- tridentatus and the Atlantic horseshoe crab Limulus polyphemus have the most orthologues shared among two species, including genes involved in the immune-related JAK-STAT signalling pathway. - polyphemus appeared approximately 130 Mya and the split of the two Asian horseshoe crabs was dated to approximately 63 Mya (57 – 69). - Genes involved in the IMD and JAK-STAT signal transduction pathways also exhibited a certain degree of expansion in both genomes. - Intact coagulation cascade-related genes were present in the T. - tridentatus constitutes its robust and effective innate immunity for self-defence in marine environments with an enormous number of invading pathogens and may affect the quality of the adaptive properties with regard to complicated marine environments.. - 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - 3 Institute of Oceanography, Minjiang University, Fuzhou 350108, China Full list of author information is available at the end of the article. - tri- dentatus but also of the xiphosuran lineage and try to reduce errors of only using a single draft-quality gen- ome, the comparative genomic study of immune systems within T. - Here, we present an analysis of the T. - The GC content of the genome is 32.03% (Table 1). - A total of 24,222 protein-coding genes were conservatively predicted in the T. - A total of 88.25% of the predicted genes were assigned and annotated by comparing to the NCBI non-redundant database, KEGG database [16] and InterPro database [17].. - tridentatus, representing 0.99% of the genome size. - Most of the identified repeat sequences were simple repeats (0.77. - To estimate of repeat se- quences which are more difficult to detect in the draft. - Table 1 Summary of the Tachypleus tridentatus genome assembly and annotation statistic. - Summary of the Tachypleus tridentatus genome assembly and annotation statistics.. - a of 1066 arthropod BUSCOs Complete [Duplicated], Fragmented, Missing, in the assembly. - To determine the reliabil- ity of the repeat contents screening by RepeatMasker and RepeatModeler, we also performed repeat analysis of the L. - The completeness of the T. - tridentatus genome assembly was assessed using the transcriptome data of the embry- onic sample at Stage 21 (the hatch-out stage) of T. - It was found that 99.04% of the transcriptome contigs were aligned to the assembly scaf- folds, with an e-value cut-off of 10 − 30 . - To further con- firm the completeness of the predicted genes, the commonly used genome assembly validation pipeline BUSCO [21] gene mapping method with 1066 BUSCO Arthropoda gene sets were utilized. - Only 1.3% of the benchmarked universal single-copy orthologous groups of arthropod genes were missing in the assembly. - This demonstrated that most of the evolutionarily conserved core genes were found in T. - moreover, approxi- mately 6880 of the shared genes were single-copy. - tridentatus with the most current understanding of the evolution of Chelicer- ata species, phylogenetic and comparative genomic ana- lyses of T. - The comparative genomic analysis of the 14 species re- vealed 14,479 orthologous groups containing genes in at least two different species, among which 1993 shared groups were commonly distributed in all sampled spe- cies, with 111 single-copy orthologues (Fig. - Nevertheless, considering the fragmentation of the draft genome, there may be uniden- tified coding genes in the analysed genomes. - polyphemus was dated to 130 Mya (121–141) and that the split of the Asian horseshoe crabs T. - On the time axis, the green bar shows the divergence time for split of the scorpion from horseshoe crabs. - the brown bar shows the inner split time of the three spiders. - the blue bar shows the origin of the the last common ancestor of Asian horseshoe crabs (including T. - Analysis of the Hox gene family showed that the T. - We further examined the positions of the identified Hox genes in the two genomes and found two clusters of adjacently distributed Hox1 and Hox4 in the T. - Expansion of crucial gene families of the innate immune signalling pathways in T. - pathways) [39–41] are present in the genomes of T. - For Dredds, the phylogeny tree shows one branch including 7 corre- sponding genes identified in the two horseshoe crabs and 1 gene in C. - More- over, main components of the JAK-STAT signalling pathway, including the receptor Domeless and the Janus Kinase and STAT transcription factor, were identified in both T. - Two STAT homologue candidates were identified in the T. - Plausible ho- mologs of major components of the JNK signalling were also identified in both T. - A hallmark of the T. - tri- dentatus genome for antimicrobial peptide genes and identified most of the antibacterial peptides that have been reported, including one anti-LPS, two tachyplesin and two big defensin peptides (Fig. - The anti-LPS gene found in the T. - poly- phemus have all the