Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(8)

Published: Aug. 1, 2023

Standing genetic variation is a major driver of fitness and resilience therefore fundamental importance for threatened species such as stony corals. We analyzed RNA-seq data generated from 132 Montipora capitata 119 Pocillopora acuta coral colonies collected Kāne'ohe Bay, O'ahu, Hawai'i. Our goals were to determine the extent colony study reproductive strategies in these two sympatric species. Surprisingly, we found that 63% P. triploid, with putative independent origins different triploid clades. These corals have spread primarily via asexual reproduction are descended small number genotypes, whose diploid ancestor invaded bay. In contrast, all M. outbreeding, almost genetically distinct. Only cases reproduction, likely fragmentation, identified this report distinct inhabit largest sheltered body water main Hawaiian Islands. highlight divergence behavior genome biology, both which contribute persistence.

Language: Английский

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Facultative lifestyle drives diversity of coral algal symbionts

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 39(3), P. 239 - 247

Published: Nov. 10, 2023

The photosynthetic symbionts of corals sustain biodiverse reefs in nutrient-poor, tropical waters. Recent genomic data illuminate the evolution coral under genome size constraints and suggest that retention facultative lifestyle, widespread among these algae, confers a selective advantage when compared with strict symbiotic existence. We posit symbiosis is analogous to 'bioreactor' selects winner genotypes allows them rise high numbers sheltered habitat prior release by host. Our observations lead novel hypothesis, 'stepping-stone model', which predicts local adaptation both free-living stages, stepwise fashion, accelerates alga diversity origin endemic strains species.

Language: Английский

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Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Nov. 20, 2024

Abstract Background Over their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond rapid change. Genome structure genetic diversity contained within highlight adaptive potential. Results We present chromosome-scale genome assemblies linkage maps of the critically endangered Atlantic acroporids, Acropora palmata A. cervicornis . Both were resolved into 14 chromosomes with gene content colinearity. Repeats chromosome arrangements largely preserved between species. The family Acroporidae genus exhibited many phylogenetically significant expansions. Macrosynteny decreased phylogenetic distance. Nevertheless, scleractinians shared six 21 cnidarian ancestral groups as well numerous fission fusion events compared other distantly related cnidarians. Genetic constructed from one 16 families using a genotyping array. consensus span 1,013.42 cM 927.36 for , respectively. species high genome-wide recombination rates (3.04 3.53 cM/Mb) pronounced sex-based differences, known heterochiasmy, 2 2.5X higher estimated in female maps. Conclusions Together, we here are first detailed look at genomic landscapes acroporids. These data sets revealed that capacity acroporids not limited by rates. sister maintain macrosynteny few genes sequence divergence act reproductive barriers them. In hybridization two yields an F1 hybrid fertility despite levels colinearity genomes. these resources now enable association studies discovery quantitative trait loci, tools can aid conservation

Language: Английский

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High-quality genome assemblies from key Hawaiian coral species

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Abstract Background Coral reefs house about 25% of marine biodiversity and are critical for the livelihood many communities by providing food, tourism revenue, protection from wave surge. These magnificent ecosystems under existential threat anthropogenic climate change. Whereas extensive ecological physiological studies have addressed coral response to environmental stress, high-quality reference genome data lacking these species. The latter issue hinders efforts understand genetic basis stress resistance design informed conservation strategies. Results We report assemblies 4 key Hawaiian species, Montipora capitata, Pocillopora acuta, meandrina, Porites compressa. or members genera, distributed worldwide therefore broad scientific importance. For M. an initial assembly was generated short-read Illumina long-read PacBio data, which then scaffolded into 14 putative chromosomes using Omni-C sequencing. P. compressa, were data. acuta is a triploid individual, making it first nondiploid animal. Conclusions significant improvements over available provide invaluable resources supporting multiomics biology, not just in Hawaiʻi but also other regions, where related species exist. provides platform studying polyploidy corals its role evolution adaptation organisms.

Language: Английский

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A draft genome assembly of reef-building octocoral Heliopora coerulea

Scientific Data, Journal Year: 2023, Volume and Issue: 10(1)

Published: June 14, 2023

Abstract Coral reefs are under existential threat from climate change and anthropogenic impacts. Genomic studies have enhanced our knowledge of resilience responses some coral species to environmental stress, but reference genomes lacking for many species. The blue Heliopora is the only reef-building octocoral genus exhibits optimal growth at a temperature close bleaching threshold scleractinian corals. Local high-latitude expansions coerulea were reported in last decade, little known about molecular mechanisms underlying its thermal resistance. We generated draft genome H. with an assembled size 429.9 Mb, scaffold N50 1.42 Mb BUSCO completeness 94.9%. contains 239.1 repetitive sequences, 27,108 protein coding genes, 6,225 lncRNAs, 79 miRNAs. This provides valuable resource in-depth on adaptive corals evolution skeleton cnidarian.

