Shunping He

Summary

Affiliation: Institute of Hydrobiology
Country: China

Publications

  1. pmc Basal jawed vertebrate phylogenomics using transcriptomic data from Solexa sequencing
    Ming Chen
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 7:e36256. 2012
  2. pmc Parallel expansions of Sox transcription factor group B predating the diversifications of the arthropods and jawed vertebrates
    Lei Zhong
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 6:e16570. 2011
  3. pmc Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing
    Beide Fu
    The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China
    DNA Res 19:131-42. 2012
  4. pmc Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii)
    Ming Zou
    The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
    Sci Rep 2:665. 2012
  5. pmc Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes)
    Wenjing Tao
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 5:e13508. 2010
  6. pmc Characterization and comparative profiling of MiRNA transcriptomes in bighead carp and silver carp
    Wei Chi
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People s Republic of China
    PLoS ONE 6:e23549. 2011
  7. ncbi request reprint Phylogenetic relationships of Cyprinidae (Teleostei: Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1
    XiangHui Kong
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
    Sci China C Life Sci 50:780-8. 2007
  8. doi request reprint Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family
    Shunping He
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Mol Phylogenet Evol 46:818-29. 2008
  9. ncbi request reprint Molecular phylogenetic relationships of Eastern Asian Cyprinidae (pisces: cypriniformes) inferred from cytochrome b sequences
    Shunping He
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Sci China C Life Sci 47:130-8. 2004
  10. ncbi request reprint Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics
    Xuzhen Wang
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Sci China Life Sci 55:761-73. 2012