coagulation-related genes while other related species lack a part of the coagulation path- way (Table 2), indicating a wider diversity of coagulation factors and a relatively intact coagulation cascade present in horseshoe crabs. - We further investi- gated the divergence time using mitochondrial coding se- quences from 7 Chelicerata species, and our analyses suggest that the diversification of the Limulidae and T. - tri- dentatus lineages was congruent approximately 121–141 Mya, and the lineages of the two Asian horseshoe crabs T.. - After the final breakup of the Eurasian and North Ameri- can plates, the European land mass formed as the shallow seas disappeared and the ancestors of the horseshoe crab migrated. - The diversity of the Asian horseshoe crabs T.. - Examination of Hox cluster genes with detailed scaffold positions in the T. - Some clues could be found from the comparison of the previously determined L. - Genes that are not found in the T. - Homologs of the FREP and Dscam families play an important role, and pattern recognition receptors with their corresponding functional domains were exten- sively present in the two horseshoe crab genomes. - The abundantly expressed PRRs in the T. - Several gene family members in the IMD and JAK-STAT signalling transduction pathway exhibit a certain degree of expansion in T. - We identified most of the antimicrobial peptides isolated in previous studies in T. - However, in the L. - polyphe- mus genome, we failed to find any of the tachyplesin family genes, probably because these antimicrobial pep- tides are usually shorter and have a high degree of spe- cies specificity. - Thus, more work needs to be undertaken to study the specific function of the AMPs in T. - Serine protease-dependent haemolymph coagulation is a major component of the innate immune system in horseshoe crabs. - Activation of the horseshoe crab coagulation cascade consists of four coagulation fac- tors including factor C, factor B, factor G and pro- clotting enzyme [73, 74]. - Factor C and factor G are two serine protease zymogens that act as biosensors and can be activated by LPS or (1 → 3)-β-D-glucan, which are major components of the cell walls of Gram-negative bacteria and fungi, respectively. - We found relatively high number of genes for all four co- agulation factors in the T. - This might be because of a limited annotation of the draft genome assemblies or there might be other special biosensors involved in their antifungal recognition process. - In total, 24,222 protein- coding genes were conservatively predicted as present in the T. - Further analysis of the T. - More- over, all of the antibacterial peptides reported in previ- ous studies, as well as their effective antimicrobial sites, have also been identified in the T. - Beyond that, according to our analysis, intact coagula- tion cascade-related genes were identified in the T. - The use of the T. - The generated clean reads from the 400 bp, 800 bp and 3- kb insert size libraries were used for the estimation of the genome size via JELLYFISH v1.116 [79] with a k-mer length of 17. - The three annotation results were combined as the annotation of the predicted genes. - The bench- marking sets of universal single-copy orthologues (BUS- COs) [21] were used to assess the completeness of the predicted genes with 1066 Arthropoda datasets. - De novo assembly of the tran- scriptome was performed with Trinity [85] with default parameters. - Tblastn was used with an e-value of 10 − 15 to search for corresponding transcripts in the T. - Tran- scripts found in the transcriptome were further com- pared to the genome of T. - The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.. - On the presence of prophenoloxidase in the hemolymph of the horseshoe crab, Limulus. - Recent advances in the innate immunity of invertebrate animals. - De novo assembly and characterization of early embryonic transcriptome of the horseshoe crab Tachypleus tridentatus. - The draft genome and transcriptome of the Atlantic horseshoe crab, Limulus polyphemus. - Homeotic genes, the homeobox, and the spatial organization of the embryo. - A history of the homeobox. - The organization and evolution of the dipteran and hymenopteran Down syndrome cell adhesion molecule (Dscam) genes. - The Dscam homologue of the crustacean Daphnia is diversified by alternative splicing like in insects. - An evolutionary conserved function of the JAK-STAT pathway in anti-dengue defense. - Ancestral whole- genome duplication in the marine chelicerate horseshoe crabs. - Hox genes and the evolution of the arthropod body plan. - The components of the Daphnia pulex immune system as revealed by complete genome sequencing. - 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In: Proceedings of the Eleventh International Conference on Language Resources and Evaluation (LREC 2018)
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