Cited by 265

The DOI matches its Crossref record; 99 of the 99 references it cites were found in a registry or an index.

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

Open access

Zhang, Xiaojun, Sun, Lina, Yuan, Jianbo, Sun, Yamin, Gao, Yi, Zhang, Libin, Li, Shihao, Dai, Hui, Hamel, Jean-François, Liu, Chengzhang, Yu, Yang, Liu, Shilin, Lin, Wenchao, Guo, Kaimin, Jin, Songjun, Xu, Peng, Storey, Kenneth B., Huan, Pin, Zhang, Tao, Zhou, Yi, Zhang, Jiquan, Lin, Chenggang, Li, Xiaoni, Xing, Lili, Huo, Da, Sun, Mingzhe, Wang, Lei, Mercier, Annie, Li, Fuhua, Yang, Hongsheng, Xiang, Jianhai·2017·PLOS Biology

DOI 10.1371/journal.pbio.2003790

Open this paper in CoChat — free account

Abstract

Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1371/journal.pbio.2003790

Cites

99 of 99 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm092 · Cited by 28,730
Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
Takahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 21,039
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,806
jModelTest 2: more models, new heuristics and parallel computing
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012) · Nature Methods · doi:10.1038/nmeth.2109 · Cited by 16,785
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,116
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,617
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti610 · Cited by 11,495
Circos: An information aesthetic for comparative genomics
Krzywinski, M., Schein, J., Birol, İ., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,964
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
The State of World Fisheries and Aquaculture 2022
(2022) · FAO eBooks · doi:10.4060/cc0461en · Cited by 5,689
CAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
The Evolutionary Fate and Consequences of Duplicate Genes
Lynch, M., & Conery, J. S. (2000) · Science · doi:10.1126/science.290.5494.1151 · Cited by 4,988
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
Marçais, G., & Kingsford, C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr011 · Cited by 4,661
KAAS: an automatic genome annotation and pathway reconstruction server
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C., & Kanehisa, M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm321 · Cited by 4,153
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., Orvis, J., White, O., Buell, C. R., & Wortman, J. R. (2008) · Genome Biology · doi:10.1186/gb-2008-9-1-r7 · Cited by 4,079
Infernal 1.1: 100-fold faster RNA homology searches
Nawrocki, E. P., & Eddy, S. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt509 · Cited by 3,591
Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
Tarailo‐Graovac, M., & Chen, N. (2009) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0410s25 · Cited by 3,398
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
Friedländer, M. R., Mackowiak, S. D., Li, N., Chen, W., & Rajewsky, N. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr688 · Cited by 3,207
Automated generation of heuristics for biological sequence comparison
Slater, G. S. C., & Birney, E. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-31 · Cited by 2,933
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
Self-citation
NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data
Patel, R. K., & Jain, M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030619 · Cited by 2,917
GeneWise and genomewise
Birney, E., Clamp, M., & Durbin, R. (2004) · Genome Research · doi:10.1101/gr.1865504 · Cited by 2,542
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M., & Blaxter, M. L. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3012 · Cited by 2,481
The oyster genome reveals stress adaptation and complexity of shell formation
Zhang, G., Fang, X., Guo, X., Li, L., Luo, R., Xu, F., Yang, P., Zhang, L., Wang, X., Qi, H., et al. (2012) · Nature · doi:10.1038/nature11413 · Cited by 2,246
Self-citation
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
Parra, G., Bradnam, K., & Korf, I. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm071 · Cited by 2,184
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., & the UniProt Consortium (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu739 · Cited by 1,928
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
CAFE: a computational tool for the study of gene family evolution
De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl097 · Cited by 1,790
The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins
Dehal, P., Satou, Y., Campbell, R. K., Chapman, J., Degnan, B., De Tomaso, A., Davidson, B., Di Gregorio, A., Gelpke, M., Goodstein, D. M., et al. (2002) · Science · doi:10.1126/science.1080049 · Cited by 1,641
JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations
van Ooijen, J. W., Verlaat, J. V. '., Ooijen, J. W. V., Tol, J., van Dalen, J., van Buren, J., van der Meer, J., van Krieken, J., van Ooijen, J. W., van Kessel, J., et al. (2006) · Cited by 1,580
The Genome of the Sea Urchin Strongylocentrotus purpuratus
Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., et al. (2006) · Science · doi:10.1126/science.1133609 · Cited by 1,132
Self-citation
Tree of Life Reveals Clock-Like Speciation and Diversification
Hedges, S. B., Marin, J., Suleski, M., Paymer, M., & Kumar, S. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv037 · Cited by 972
The dynamic genome of Hydra
Chapman, J. A., Kirkness, E. F., Simakov, O., Hampson, S. E., Mitros, T., Weinmaier, T., Rattei, T., Balasubramanian, P. G., Borman, J., Busam, D., et al. (2010) · Nature · doi:10.1038/nature08830 · Cited by 810
Self-citation
Fossil steroids record the appearance of Demospongiae during the Cryogenian period
Love, G. D., Grosjean, E., Stalvies, C., Fike, D. A., Grotzinger, J. P., Bradley, A. S., Kelly, A. E., Bhatia, M., Meredith, W., Snape, C. E., et al. (2009) · Nature · doi:10.1038/nature07673 · Cited by 731
The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
Douzery, E. J. P., Snell, E. A., Bapteste, E., Delsuc, F., & Philippe, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403984101 · Cited by 638
Sea cucumber fisheries: global analysis of stocks, management measures and drivers of overfishing
Purcell, S. W., Mercier, A., Conand, C., Hamel, J., Toral‐Granda, M. V., Lovatelli, A., & Uthicke, S. (2013) · Fish and Fisheries · doi:10.1111/j.1467-2979.2011.00443.x · Cited by 494
Self-citation
Molecular Phylogeny and Divergence Times of Deuterostome Animals
Blair, J. E., & Hedges, S. B. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi225 · Cited by 449
The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation
Wang, Y., Lu, Y., Zhang, Y., Ning, Z., Li, Y., Zhao, Q., Lu, H., Huang, R., Xia, X., Feng, Q., et al. (2015) · Nature Genetics · doi:10.1038/ng.3280 · Cited by 434
Self-citation
Using <tt>GeneWise</tt> in the Drosophila Annotation Experiment
Birney, E., & Durbin, R. (2000) · Genome Research · doi:10.1101/gr.10.4.547 · Cited by 398
A genomic view of the sea urchin nervous system
Burke, R. D., Angerer, L. M., Elphick, M. R., Humphrey, G. W., Yaguchi, S., Kiyama, T., Liang, S., Mu, X., Agca, C., Klein, W. H., et al. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.007 · Cited by 293
Hemichordate genomes and deuterostome origins
Simakov, O., Kawashima, T., Marlétaz, F., Jenkins, J., Koyanagi, R., Mitros, T., Hisata, K., Bredeson, J., Shoguchi, E., Gyoja, F., et al. (2015) · Nature · doi:10.1038/nature16150 · Cited by 255
Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives
Swalla, B. J., & Smith, A. B. (2008) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2007.2246 · Cited by 252
A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus
Livingston, B. T., Killian, C. E., Wilt, F., Cameron, A., Landrum, M. J., Ermolaeva, O., Sapojnikov, V., Maglott, D. R., Buchanan, A. M., & Ettensohn, C. A. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.07.047 · Cited by 243
The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest
Hall, M. R., Kocot, K. M., Baughman, K. W., Fernandez-Valverde, S. L., Gauthier, M. E. A., Hatleberg, W. L., Krishnan, A., McDougall, C., Motti, C. A., Shoguchi, E., et al. (2017) · Nature · doi:10.1038/nature22033 · Cited by 204
The cost of being valuable: predictors of extinction risk in marine invertebrates exploited as luxury seafood
Purcell, S. W., Polidoro, B. A., Hamel, J.-F., Gamboa, R. U., & Mercier, A. (2014) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2013.3296 · Cited by 180
Self-citation
Unusual gene order and organization of the sea urchin hox cluster
Cameron, R. A., Rowen, L., Nesbitt, R., Bloom, S., Rast, J. P., Berney, K., Arenas‐Mena, C., Martinez, P., Lucas, S., Richardson, P. M., et al. (2006) · Journal of Experimental Zoology Part B: Molecular and Developmental Evolution · doi:10.1002/jez.b.21070 · Cited by 173
FGF signals guide migration of mesenchymal cells, control skeletal morphogenesis and regulate gastrulation during sea urchin development
Röttinger, É., Saudemont, A., Duboc, V., Besnardeau, L., McClay, D. R., & Lepage, T. (2007) · Development · doi:10.1242/dev.014282 · Cited by 158
Extracellular matrix protein tenascin-C is required in the bone marrow microenvironment primed for hematopoietic regeneration
Nakamura‐Ishizu, A., Okuno, Y., Omatsu, Y., Okabe, K., Morimoto, J. O., Uede, T., Nagasawa, T., Suda, T., & Kubota, Y. (2012) · Blood · doi:10.1182/blood-2011-11-393645 · Cited by 142
Phylogenomic analysis of echinoderm class relationships supports Asterozoa
