Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses

Davidson, Phillip L.; Guo, Hao; Wang, Lingyu; Berrío, Alejandro; Zhang, He; Chang, Yue; Soborowski, Andrew; McClay, David R.; Fan, Guangyi; Wray, Gregory A.

doi:10.1093/gbe/evaa101

Cited by 64 publications

(64 citation statements)

References 33 publications

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“…In this study, a large number of genome fragments were obtained for M. nudus by using GBS. By analyzing the DNA base composition, the percentage of GC content was up to 41%, which was higher than that of the reported sea urchin, including Strongylocentrotus purpuratus (36.9%) ( Sodergren et al, 2006 ), and Lytechinus variegatus (36.1%) ( Davidson et al, 2020 ). Considering that genomic GC content is closely associated with genome size and significantly affects the genome functioning and species ecology ( Šmarda et al, 2014 ), this result suggested that M. nudus may have a more complex genome than S. purpuratus and L. variegatus .…”

Section: Discussioncontrasting

confidence: 57%

Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas

et al. 2021

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Mesocentrotus nudus is an important commercially aquatic species because of its high edible and medicinal values. However, wild stocks have dramatically decreased in recent decades. Understanding the population structure and genetic diversity can provide vital information for genetic conservation and improvement. In the present study, the genotyping-by-sequencing (GBS) approach was adopted to identify the genome-wide single-nucleotide polymorphisms (SNPs) from a collection of 80 individuals consisting of five geographical populations (16 individuals from each population), covering the natural habitats of M. nudus in China seas. An average of 0.96-Gb clean reads per sample were sequenced, and a total of 51,738 biallelic SNPs were identified. Based on these SNPs, diversity index analysis showed that all populations have a similar pattern with positive Fis (0.136) and low Ne (724.3). Low genetic differentiation and high genetic connectivity among five geographical populations were detected by pairwise Fst, principal component analysis (PCA), admixture, and phylogenetic analysis. Besides, two YWL individuals originating from an isolated ancestor may imply that there is a genetically differentiated population in the adjacent sea. Overall, the results showed that GBS is an effective method to detect genome-wide SNPs for M. nudus and suggested that the protective measures and the investigation with larger spatial scale and sample size for M. nudus should be carried out in the future.

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Section: Discussioncontrasting

confidence: 57%

Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas

et al. 2021

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“…According to a standard analysis pipeline (Massri et al, 2021), we mapped reads to the Lv3.0 genome (Davidson et al, 2020), with the 10x Cellranger pipeline and filtered out low quality cells using Seurat (Butler et al, 2018; Stuart et al, 2019). In total 50,935 cells remained and were used for the analysis.…”

Section: Resultsmentioning

confidence: 99%

“…The optimal transport method was then used to follow temporal profiles of cell fate specification, and to address several unanswered questions related to gene regulation in development. It was of great value to have a well annotated, high quality genome in order to produce gene calls with high fidelity (Davidson et al, 2020). With these quality checks complete, we built on Waddington-OT (Schiebinger et al, 2019) to devise a number of novel computational analyses.…”

Section: Discussionmentioning

confidence: 99%

“…Data download, FastQ file generation, Genome Indexing, Genome Mapping and Counting, production of raw csv counts files Following sequencing, we used Cellranger 3.1.0 to convert Illumina-generated BCL files to fastq files using the Cellranger "mkfastq" command. We then applied the "mkref" command to index the most recent Lv3.0 Genome (Davidson et al, 2020). We then used the "count" command to demultiplex and count reads mapping to the reference Lv genome.…”

Section: Computational Analysismentioning

confidence: 99%

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Developmental Single-cell transcriptomics in theLytechinus variegatusSea Urchin Embryo

Massri

Greenstreet

Afanassiev

et al. 2020

Preprint

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Here we employed scRNA-seq coupled with computational approaches to examine molecular changes in cells during specification and differentiation. We examined the first 24 hours of development of the sea urchin Lytechinus variegatus (Lv) with 18 time points during which the embryo develops to the larval stage. Using Waddington-OT, the time points were computationally “stitched” together to calculate developmental trajectories. Skeletogenic cells displayed the expected immediate early divergence while other lineages diverged asynchronously, with many cells retaining an intermediate specification status until late in gastrulation. The Lv-scRNA-seq dataset was compared to the developmental Gene Regulatory Network (dGRN) model of specification in Strongylocentrotus purpuratus (Sp). 79 of 80 genes (98%) in that dGRN are present in the Lv-scRNA-seq dataset, and expressed in the correct lineages in which the dGRN circuits operate. Surprisingly, however, many heterochronies in timing of first expression of dGRN genes have evolved between the two species. Replotting the two dGRNs with precise attention to time of expression revealed a number of feedback inputs that likely buffer the dGRNs, allowing them to maintain function in the face of accumulating heterochronies.Summary statementThe early development of the sea urchin embryo was followed using scRNA-seq plus computational methods to trace lineage diversifications. These were matched to gene regulatory network changes over time.

