectensis has emerged as a slow evolving model for investigating characteristics of the cnidarian-bilaterian common ancestor, which diverged near the Cambrian explosion. Here, using long read sequencing and high throughput chromosome conformation capture, we generate high quality chromosome-level genome assemblies for N. vectensis and the closely related edwardsiid sea anemone, Scolanthus callimorphus. In both cases we find a robust set of 15 chromosomes comprising a stable linkage group detectable within all major clades of sequenced cnidarian genomes. Further, both genomes show remarkable chromosomal conservation with chordates. In contrast with Bilateria, we report that extended Hox and NK gene clusters are chromosomally linked but do not retain a tight spatial conservation. Accordingly, there is a lack of evidence for topologically associated domains, which have been implicated in the evolutionary pressure to retain tight microsyntenic gene clusters. We also uncover ultra-conserved noncoding elements at levels previously undetected in non-chordate lineages. Both genomes are accessible through an actively updated genome browser and database at https://simrbase.stowers.org

scholarly journals Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1336
Author(s):  
Azamat Totikov ◽  
Andrey Tomarovsky ◽  
Dmitry Prokopov ◽  
Aliya Yakupova ◽  
Tatiana Bulyonkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Biology ◽  
Threatened Species ◽  
Mammalian Species ◽  
Draft Genome ◽  
Chromosome Length ◽  
Chromosome Conformation ◽  
Genome Wide ◽  
Genome Assemblies ◽  
Chromosome Level

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

scholarly journals Chromosome-Level Genome Assemblies: Expanded Capabilities for Conservation Biology Research

Proceedings ◽  
2020 ◽  
Vol 76 (1) ◽  
pp. 10
Author(s):  
Azamat Totikov ◽  
Andrey Tomarovsky ◽  
Lorena Derezanin ◽  
Olga Dudchenko ◽  
Erez Lieberman-Aiden ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
Conservation Biology ◽  
Threatened Species ◽  
Draft Genome ◽  
Chromosome Conformation ◽  
Genome Wide ◽  
Genome Assemblies ◽  
Biology Research ◽  
Chromosome Level

Genome assemblies are becoming increasingly important for understanding genetic diversity in threatened species. However, due to limited budgets in the area of conservation biology, genome assemblies, when available, tend to be highly fragmented with tens of thousands of scaffolds. The recent advent of high throughput chromosome conformation capture (Hi-C) makes it possible to generate more contiguous assemblies containing scaffolds that are length of entire chromosomes. Such assemblies greatly facilitate analyses and visualization of genome-wide features. We compared genetic diversity in seven threatened species that had both draft genome assemblies and newer chromosome-level assemblies available. Chromosome-level assemblies allowed better estimation of genetic diversity, localization, and, especially, visualization of low heterozygosity regions in the genomes.

scholarly journals A chromosome-level genome of Antechinus flavipes provides a reference for an Australasian marsupial genus with suicidal reproduction

2021 ◽  
Author(s):  
Ran Tian ◽  
Kai Han ◽  
Yuepan Geng ◽  
Chen Yang ◽  
Patrick Thomas ◽  
...  
Keyword(s):  
Life History ◽  
Breeding Season ◽  
Dna Sequences ◽  
Draft Genome ◽  
Life History Strategy ◽  
Demographic Analysis ◽  
Genome Draft ◽  
Genome Assemblies ◽  
Chromosome Level ◽  
Isolated Species

The 15 species of small carnivorous marsupials that comprise the genus Antechinus exhibit semelparity, a rare life-history strategy where death occurs after one breeding season. Antechinus males, but not females, age rapidly (demonstrate organismal senescence) during the breeding season and show promise as new animal models of ageing. Some antechinus species are also threatened or endangered. Here, we report chromosome-level genomes of the yellow-footed antechinus Antechinus flavipes. The genome assembly has a total length of 3.2 Gb with a contig N50 of 51.8 Mb and a scaffold N50 of 636.7 Mb. We anchored and oriented 99.7% of the assembly on seven pseudochromosomes and found that repetitive DNA sequences occupy 51.8% of the genome. Draft genome assemblies of three related species in the subfamily Phascogalinae, two additional antechinus species (A. argentus and A. arktos) and the iteroparous sister species Murexia melanurus were also generated. Preliminary demographic analysis supports the hypothesis that climate change during the Pleistocene isolated species in Phascogalinae and shaped their population size. A transcriptomic profile across the A. flavipes breeding season allowed us to identify genes associated with aspects of the male die-off. The chromosome-level A. flavipes genome provides a steppingstone to understanding an enigmatic life-history strategy and a resource to assist the conservation of antechinuses.

scholarly journals Identification of the conserved long non-coding RNAs in myogenesis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anupam Bhattacharya ◽  
Simang Champramary ◽  
Tanya Tripathi ◽  
Debajit Thakur ◽  
Ilya Ioshikhes ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Muscle Development ◽  
Three Dimensional ◽  
C2c12 Cells ◽  
Mouse Muscle ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Topologically Associated Domains