Telford, M. J., Lowe, C. J., Cameron, C. B., Ortega‐Martinez, O., Aronowicz, J., Oliveri, P., & Copley, R. R. (2014) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2014.0479 · Cited by 142
Regeneration, tissue injury and the immune response
Godwin, J. W., & Brockes, J. P. (2006) · Journal of Anatomy · doi:10.1111/j.1469-7580.2006.00626.x · Cited by 134
The Role of Brachyury (T) during Gastrulation Movements in the Sea Urchin Lytechinus variegatus
Gross, J. M., & McClay, D. R. (2001) · Developmental Biology · doi:10.1006/dbio.2001.0426 · Cited by 130
Red sea urchins (Strongylocentrotus franciscanus) can live over 100 years: confirmation with A-bomb 14 carbon
Ebert, T. A., & Southon, J. R. (2003) · AquaDocs (United Nations Educational, Scientific and Cultural Organization) · Cited by 123
Paired gill slits in a fossil with a calcite skeleton
Alonso, P. D., Jacobson, A. G., & Jefferies, R. P. S. (2002) · Nature · doi:10.1038/nature00805 · Cited by 115
Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus
Sun, L., Chen, M., Yang, H., Wang, T., Liu, B., Shu, C., & Gardiner, D. M. (2011) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2011.03.002 · Cited by 113
Self-citation
Evolution of Hoxgene clusters in deuterostomes
Pascual‐Anaya, J., D’Aniello, S., Kuratani, S., & García‐Fernàndez, J. (2013) · BMC Developmental Biology · doi:10.1186/1471-213x-13-26 · Cited by 110
Gene expression profiling of intestinal regeneration in the sea cucumber
Ortíz-Pineda, P. A., Ramírez-Gómez, F., Ortiz, J. P., González-Díaz, S., Jesús, F. S.-D., Hernández‐Pasos, J., Valle-Avila, C. D., Rojas‐Cartagena, C., Suárez‐Castillo, E. C., Tossas, K., et al. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-262 · Cited by 101
Gut Regeneration in Holothurians: A Snapshot of Recent Developments
Mashanov, V. S., & García‐Arrarás, J. E. (2011) · Biological Bulletin · doi:10.1086/bblv221n1p93 · Cited by 101
Transcriptomic changes during regeneration of the central nervous system in an echinoderm
Mashanov, V. S., Zueva, O. R., & García‐Arrarás, J. E. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-357 · Cited by 90
Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity and morphogenesis
Ettensohn, C. A. (2008) · Development · doi:10.1242/dev.023564 · Cited by 88
The Fox/Forkhead transcription factor family of the hemichordate Saccoglossus kowalevskii
Fritzenwanker, J. H., Gerhart, J. C., Freeman, R. M., & Lowe, C. J. (2014) · EvoDevo · doi:10.1186/2041-9139-5-17 · Cited by 85
Genomic Approaches Reveal Unexpected Genetic Divergence Within Ciona intestinalis
Suzuki, M. M., Nishikawa, T., & Bird, A. P. (2005) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0009-3 · Cited by 80
A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos
McCauley, B. S., Weideman, E. P., & Hinman, V. F. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2009.11.020 · Cited by 79
Prostate secretory protein PSP-94 decreases tumor growth and hypercalcemia of malignancy in a syngenic in vivo model of prostate cancer.
Shukeir, N., Arakelian, A., Kadhim, S., Garde, S. V., & Rabbani, S. A. (2003) · PubMed · Cited by 79
How was the notochord born?
Satoh, N., Tagawa, K., & Takahashi, H. (2012) · Evolution & Development · doi:10.1111/j.1525-142x.2011.00522.x · Cited by 79
Longevity and lack of senescence in the red sea urchin Strongylocentrotus franciscanus
Ebert, T. A. (2008) · Experimental Gerontology · doi:10.1016/j.exger.2008.04.015 · Cited by 76
Signal-dependent regulation of the sea urchin skeletogenic gene regulatory network
Sun, Z., & Ettensohn, C. A. (2014) · Gene Expression Patterns · doi:10.1016/j.gep.2014.10.002 · Cited by 76
Netrins and netrin receptors
Livesey, F. J. (1999) · Cellular and Molecular Life Sciences · doi:10.1007/s000180050006 · Cited by 74
Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms
McCauley, B. S., Wright, E. P., Exner, C. R. T., Kitazawa, C., & Hinman, V. F. (2012) · EvoDevo · doi:10.1186/2041-9139-3-17 · Cited by 72
Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera of Daphniaand their coevolution with chaoborid predators
Kotov, A. A., & Taylor, D. J. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-129 · Cited by 72
RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas
Sun, L., Yang, H., Chen, M., Ma, D., & Lin, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069441 · Cited by 71
Self-citation
P16 is an essential regulator of skeletogenesis in the sea urchin embryo
Cheers, M. S., & Ettensohn, C. A. (2005) · Developmental Biology · doi:10.1016/j.ydbio.2005.02.037 · Cited by 71
Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants
Jo, J., Oh, J., Lee, H.-G., Hong, H.-H., Lee, S., Cheon, S., Kern, E., Jin, S., Cho, S.-J., Park, J., et al. (2017) · GigaScience · doi:10.1093/gigascience/giw006 · Cited by 70
