Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

Li, Chunyan; Olave, Melisa; Hou, Yali; Qin, Geng; Schneider, Ralf; Gao, Zexia; Tu, Xiaolong; Wang, Xin; Qi, Furong; Nater, Alexander; Kautt, Andreas F.; Wan, Shiming; Zhang, Yanhong; Liu, Yali; Zhang, Huixian; Zhang, Bo; Zhang, Hao; Qu, Meng; Liu, Shuaishuai; Chen, Zeyu; Zhong, Jia; Zhang, He; Meng, Lingfeng; Wang, Kai; Yin, Jingdong; Huang, Liangmin; Venkatesh, Byrappa; Meyer, Axel; Lu, Xuemei; Lin, Qiang

doi:10.1038/s41467-021-21379-x

Cited by 40 publications

(51 citation statements)

References 90 publications

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“…3a ). These findings indicate that ocean currents play important role in shaping and maintaining population structure of the estuarine oyster 12 , 43 . The exceptionally high divergence between SC and NC populations can be explained by the fact that currents from the south and north do not cross over and cannot facilitate gene flow.…”

Section: Resultsmentioning

confidence: 73%

Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

Dai

Zhang

et al. 2021

Commun Biol

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Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology and important for assessing adaptive potential of species under climate change. Analysis of a chromosome-level assembly and resequencing of individuals across wide latitude distribution in the estuarine oyster (Crassostrea ariakensis) revealed unexpectedly low genomic diversity and population structures shaped by historical glaciation, geological events and oceanographic forces. Strong selection signals were detected in genes responding to temperature and salinity stress, especially of the expanded solute carrier families, highlighting the importance of gene expansion in environmental adaptation. Genes exhibiting high plasticity showed strong selection in upstream regulatory regions that modulate transcription, indicating selection favoring plasticity. Our findings suggest that genomic variation and population structure in marine bivalves are heavily influenced by climate history and physical forces, and gene expansion and selection may enhance phenotypic plasticity that is critical for the adaptation to rapidly changing environments.

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Section: Resultsmentioning

confidence: 73%

Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

Dai

Zhang

et al. 2021

Commun Biol

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“…Syngnathus pipefish have genomes that rival green spotted puffer in genomic compactness, with assembly lengths of 307.0 Mb for the Gulf pipefish (Small et al, 2016) (S. scovelli), and 324.33 Mb for the greater pipefish (S. acus) (NCBI RefSeq Genome GCF_901709675.1). In the spectrum of vertebrate genomes, known seahorse genomes are also diminutive, estimated at 421 Mb for the lined seahorse (H. erectus) (Li et al, 2021) and 494 Mb for the tiger tail seahorse (H. comes) (Lin et al, 2016).…”

Section: Seadragon Genomes Are Highly Repetitive For Their Compact Size With Large Contributions From Relatively Recent Te Expansionsmentioning

confidence: 99%

“…Hippocampus (Li et al, 2021;Lin et al, 2016), Microphis (Zhang et al, 2020), and most recently (published as of the writing of this paper) Phyllopteryx and Syngnathoides (Qu et al, 2021). We add to this quiver of syngnathid genomes useful in illuminating the evolution and development of puzzling syngnathid novelties such as male pregnancy and leaf-like appendages.…”

mentioning

confidence: 94%

“…With these new genome models and rich accompanying data, we grow the existing collection of high-quality genomic tools and insights for several syngnathid groups including genera Syngnathus (Roth et al, 2020;Small et al, 2016), Hippocampus (Li et al, 2021;Lin et al, 2016), Microphis (Zhang et al, 2020), and most recently (published as of the writing of this paper) Phyllopteryx and Syngnathoides (Qu et al, 2021). We add to this quiver of syngnathid genomes useful in illuminating the evolution and development of puzzling syngnathid novelties such as male pregnancy and leaf-like appendages.…”

Section: Introductionmentioning

confidence: 99%

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Leafy and Weedy Seadragon Genomes Connect Genic and Repetitive DNA Features to the Extravagant Biology of Syngnathid Fishes

Small

Healey

Currey

et al. 2021

Preprint

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Seadragons are a remarkable lineage of teleost fishes, and they are members of the family Syngnathidae renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations into evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent non-coding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve re-organization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and will be a key resource for conservation studies of the extravagant seadragons and their relatives.

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“…Whereas several high-quality assemblies within family Syngnathidae, i.e. , seahorses, pipefishes, and seadragons have been published in the last few years ( Lin et al 2016 ; Small et al 2016 ; Vertebrate Genomes Project 2019 ; Roth et al 2020 ; Zhang et al 2020 ; Li et al 2021 ), nonsyngnathid syngnathiform species are generally represented by relatively fragmented assemblies (scaffold N50 17–116 Kbp) of low coverage (29–58×; Roth et al 2020 ). An exception with intermediate contiguity and coverage is the striped red mullet Mullus surmuletus (scaffold N50 483 Kbp, 73× coverage; Fietz et al 2020 ), and importantly, the recent chromosome-level genome assembly of the common dragonet Callionymus lyra that was produced by Winter et al (2020) , based on MinION sequencing.…”

Section: Introductionmentioning

confidence: 99%

A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae)

Stervander

Cresko

2021

G3 Genes|Genomes|Genetics

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The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons—the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4,584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.

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Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

Cited by 40 publications

References 90 publications

Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

Leafy and Weedy Seadragon Genomes Connect Genic and Repetitive DNA Features to the Extravagant Biology of Syngnathid Fishes

A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae)

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