Erratum to: draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus smith 1828

Read, Timothy D.; Petit, Robert A.; Joseph, Sandeep J.; Alam, Tauqeer; Weil, M. Ryan; Ahmad, Maida; Bhimani, Ravila; Vuong, Jocelyn S.; Haase, Chad P; Webb, D. Harry; Tan, Milton; Dove, Alistair D. M.

doi:10.1186/s12864-017-4138-z

Cited by 11 publications

(4 citation statements)

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“…TLR2, TLR3, TLR6, and TLR9 have been identified in the gray bamboo shark ( Chiloscyllium griseum ) genome whereas no TLR6 or TLR10 homolog has been identified in teleost fish. In addition, a novel TLR with sequence similarity to TLR4 and TLR13 in mammals, and TLR21 in teleost fish, has been identified in the whale shark ( Rhincodon typus ) (80, 83).…”

Section: Recognition Of Non-selfmentioning

confidence: 99%

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

2019

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The immune system is composed of two subsystems—the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates—the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.

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Section: Recognition Of Non-selfmentioning

confidence: 99%

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

2019

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“…While mostly confined to marine environments, species in the taxon Chondrichthyes (cartilaginous fishes) exhibit a wide variety of body size, longevity, and habitat depth. Despite their diversity, genome analysis has concentrated on species with high public visibility (Read et al, 2017;Marra et al, 2019). Previously, a study reporting whole genome sequencing of the white shark, Carcharodon carcharias (Marra et al, 2019) suggested unique molecular evolution accounted for the maintenance of genome stability and the elongated lifespan of the whale shark, Rhincodon typus as well as the white shark.…”

Section: Introductionmentioning

confidence: 99%

Unbiasing Genome-Based Analyses of Selection: An Example Using Iconic Shark Species

Yamaguchi

Kuraku

2021

Front. Mar. Sci.

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“…Moreover, especially in studying elasmobranchs, genome analysis can encounter inherent difficulty incurred by their large genome sizes (for review, see Kuraku 2021 ). These factors have prevented previous efforts on cartilaginous fishes from obtaining a suite of genome sequences supported by karyotype and genome size estimate as well as transcriptome sequencing ( Read et al 2017 ; Marra et al 2019 ; Weber et al 2020 ; Zhang et al 2020 ; Rhie et al 2021 ; Tan et al 2021 ).…”

mentioning

confidence: 99%

“…Each of the resultant chromosome-scale genome assemblies of the zebra shark, as well as the whale shark ( Fig. 1 B), have been constructed using samples from a single individual (which was not achieved in earlier efforts: Read et al 2017 ; Weber et al 2020 ; Tan et al 2021 ) and controlled by referring to their karyotypes. Using the obtained sequences, we performed comparative investigations to characterize the diversity of chromosomal organization.…”

mentioning

confidence: 99%

Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization

Yamaguchi,

Uno,

Kadota

et al. 2023

Genome Res.

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Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra sharkStegostoma tigrinum, an endangered species that has a relatively small genome among sharks (3.71 Gb), as well as for the whale sharkRhincodon typus. Our analysis employing a male-female comparison identified an X Chromosome, the first genomically characterized shark sex chromosome. The X Chromosome harbors the Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes exhibit a gradualism of chromosome length with remarkable length-dependent characteristics—shorter chromosomes tend to have higher GC-content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length and lower interspersed repeat content. We challenge the traditional binary classification of karyotypes as with and without so-called microchromosomes. Even without microchromosomes, the length-dependent characteristics persist widely in some other vertebrate lineages. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout. It also paves the way to dissecting more genomes with variable sizes to be sequenced on high quality.

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Erratum to: draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus smith 1828

Cited by 11 publications

References 1 publication

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

Unbiasing Genome-Based Analyses of Selection: An Example Using Iconic Shark Species

Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization

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