Language: Английский

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Genome assemblies and genetic maps highlight chromosome-scale macrosynteny in Atlantic acroporids

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 23, 2023

Abstract Background Corals belong to the Cnidaria, an early branching phylum of metazoans. Over course their long evolutionary history, they have adapted changing environments, such as rising sea levels and increasing ocean temperatures. While history speaks capacity, it is less clear how quickly may respond rapid changes. A critical aspect adaptive capacity structure genome genetic diversity contained within. Findings Here, we present chromosome-scale assemblies linkage maps two critically endangered coral species, Acropora palmata A. cervicornis, extant Atlantic acroporid corals. Genomes both species were resolved into 14 chromosomes with comparable assembly sizes ( , 287Mb; cervicornis 305Mb). Gene content, repeat gene collinearity macrosynteny largely preserved between acroporids but a 2.5 Mb inversion 1.4 translocation detected chromosome pairs. Macrosynteny decreased when comparing Pacific acroporids. Paracentric inversions whole arms characterized hyacinthus specifically. In larger context cnidarian evolution, four another scleractinian chromosome-resolved retained six 21 ancestral groups, while also privately sharing numerous ALG fission fusion events compared other distantly related cnidarians. Genetic built using 30K genotyping array 105 offspring in one family for 154 across 16 families . The consensus map spans 1,013.42 cM includes 2,114 informative markers. 927.36 4,859 exhibited similarly high sex-averaged genome-wide recombination rates (3.53 cM/Mb 3.04 cM/Mb, respectively) relative animals. our gamete-specific maps, found pronounced sex-based differences recombination, known heterochiasmy, this simultaneous hermaphrodite, showing 2-2.5X higher eggs sperm. Conclusions genomic resources presented here are first kind available species. These data sets revealed that corals not limited by rates, exhibiting heterochiasmy. Nevertheless, sister maintain them. few large-scale rearrangements deserve further study potential cause fertilization barriers Together, now enable association studies discovery quantitative trait loci; tools can aid conservation these

Language: Английский

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Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(7)

Published: July 1, 2024

Transcriptome data are frequently used to investigate coral bleaching; however, the factors controlling gene expression in natural populations of these species poorly understood. We studied two corals,

Language: Английский

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Genome assembly of the deep-sea coral Lophelia pertusa

Gigabyte, Journal Year: 2023, Volume and Issue: 2023, P. 1 - 12

Published: March 16, 2023

Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from southeastern coast USA, first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data an initial proximity ligation scaffolding. The was annotated using evidence transcripts, proteins, ab initio gene model predictions. This is comparable high-quality reference genomes corals. comprises 2,858 scaffolds (N50 1.6 Mbp) has size 556.9 Mbp. Approximately 57% repetitive elements 34% coding DNA. predicted 41,089 genes, including 91.1% complete metazoan orthologs. will facilitate investigations into ecology this species evolution

Language: Английский

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Nutritional exchange between reef-building corals and algal endosymbionts buffers the energetic demand of larval development and metamorphosis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 23, 2023

Abstract Anthropogenic climate change threatens the persistence of coral reefs by impacting reproduction and accelerating loss. Adult corals depend on nutritional exchange with their endosymbiotic algae (Symbiodiniaceae) to fulfill energetic demands. However, mechanisms underlying onset this during early life stages how it contributes developmental energy demands are unclear. We conducted an integrative analysis metabolism across in Montipora capitata , a vertically transmitting (Symbiodiniaceae passed from parent offspring) Hawai□i. applied physiological (metabolism symbiont density) multi-omic (metabolomics, transcriptomics, microbial amplicon sequencing) approaches over 13 time points between 1-255 hours post-fertilization eggs settled recruits. Energetic demand (respiration) increased as embryos developed into larvae progressed through metamorphosis. Symbiont photosynthetic capacity (photosynthesis cell ontogeny, demonstrating potential for symbiont-derived nutrition fuel development growth. Indeed, gene expression metabolomic analyses revealed that is metabolized starting motile larval stage increasing utilization metamorphosis following settlement. Specifically, metabolic pathways associated organic compound transport glucose fatty acid were enriched there was expanded use carbohydrate lipid metamorphosed polyps Larvae also demonstrate cellular processes maintain nutrient balance host regulate populations genes nitrogen assimilation response reactive oxygen species. Collectively, our characterization reveals becomes increasingly important buffer required In environmentally stressful conditions, species may be vulnerable loss nutrition. Therefore, interventions reduce symbiotic stress sensitive could enhance reef recruitment recovery intensifies.

Language: Английский

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Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 29, 2024

Abstract Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, long-read assemblies now starting to be publicly available, opening the door a wide array of ‘omics-based research. Here we present new assembly endangered Caribbean star coral, Orbicella faveolata , using PacBio circular consensus reads. Our improved contiguity (51 versus 1,933 contigs) and complete single copy BUSCO orthologs (93.6% 85.3%, database metazoa_odb10), compared currently reference generated short-read methodologies. assembled also showed comparable quality metrics other coral genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, these repeats at either one, or both ends, contigs. We 32,172 protein coding genes through use RNA (ISO-seq) additional O. fragments exposed range abiotic biotic treatments, RNA-seq data. With anthropogenic influences heavily affecting as well s increasing incorporation into reef restoration activities, this updated resource can used population genomics ‘omics analyses aid conservation species.

Language: Английский

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