Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution

Shingate, Prashant; Ravi, Vydianathan; Prasad, Aravind; Tay, Boon-Hui; Garg, Kritika M.; Chattopadhyay, Balaji; Yap, L. F.; Çilingir, F. Gözde; Venkatesh, Byrappa

doi:10.1038/s41467-020-16180-1

Cited by 70 publications

(88 citation statements)

References 65 publications

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“…These repetitive sequences belonged to four major repeat classes: DNA elements (7.1%), long interspersed nuclear elements (LINEs, 6.8%), short interspersed nuclear elements (SINEs, 5.1%) and long terminal repeats (LTRs, 2.8%) ( Table 2). The total repeat content of the T. gigas genome (33%) is comparable to those of T. tridentatus (34%) (Gong et al, 2019) and C. rotundicauda (33%) (Shingate et al, 2020). However, the repeat content of the L. polyphemus genome is lower (25.5%) than that in the other three horseshoe crab genomes, presumably due to the highly fragmented L. polyphemus genome assembly in which the dispersed repetitive sequences might have collapsed, resulting in the assembly of fewer consensus sequences.…”

Section: Repetitive Sequencesmentioning

confidence: 83%

“…A highly contiguous, error‐free chromosome‐level genome assembly is an important requirement for effective population genomic study. At present, genome assemblies of varying quality and contiguity exist for three of the four horseshoe crab species ( L. polyphemus , T. tridentatus and C. rotundicauda ) (Gong et al., 2019; Kenny et al., 2016; Liao et al., 2019; Nossa et al., 2014; Shingate et al, 2020). However, a genome assembly is lacking for the fourth species, T. gigas .…”

Section: Introductionmentioning

confidence: 99%

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Chromosome‐level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

Shingate

Ravi

Prasad

et al. 2020

Molecular Ecology Resources

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Horseshoe crabs (order: Xiphosura, family: Limulidae) are marine chelicerates that are closely related to spiders, scorpions, ticks and mites rather than "true" crabs. Only four extant species of horseshoe crabs exist globally of which three (mangrove horseshoe crab, Carcinoscorpius rotundicauda; coastal horseshoe crab, Tachypleus gigas; and tri-spine horseshoe crab, Tachypleus tridentatus) inhabit the waters of tropical and subtropical Asia, while the fourth species (Atlantic horseshoe crab, Limulus polyphemus) is found along the Atlantic coast of North America as well as the Gulf of Mexico. The discovery of horseshoe crabs' highly sensitive immune response to

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Section: Repetitive Sequencesmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Chromosome‐level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

Shingate

Ravi

Prasad

et al. 2020

Molecular Ecology Resources

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“…On the other hand, genome and Hox cluster duplications are considered rare in Arthropoda [80]. Complete Hox cluster duplication in the phylum has only been reported in horseshoe crabs (Xiphosura) [34,35,81,82], and in spiders and scorpions (presumed ancestral in Arachnopulmonata). The phylogenetic placement of Amblypygi makes this group an opportune system to test the downstream prediction that P. marginemaculatus retains and expresses Hox paralogs shared by spiders and scorpions.…”

Section: Genomic Resources For Whip Spiders Corroborate Widespread Rementioning

confidence: 99%

“…Empty squares in Parasteatoda, Centruroides, and Tetranychus indicate absence from the genome. Number of Hox genes in Carcinoscorpius rotundicauda after[35] (but see[102] for evidence of additional copies). b Tree topology inferred from maximum likelihood analysis of a conserved region (71 amino acid characters) using the same terminals of the schematics (ln L = − 3442.810).…”

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confidence: 99%

Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning

Gainett

Sharma

2020

EvoDevo

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Background: The resurgence of interest in the comparative developmental study of chelicerates has led to important insights, such as the discovery of a genome duplication shared by spiders and scorpions, inferred to have occurred in the most recent common ancestor of Arachnopulmonata (a clade comprising the five arachnid orders that bear book lungs). Nonetheless, several arachnid groups remain understudied in the context of development and genomics, such as the order Amblypygi (whip spiders). The phylogenetic position of Amblypygi in Arachnopulmonata posits them as an interesting group to test the incidence of the proposed genome duplication in the common ancestor of Arachnopulmonata, as well as the degree of retention of duplicates over 450 Myr. Moreover, whip spiders have their first pair of walking legs elongated and modified into sensory appendages (a convergence with the antennae of mandibulates), but the genetic patterning of these antenniform legs has never been investigated. Results: We established genomic resources and protocols for cultivation of embryos and gene expression assays by in situ hybridization to study the development of the whip spider Phrynus marginemaculatus. Using embryonic transcriptomes from three species of Amblypygi, we show that the ancestral whip spider exhibited duplications of all ten Hox genes. We deploy these resources to show that paralogs of the leg gap genes dachshund and homothorax retain arachnopulmonate-specific expression patterns in P. marginemaculatus. We characterize the expression of leg gap genes Distal-less, dachshund-1/2 and homothorax-1/2 in the embryonic antenniform leg and other appendages, and provide evidence that allometry, and by extension the antenniform leg fate, is specified early in embryogenesis. Conclusion: This study is the first step in establishing P. marginemaculatus as a chelicerate model for modern evolutionary developmental study, and provides the first resources sampling whip spiders for comparative genomics. Our results suggest that Amblypygi share a genome duplication with spiders and scorpions, and set up a framework to study the genetic specification of antenniform legs. Future efforts to study whip spider development must emphasize the development of tools for functional experiments in P. marginemaculatus.

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“…This genome duplication is inferred to trace back to the most recent common ancestor of the recently proposed clade Arachnopulmonata, which includes spiders, scorpions, and three other arachnid orders with book lungs [6,26,[31][32][33]. This duplication event is also inferred to be independent from the multiple rounds of whole genome duplication undergone by horseshoe crabs (Xiphosura) [34,35]. The duplication in spiders and scorpions encompasses several important developmental genes, such as the homeobox family [6,32].…”

Section: Introductionmentioning

confidence: 92%

Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning

Gainett

Sharma

2020

Preprint

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AbstractThe resurgence of interest in the comparative developmental study of chelicerates has led to important insights, such as the discovery of a genome duplication shared by spiders and scorpions, inferred to have occurred in the newly proposed clade Arachnopulmonata. Nonetheless, several groups remain understudied in the context of development and genomics, such as the order Amblypygi (whip spiders). The phylogenetic position of Amblypygi in Arachnopulmonata poses them as an interesting group to test the extent of conservation of the proposed genome duplication in the history of arachnids. Moreover, whip spiders have their first pair of walking legs elongated and modified into sensory appendages (a convergence with the antenna of mandibulates), but the genetic patterning of these antenniform legs has never been investigated. Here, we break a 45-year hiatus of embryological studies in Amblypygi, by establishing genomic resources and protocols for cultivation of embryos and gene expression assays by in situ hybridization to study the development of the whip spider Phrynus marginemaculatus. We provide evidence that P. marginemaculatus retains duplicates of most Hox genes, and that paralogs of the leg gap genes dachshund and homothorax retain arachnopulmonate-specific expression patterns. We characterize the expression of leg gap genes Distal-less, dachshund1/2 and homothorax1/2 in the embryonic antenniform leg and other appendages, and provide evidence that allometry, and by extension the antenniform leg fate, is already specified very early in embryogenesis.

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Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution

Cited by 70 publications

References 65 publications

Chromosome‐level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

Chromosome‐level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning

Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning

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