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“…Sequences for insulin related peptides and their likely receptors were identified from a number of Ambulacraria species. This was done using the Artemis program ( Rutherford et al, 2000 ) and the BLAST+ program ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ) on publicly available genome sequences from the feather star Anneissia japonica , the sea urchins Lytechinus variegatus ( Davidson et al, 2020 ) and Strongylocentrus purpuratus ( Sea Urchin Genome Sequencing Consortium, 2006 ), the sea cucumbers Apostichopus japonicus ( Jo et al, 2017 ; Zhang et al, 2017 ) and Holothuria glaberrima , the sea stars Acanthaster planci ( Hall et al, 2017 ) , Pisaster ochraceus ( Ruiz-Ramos et al, 2020 ) and Patiria miniata , the brittle star Ophiothrix spiculata and the hemichordates Saccoglossus kowalevskii and Ptychodera flava ( Simakov et al, 2015 ). The genomes were downloaded from https://www.ncbi.nlm.nih.gov/genome .…”

Section: Methodsmentioning

confidence: 99%

Ambulacrarian insulin-related peptides and their putative receptors suggest how insulin and similar peptides may have evolved from insulin-like growth factor

Veenstra

2021

PeerJ

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Background Some insulin/IGF-related peptides (irps) stimulate a receptor tyrosine kinase (RTK) that transfers the extracellular hormonal signal into an intracellular response. Other irps, such as relaxin, do not use an RTK, but a G-protein coupled receptor (GPCR). This is unusual since evolutionarily related hormones typically either use the same or paralogous receptors. In arthropods three different irps, i.e. arthropod IGF, gonadulin and Drosophila insulin-like peptide 7 (dilp7), likely evolved from a gene triplication, as in several species genes encoding these three peptides are located next to one another on the same chromosomal fragment. These arthropod irps have homologs in vertebrates, suggesting that the initial gene triplication was perhaps already present in the last common ancestor of deuterostomes and protostomes. It would be interesting to know whether this is indeed so and how insulin might be related to this trio of irps. Methodology Genes encoding irps as well as their putative receptors were identified in genomes and transcriptomes from echinoderms and hemichordates. Results A similar triplet of genes coding for irps also occurs in some ambulacrarians. Two of these are orthologs of arthropod IGF and dilp7 and the third is likely a gonadulin ortholog. In echinoderms, two novel irps emerged, gonad stimulating substance (GSS) and multinsulin, likely from gene duplications of the IGF and dilp7-like genes respectively. The structures of GSS diverged considerably from IGF, which would suggest they use different receptors from IGF, but no novel irp receptors evolved. If IGF and GSS use different receptors, and the evolution of GSS from a gene duplication of IGF is not associated with the appearance of a novel receptor, while irps are known to use two different types of receptors, the ancestor of GSS and IGF might have acted on both types of receptors while one or both of its descendants act on only one. There are three ambulacrarian GPCRs that have amino acid sequences suggestive of being irp GPCRs, two of these are orthologs of the gonadulin and dilp7 receptors. This suggests that the third might be an IGF receptor, and that by deduction, GSS only acts on the RTK. The evolution of GSS from IGF may represent a pattern, where IGF gene duplications lead to novel genes coding for shorter peptides that activate an RTK. It is likely this is how insulin and the insect neuroendocrine irps evolved independently from IGF. Conclusion The local gene triplication described from arthropods that yielded three genes encoding irps was already present in the last common ancestor of protostomes and deuterostomes. It seems plausible that irps, such as those produced by neuroendocrine cells in the brain of insects and echinoderm GSS evolved independently from IGF and, thus, are not true orthologs, but the result of convergent evolution.

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Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses

Cited by 64 publications

References 33 publications

Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas

Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas

Developmental Single-cell transcriptomics in theLytechinus variegatusSea Urchin Embryo

Ambulacrarian insulin-related peptides and their putative receptors suggest how insulin and similar peptides may have evolved from insulin-like growth factor

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