De novo Assembly of the Brain Coral Platygyra sinensis Genome

Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat; Kongjandtre, Narinratana; Putchim, Lalita; Sangsrakru, Duangjai; Yoocha, Thippawan; Tangphatsornruang, Sithichoke

doi:10.3389/fmars.2021.732650

Cited by 3 publications

(1 citation statement)

References 24 publications

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“…Pocillopora acuta, Stephens et al 2022). The ancestral cnidarian chromosome number is seventeen (Zimmermann et al 2023), but coral genomes generally have fourteen chromosomes (2n = 28; Kenyon 1997) and genome sizes are between 300Mb – 1Gb (eg., Prada et al 2016, Fuller et al 2020, Pootakham et al 2021, Bongaerts et al 2021). The number of genes is typically 30,000-40,000 but exceptions exist (e.g.…”

Section: Introductionmentioning

confidence: 99%

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

Locatelli,

Kitchen,

Stankiewicz

et al. 2023

Preprint

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

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Section: Introductionmentioning

confidence: 99%

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

Locatelli,

Kitchen,

Stankiewicz

et al. 2023

Preprint

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A first genomic portrait of the deep-water azooxanthellate reef-building coral Madracis myriaster: genome size, repetitive elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Pocilloporidae

Tucker,

Barrios,

Preziosi

et al. 2023

Coral Reefs

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

Locatelli,

Kitchen,

Stankiewicz

et al. 2024

BMC Genomics

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

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De novo Assembly of the Brain Coral Platygyra sinensis Genome

Cited by 3 publications

References 24 publications

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

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

A first genomic portrait of the deep-water azooxanthellate reef-building coral Madracis myriaster: genome size, repetitive elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Pocilloporidae

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

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