Self-citation
PTGBase: an integrated database to study tandem duplicated genes in plants
Yu, J., Ke, T., Tehrim, S., Sun, F., Liao, B., & Hua, W. (2015) · Database · doi:10.1093/database/bav017 · Cited by 63
Antithrombotic and Anticoagulant Activity of Depolymerized Fragment of the Glycosaminoglycan Extracted from Stichopus japonicus Selenka
Suzuki, N., Kitazato, K., Takamatsu, J., et al. (1991) · Thrombosis and Haemostasis · doi:10.1055/s-0038-1648154 · Cited by 61
Radial glial cells play a key role in echinoderm neural regeneration
Mashanov, V. S., Zueva, O. R., & García‐Arrarás, J. E. (2013) · BMC Biology · doi:10.1186/1741-7007-11-49 · Cited by 60
Angiopoietin-1 enhances skeletal muscle regeneration in mice
Mofarrahi, M., McClung, J. M., Kontos, C. D., Davis, E. C., Tappuni, B., Moroz, N., Pickett, A., Huck, L., Harel, S., Danialou, G., et al. (2015) · American Journal of Physiology-Regulatory, Integrative and Comparative Physiology · doi:10.1152/ajpregu.00267.2014 · Cited by 60
Multiple global radiations in tadpole shrimps challenge the concept of ‘living fossils’
Mathers, T. C., Hammond, R. L., Jenner, R. A., Hänfling, B., & Gómez, Á. (2013) · PeerJ · doi:10.7717/peerj.62 · Cited by 53
Evolution of a pentameral body plan was not linked to translocation of anterior Hox genes: the echinoderm HOX cluster revisited
Byrne, M., Martínez, P., & Morris, V. B. (2016) · Evolution & Development · doi:10.1111/ede.12172 · Cited by 52
Genomic organization of H ox and P ara H ox clusters in the echinoderm, A canthaster planci
Baughman, K. W., McDougall, C., Cummins, S. F., Hall, M., Degnan, B. M., Satoh, N., & Shoguchi, E. (2014) · genesis · doi:10.1002/dvg.22840 · Cited by 49
A critical role for thrombin in vertebrate lens regeneration
Imokawa, Y., Simon, A., & Brockes, J. P. (2004) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2004.1467 · Cited by 44
On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates
Satoh, N., Tagawa, K., Lowe, C. J., Yu, J., Kawashima, T., Takahashi, H., Ogasawara, M., Kirschner, M. W., Hisata, K., Su, Y., et al. (2014) · genesis · doi:10.1002/dvg.22831 · Cited by 41
MSMB variation and prostate cancer risk: Clues towards a possible fungal etiology
Sutcliffe, S., Marzo, A. M. D., Sfanos, K. S., & Laurence, M. (2014) · The Prostate · doi:10.1002/pros.22778 · Cited by 40
Hepassocin regulates cell proliferation of the human hepatic cells L02 and hepatocarcinoma cells through different mechanisms
Cao, M.-M., Xu, W., Li, C., Cao, C.-Z., Wang, Z., Yao, J., Yu, M., Zhan, Y., Wang, X., Tang, L., et al. (2011) · Journal of Cellular Biochemistry · doi:10.1002/jcb.23202 · Cited by 40
Brief review of the stylophoran debate
Ruta, M. (1999) · Evolution & Development · doi:10.1046/j.1525-142x.1999.99008.x · Cited by 38
Hemichordata (Pterobranchia, Enteropneusta) and the fossil record
Maletz, J. (2013) · Palaeogeography Palaeoclimatology Palaeoecology · doi:10.1016/j.palaeo.2013.06.010 · Cited by 37
Cloning and characterization of a mouse liver-specific gene mfrep-1, upregulated in liver regeneration
Yan, J., Ying, H., Gu, F., He, J., Yu Li, L. I., Liu, H. M., & Xu, Y. (2002) · Cell Research · doi:10.1038/sj.cr.7290137 · Cited by 37
Regeneration in Hemichordates and Echinoderms
Rychel, A. L., & Swalla, B. J. (2009) · Springer eBooks · doi:10.1007/978-90-481-2767-2_10 · Cited by 29
Postembryonic Organogenesis of the Digestive Tube
Mashanov, V. S., Zueva, O. R., & García‐Arrarás, J. E. (2014) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/b978-0-12-391498-9.00006-1 · Cited by 26
Specification to Biomineralization: Following a Single Cell Type as It Constructs a Skeleton
Lyons, D. C., Martik, M. L., Saunders, L. R., & McClay, D. R. (2014) · Integrative and Comparative Biology · doi:10.1093/icb/icu087 · Cited by 26
Expression of Hox4 during development of the pentamerous juvenile sea star, Parvulastra exigua
Cisternas, P., & Byrne, M. (2009) · Development Genes and Evolution · doi:10.1007/s00427-010-0318-4 · Cited by 26
Impact of family structure and common environment on heritability estimation for neuroimaging genetics studies using Sequential Oligogenic Linkage Analysis Routines
Koran, M. E. I., Thornton‐Wells, T. A., Jahanshad, N., Glahn, D. C., Thompson, P. M., Blangero, J., Nichols, T. E., Kochunov, P., & Landman, B. A. (2014) · Journal of medical imaging · doi:10.1117/1.jmi.1.1.014005 · Cited by 19
FGF signals guide migration of mesenchymal cells, control skeletal morphogenesis and regulate gastrulation during sea urchin development
Röttinger, É., Saudemont, A., Duboc, V., Besnardeau, L., McClay, D. R., & Lepage, T. (2008) · Development · doi:10.1242/dev.020016 · Cited by 11

