Fish genomes: Sequencing trends, taxonomy and influence of taxonomy on genome attributes

Randhawa, Swarajpal S.; Pawar, R. A.

doi:10.1111/jai.14227

Cited by 13 publications

(10 citation statements)

References 37 publications

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“…could accomplish more with more). For example, birds (637 assemblies representing 11,162 species; Bravo et al 2021) and fishes (594 assemblies representing 32,000 species; Randhawa & Pawar, 2021) each possess some of the smallest vertebrate genomes described—most within the ~0.4-1.4Gb range. While far larger genome sizes occur in mammals (~2.5-3.5Gb), applied funding from health and agricultural sources (far exceeding that allocated to other vertebrate groups, such as squamates) have offset similar phenomena in the field of mammal genome sequencing (Supplemental Table 1).…”

Section: (1a) Why Have Squamate Genomics Lagged Behind Other Groups?mentioning

confidence: 99%

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

Pinto

Gamble

Smith

et al. 2023

Preprint

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In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012-2017. However, since 2018, an exponential increase in high quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.

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Section: (1a) Why Have Squamate Genomics Lagged Behind Other Groups?mentioning

confidence: 99%

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

Pinto

Gamble

Smith

et al. 2023

Preprint

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“…The size and repetitive content of amphibian genomes has hindered wholegenome sequencing efforts (Sun et al, 2020). For comparison, >500 fish genomes (Randhawa and Pawar, 2021; average size of 808 Mb) and >300 bird genomes have been sequenced (Feng et al, 2020; Although there is a wealth of accessible amphibian data online (Fig. 5), we still lack basic natural history and phenotypic data for a large portion of amphibian genera and families.…”

Section: Challenges and Opportunities In Amphibian Research-mentioning

confidence: 99%

“…average size of 1.13 Gb,(Randhawa and Pawar, 2021), yet only 28 amphibian genomes are available. The average sizes of sequenced Gymnophiona, based on values reported inLiedtke et al, 2018. Nevertheless, the number of species represented in NCBI sequence databases continues to increase, as does the use of high-throughput technologies for non-model species.…”

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confidence: 99%

State of the Amphibia 2020: A review of five years of amphibian research and existing resources

Womack¹,

Steigerwald²,

Blackburn³

et al. 2021

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Amphibians are a clade of over 8,400 species that provide unique research opportunities and challenges. With amphibians undergoing severe global declines, taking stock of our current understanding of amphibians is imperative. Focusing on 2016–2020, we assessed trends in amphibian publishing, conservation research, systematics, and community resources. We show that while research and data availability are increasing rapidly, information is not evenly distributed across research fields, clades, or geographic regions, leading to substantial knowledge gaps. A complete review of amphibian NCBI resources indicates that genomic data are poised for rapid expansion, but amphibian genomes pose significant challenges. A review of recent conservation literature and cataloged threats on 1,261 species highlight the need to address land use change and disease using adaptive management strategies. We underscore the importance of database integration for advancing amphibian research and conservation and suggest other understudied or imperiled clades would benefit from similar assessments.

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“…Elliott & Gregory (2015) emphasized that the lack of reporting of metrics like the number and proportion of coding regions and introns is an issue that should be addressed. A recent study that explored the patterns of size, GC content, number of chromosomes and number of genes in fish genomes (Randhawa & Pawar, 2021) highlighted that “surprisingly, no study exists on record that has used the WGS annotation data to defines the trends, effects of taxonomic distribution and interrelation of genome attributes”. Yet, such studies have successfully unveiled inter-lineage genomic characteristic patterns in e.g.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of tarakihi (Nemadactylus macropterus) and five New Zealand fish species: assembly contiguity affects the identification of genic features but not transposable elements

Papa

Wellenreuther

Morrison

et al. 2022

Preprint

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Comparative analysis of whole-genome sequences can provide valuable insights into the evolutionary patterns of diversification and adaptation of species, including the genome contents and the regions under selection. However, such studies are lacking for fishes in New Zealand. To supplement the recently sequenced genome of tarakihi (Nemadactylus macropterus), the genomes of five additional percomorph species native to New Zealand (king tarakihi (Nemadactylus n.sp.), blue moki (Latridopsis ciliaris), butterfish (Odax pullus), barracouta (Thyrsites atun), and kahawai (Arripis trutta)) were determined and assembled using Illumina sequencing. While the proportion of repeat elements was highly correlated with the genome size (R2 = 0.97, P < 0.01), most of the metrics for the genic features (e.g. number of exons or intron length) were significantly correlated with assembly contiguity (|R2| = 0.79–0.97). A phylogenomic tree including eight additional high-quality fish genomes was reconstructed from sequences of shared gene families. The radiation of Percomorpha was estimated to have occurred c. 112 mya (mid-Cretaceous), while the Latridae have diverged from true Perciformes c. 83 mya (late Cretaceous). Evidence of positive selection was found in 65 genes in tarakihi and 209 genes in Latridae: the largest portion of these are involved in the ATP binding pathway and the integral structure of membranes. These results and the de novo genome sequences can be used to (1) inform future studies on both the strength and shortcomings of scaffold-level assemblies for comparative genomics and (2) provide insights into the evolutionary patterns and processes of genome evolution in bony fishes.

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Fish genomes: Sequencing trends, taxonomy and influence of taxonomy on genome attributes

Cited by 13 publications

References 37 publications

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

State of the Amphibia 2020: A review of five years of amphibian research and existing resources

Comparative genomics of tarakihi (Nemadactylus macropterus) and five New Zealand fish species: assembly contiguity affects the identification of genic features but not transposable elements

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