Abstract Background Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Therefore, we propose a novel approach to identify conserved lncRNAs and functionally annotate these molecules. Results In this study, we exploited existing myogenic transcriptome data and identified conserved lncRNAs in mice and humans. We identified the lncRNAs expressing differentially between the early and later stages of muscle development. Differential expression of these lncRNAs was confirmed experimentally in cultured mouse muscle C2C12 cells. We utilized the three-dimensional architecture of the genome and identified topologically associated domains for these lncRNAs. Additionally, we correlated the expression of genes in domains for functional annotation of these trans-lncRNAs in myogenesis. Using this approach, we identified conserved lncRNAs in myogenesis and functionally annotated them. Conclusions With this novel approach, we identified the conserved lncRNAs in myogenesis in humans and mice and functionally annotated them. The method identified a large number of lncRNAs are involved in myogenesis. Further studies are required to investigate the reason for the conservation of the lncRNAs in human and mouse while their sequences are dissimilar. Our approach can be used to identify novel lncRNAs conserved in different species and functionally annotated them.

scholarly journals Draft Genome Sequences of Fungus Aspergillus calidoustus

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Fabian Horn ◽  
Jörg Linde ◽  
Derek J. Mattern ◽  
Grit Walther ◽  
Reinhard Guthke ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Sequence ◽  
Functional Annotation ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Genome Sequences

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504) . The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

Gametogenesis and the reproductive cycle in the deep-sea anemone Paracalliactis stephensoni (Cnidaria: Actiniaria)

1990 ◽  
Vol 70 (1) ◽  
pp. 163-172 ◽  
Author(s):  
Michel Praet-Van
Keyword(s):  
Organic Matter ◽  
Shallow Water ◽  
Deep Sea ◽  
Phytoplankton Bloom ◽  
Sea Anemone ◽  
Bay Of Biscay ◽  
Sea Anemones ◽  
Spring Phytoplankton Bloom ◽  
Sea Floor ◽  
Ultrastructural Investigation

This ultrastructural investigation of gametogenesis in a deep-sea anemone of the Bay of Biscay trawled around 2000 m depth, contributes to the knowledge of biology and strategy of reproduction of deep-sea benthos.This sea anemone is dioecious. The sperm appears very similar to those of shallow water sea anemones of the genus, Calliactis. The ultrastructural investigation of oogenesis allows the characteristics of the stages of previtellogenesis and vitellogenesis to be defined. The latter begins with a period of lipogenesis correlated with the formation of a trophonema. Mature oocytes measure up to 180 (im in diameter. Study of spermatogenesis and oogenesis reveals that spawning occurs in April/May. In males, the main area of testicular cysts, full of sperm, reaches maximal development from March to May and, in females, the percentage of mature oocytes decreases from 33% in April to 1% in May.Spawning may be induced by the advent in the deep-sea of the products of the spring phytoplankton bloom. This period of spawning, during the increased deposition of organic matter to the deep-sea floor, may be an advantageous strategy for early development of Paracalliactis.

scholarly journals Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher Alan Smith
Keyword(s):  
Evolutionary History ◽  
Lentinula Edodes ◽  
Reference Genome ◽  
Genomic Change ◽  
Diverse Species ◽  
The World ◽  
Cultivated Mushroom ◽  
Genome Assemblies ◽  
High Degree ◽  
Chromosome Level

AbstractThe basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

The Behaviour and Neuromuscular System of Gonactinia Prolifera, A Swimming Sea-Anemone

1971 ◽  
Vol 55 (3) ◽  
pp. 611-640
Author(s):  
ELAINE A. ROBSON
Keyword(s):  
Electrical Stimulation ◽  
Mechanical Stimulation ◽  
Motor Units ◽  
Nerve Cells ◽  
Sea Anemone ◽  
Neuromuscular System ◽  
Sea Anemones ◽  
Nerve Net ◽  
Local Contraction ◽  
Electric Shocks

1. In Gonactinia well-developed ectodermal muscle and nerve-net extend over the column and crown and play an important part in the anemone's behaviour. 2. Common sequences of behaviour are described. Feeding is a series of reflex contractions of different muscles by means of which plankton is caught and swallowed. Walking, in the form of brief looping steps, differs markedly in that it continues after interruptions. Anemones also swim with rapid tentacle strokes after contact with certain nudibranch molluscs, strong mechanical disturbance or electrical stimulation. 3. Swimming is attributed to temporary excitation of a diffuse ectodermal pacemaker possibly situated in the upper column. 4. From the results of electrical and mechanical stimulation it is concluded that the endodermal neuromuscular system resembles that of other anemones but that the properties of the ectodermal neuromuscular system require a new explanation. The size and spread of responses to electric shocks vary with intensity, latency is variable and there is a tendency to after-discharge. There is precise radial localization, for example touching a tentacle or the column causes it to bend towards or away from the stimulus. 5. A model to explain these and other features includes multipolar nerve cells closely linked to the nerve-net which would act as intermediate motor units, causing local contraction of the ectodermal muscle. This scheme can be applied to other swimming anemones but there is no evidence that it holds for sea anemones generally.

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