Harnessing genomics to fast-track genetic improvement in aquaculture
Houston, R. D., Bean, T. P., Macqueen, D. J., Gundappa, M. K., Jin, Y. H., Jenkins, T. L., Selly, S. L. C., Martin, S. A. M., Stevens, J. R., Santos, E. M., et al. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0227-y · Cited by 622
Chromosome-level reference genome of the jellyfish Rhopilema esculentum
Li, Y., Gao, L., Pan, Y., Tian, M., Li, Y., He, C., Dong, Y., Sun, Y., & Zhou, Z. (2020) · GigaScience · doi:10.1093/gigascience/giaa036 · Cited by 31
Self-citation
Exploring Biomineralization in Echinoderms: A Review of Gene Regulatory Networks Through Bibliometrics and Comparative Genomics
Guo, X., Cong, X., Yu, Z., & Yuan, X. (2026) · Biology · doi:10.3390/biology15201796

See all 265

Authors: Zhang, X., Sun, L., Yuan, J., Sun, Y., Gao, Y., Zhang, L., Li, S., Dai, H., Hamel, J.-F., Liu, C., Yu, Y., Liu, S., Lin, W., Guo, K., Jin, S., Xu, P., Storey, K. B., Huan, P., Zhang, T., Zhou, Y., Zhang, J., Lin, C., Li, X., Xing, L., Huo, D., Sun, M., Wang, L., Mercier, A., Li, F., Yang, H., & Xiang, J.
Venue: PLOS Biology
Publisher: Public Library of Science (PLoS)
Published: 2017-10-12
Volume: 15
Issue: 10
Pages: e2003790
ISSN: 1544-9173 (ISSN-L)
1545-7885
DOI: 10.1371/journal.pbio.2003790
OpenAlex: W2761961135
Cited by: 265
References: 99
FWCI: 20.80
Type: journal article
Language: en
Open access: gold

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Self-check

Citations

Cites

Cited by

Metadata

Record

About these checks

Data sources