The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ.
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ABSTRACT:
SUBMITTER: Ketchum RN
PROVIDER: S-EPMC7799691 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E sp. EZ's life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was among the highest recorded for an echinoderm at 4.5%. We recovered 918 high-quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.
| S-EPMC7594579 | biostudies-literature
Project description:Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly, we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. Ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared E. sp. EZ gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in E. sp. EZ noncoding elements near genes involved in environmental response pathways as well as losses of transcription factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.
| S-EPMC9557091 | biostudies-literature
Project description:The complete mitochondrial genomes are sequenced in two individuals representing two morphological forms, 'usual' (U) and 'gray' (G), of the short-spined sea urchin Strongylocentrotus intermedius. The genome sequences are 15,705?bp in size, and the gene arrangement, composition, and size are very similar to the other sea urchin mitochondrial genomes published previously. A low level of sequence divergence (D xy?=?0.0083?±?0.0007) is detected between the forms. The GenBank (KC490912) mt genome of S. intermedius is much closer to the U form (D xy?=?0.0013?±?0.0003) than to the G form (D xy?=?0.0085?±?0.0006), demonstrating unique evolutionary trajectories for each form, which we previously suggested based on the bindin gene and symbiont analyses.
| S-EPMC7800726 | biostudies-literature
Project description:Tuleariocaris holthuisi and Arete indicus are two ectocommensal shrimps closely associated with the tropical sea urchin Echinometra mathaei. This study provides a comparison of these two E. mathaei symbiotic crustaceans and particularly focuses on the relationship between T. holthuisi and its host's pigments (i.e. spinochromes), and its dependency on its host. While all the analyses underline a close association between A. indicus and E. mathaei, they reveal a particularly close interaction between T. holthuisi and its host. Chemical analyses reveal that these shrimps present the same spinochrome composition as E. mathaei, and have similar colouration, allowing camouflage. Isotopic composition and pigment loss after host separation suggest that these pigments are certainly assimilated upon feeding on the urchin. Moreover, symbiont isolation experiments demonstrate the high dependency of T. holthuisi on its host and the importance of the host's pigments on their survival capacity. Finally, some host recognition mechanisms are investigated for T. holthuisi and show the probable implication of spinochromes in host selection, through chemical recognition. Hence, all the results suggest the essential roles of spinochromes for T. holthuisi, which, in turn, suggests the potential implication of these pigments in the shrimps' metabolism.
| S-EPMC6277410 | biostudies-literature
Project description:BACKGROUND:Echinometra lucunter is a common American sea urchin responsible for the majority of the marine accidents in Brazil. Although not lethal, these accidents are reported to be extremely painful. Recently, our group described the presence of toxins in its spines that contribute to the pathological reactions. Additionally, we have observed that the E. lucunter spines can regenerate when broken. In the present work we evaluated the enzymatic activities of sea urchin spine extracts in order to identify an enzyme that could contribute not only to the toxicity, but also participate in the spine growth and regeneration. RESULTS:The spine aqueous extract was tested for peptidase activity, with synthetic substrates, in the presence and absence of inhibitors and activators. For proper enzyme classification, the FRET-substrate cleavage pattern, pH-dependency activity and Western-blot analyses were performed. The spine extract was able to cleave Z-R-MCA and Abz-GIVRAK(Dnp)-OH following pre-incubation with DTT, and was inhibited by E-64. Furthermore, the double-peaked pH curve (5 and 7) and the cleavage site proportion (4:6, R?A:A?K) indicate the presence of both mono and dicarboxypeptidase activities. Moreover, in Western-blot analysis, the spine extract was positive for anti-cathepsin B antibody. CONCLUSIONS:E. lucunter spines extracts presented a cysteine peptidase activity that was identified as cathepsin B/X that would participate in the remodeling and growth processes of the spine, as well as in the inflammatory response to the accident.
| S-EPMC3880103 | biostudies-literature
Project description:The complete mitochondrial genome (mitogenome) of Ugyops sp. (Hemiptera: Delphacidae) was sequenced, making it the first determined mitogenome from the subfamily Asiracinae, the basal clade of the family Delphacidae. The mitogenome was 15,259 bp in length with A + T content of 77.65% and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region. The gene order was identical with that of the ancestral insect. The nucleotide composition analysis indicated that the whole mitogenome was strongly A-skewed (0.288) and highly C-skewed (-0.270). For PCGs on the J-strand, the AT skew was positive, and the GC skew was negative. All PCGs started with canonical ATN codons, except for cox1 and nad5, which used CTG and GTG as start codon, respectively. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnS1 (AGN), in which the dihydrouridine arm was reduced to a simple loop. The control region included a poly-T stretch downstream of the small rRNA gene (rrnS), a subregion of higher A + T content and tandemly repeated sequence near trnI. The mitogenome of Ugyops sp. could be very helpful in exploring the diversity and evolution of mitogenomes in Delphacidae.
| S-EPMC6007673 | biostudies-literature
Project description:We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
| S-EPMC3159423 | biostudies-literature
Project description:Paenibacillus species, belonging to the family Paenibacillaceae, are able to survive for long periods under adverse environmental conditions. Several Paenibacillus species produce antimicrobial compounds and are capable of biodegradation of various contaminants; therefore, more investigations at the genomic level are necessary to improve our understanding of their ecology, genetics, as well as potential biotechnological applications.In the present study, we describe the draft genome sequence of Paenibacillus sp. EZ-K15 that was isolated from nitrocellulose-contaminated wastewater samples. The genome comprises 7,258,662 bp, with a G+C content of 48.6%. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PDHM00000000. Data demonstrated here can be used by other researchers working or studying in the field of whole genome analysis and application of Paenibacillus species in biotechnological processes.
| S-EPMC5727980 | biostudies-literature
Project description:The complete nucleotide sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome has been determined. The lamprey genome is 16,201 bp in length and contains genes for 13 proteins, two rRNAs, 22 tRNAs and two major noncoding regions. The order and transcriptional polarities of protein-coding genes are basically identical to those of other chordate mtDNAs, demonstrating that the common mitochondrial gene organization of vertebrates was established at an early stage of vertebrate evolution. The two major noncoding regions are separated by two tRNA genes. The first region probably functions as the control region because it contains distinctive conserved sequence blocks (CSB-II and III) common to other vertebrate control regions. The central conserved domain observed in other vertebrate control regions is not found in the lamprey, suggesting that it is a recently evolved functional domain in vertebrates. Noncoding segments are not found in the expected position of the origin of replication for the second strand, suggesting either that one of the tRNA genes has a dual function or that the second noncoding region may function as the second-strand origin. The base composition at the wobble positions of fourfold degenerate codon families is highly biased toward thymine (32.7%). Values of GC- and AT-skew are typical of vertebrate mitochondrial genomes.
| S-EPMC1206387 | biostudies-other
Project description:The complete mitochondrial genome of the Evynnis tumifrons was 16 616?bp in length and contained 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition of E. tumifrons was A 27.05%, T 26.42%, C 29.45% and G 17.07%. Phylogenetic tree construction indicated that Evynnis tumifrons was most closely related to Parargyrops edita and Pagrus auriga. This molecular information will contribute to better understand its evolution and population genetics.
| S-EPMC7800024 | biostudies-literature