Collaborators

Detail Information

Publications40

  1. pmc Basal jawed vertebrate phylogenomics using transcriptomic data from Solexa sequencing
    Ming Chen
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 7:e36256. 2012
    ..6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences...
  2. pmc Parallel expansions of Sox transcription factor group B predating the diversifications of the arthropods and jawed vertebrates
    Lei Zhong
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 6:e16570. 2011
    ..The parallel increases in the Sox group B repertoires of the arthropods and vertebrates are consistent with the parallel increases in the complexity and diversification of these two important organismal groups...
  3. pmc Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing
    Beide Fu
    The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China
    DNA Res 19:131-42. 2012
    ..This work also provides an archive for future studies of recent speciation and evolution of Cyprinidae fishes and can be used in comparative studies of other fishes...
  4. pmc Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii)
    Ming Zou
    The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
    Sci Rep 2:665. 2012
    ..These relationships were recovered with high confidence...
  5. pmc Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes)
    Wenjing Tao
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 5:e13508. 2010
    ..The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids...
  6. pmc Characterization and comparative profiling of MiRNA transcriptomes in bighead carp and silver carp
    Wei Chi
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People s Republic of China
    PLoS ONE 6:e23549. 2011
    ..Gain and loss of family members were observed in several miRNA families, which suggests that duplication of animal miRNA genes may occur through evolutionary processes which are similar to the protein-coding genes...
  7. ncbi request reprint Phylogenetic relationships of Cyprinidae (Teleostei: Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1
    XiangHui Kong
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
    Sci China C Life Sci 50:780-8. 2007
    ..Some conserved regions in intron 1 were thought to be involved in the functional regulation. However, no correlation was found between sequence variations and species characteristic size...
  8. doi request reprint Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family
    Shunping He
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Mol Phylogenet Evol 46:818-29. 2008
    ..The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages...
  9. ncbi request reprint Molecular phylogenetic relationships of Eastern Asian Cyprinidae (pisces: cypriniformes) inferred from cytochrome b sequences
    Shunping He
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Sci China C Life Sci 47:130-8. 2004
    ..The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved...
  10. ncbi request reprint Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics
    Xuzhen Wang
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Sci China Life Sci 55:761-73. 2012
    ..Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family...
  11. ncbi request reprint The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate
    Xuzhen Wang
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Gene 399:11-9. 2007
    ..Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny...
  12. pmc Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation
    Chaobo Tong
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China
    BMC Genomics 10:83. 2009
    ....
  13. ncbi request reprint Uplift of the Tibetan plateau: evidence from divergence times of glyptosternoid catfishes
    Zuogang Peng
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Mol Phylogenet Evol 39:568-72. 2006
  14. pmc Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish
    Liandong Yang
    The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People s Republic of China
    BMC Genomics 14:65. 2013
    ..Fish-specific genome duplication cannot provide sufficient explanation for the morphological complexity of teleosts, considering the relatively large number of extinct basal ray-finned fishes...
  15. pmc Evolutionary patterns of RNA-based duplication in non-mammalian chordates
    Ming Chen
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 6:e21466. 2011
    ..Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes...
  16. pmc Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing
    Baocheng Guo
    Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
    BMC Genomics 11:396. 2010
    ..Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish...
  17. ncbi request reprint Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences
    Xuzhen Wang
    Institute of Hydrobiology, Chinese Academy of Sciences, 7 Donghu Nanlu, Wuhan, Hubei 430072, PR China
    Mol Phylogenet Evol 42:157-70. 2007
    ....
  18. pmc The rapid generation of chimerical genes expanding protein diversity in zebrafish
    Beide Fu
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P R China
    BMC Genomics 11:657. 2010
    ..Retroposition, as a special type of gene duplication- the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome...
  19. doi request reprint Evolution of MHC class I genes in two ancient fish, paddlefish (Polyodon spathula) and Chinese sturgeon (Acipenser sinensis)
    Dengqiang Wang
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    FEBS Lett 584:3331-9. 2010
    ..We also found clear evidence of recombination among class I genes of paddlefish and Chinese sturgeon...
  20. ncbi request reprint The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes
    Zuogang Peng
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, 7th Donghu South Road, Wuhan 430072, China
    Gene 376:290-7. 2006
    ..In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed...
  21. doi request reprint Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)
    Junbing Li
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People s Republic of China
    Mol Phylogenet Evol 47:472-87. 2008
    ....
  22. pmc Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE
    Chaobo Tong
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
    BMC Evol Biol 10:115. 2010
    ....
  23. ncbi request reprint Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome
    Shunping He
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
    Mol Phylogenet Evol 47:419-25. 2008
  24. pmc Ongoing speciation in the Tibetan plateau Gymnocypris species complex
    Renyi Zhang
    Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China University of Chinese Academy of Sciences, Beijing, China
    PLoS ONE 8:e71331. 2013
    ..This study provides the first genetic evidence for the occurrence of convergence or reversal in the schizothoracine fish of the Tibetan Plateau at small temporal scales. ..
  25. ncbi request reprint Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes)
    Zuogang Peng
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Mol Phylogenet Evol 42:854-62. 2007
  26. doi request reprint Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative
    Baocheng Guo
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
    Gene 439:102-12. 2009
    ..Genealogical analysis revealed that T. qiaojiensis was tetraploid, and T. douronensis, T. qiaojiensis as well as T. sinensis had an allotetraploid ancestor...
  27. doi request reprint Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): a proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses
    Wenjing Tao
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
    Mol Phylogenet Evol 66:603-16. 2013
    ..Future studies should include higher levels of taxon sampling and partitioned, model-based analyses...
  28. ncbi request reprint Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces: Teleostei): A new insight
    Zuogang Peng
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, 7 Donghu South Road, Wuhan 430072, China
    Gene 370:113-24. 2006
    ..The origin of the Otocephala is estimated as having occurred about 282 Mya, with the origin of the Otophysi being estimated at about 251 Mya...
  29. doi request reprint Distinct evolutionary patterns between two duplicated color vision genes within cyprinid fishes
    Zhiqiang Li
    Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 7th Donghu South Road, 430072, Wuhan, Hubei Province, People s Republic of China
    J Mol Evol 69:346-59. 2009
    ..Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes...
  30. doi request reprint Phylogenetic relationships and estimation of divergence times among Sisoridae catfishes
    Meiling Yu
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 400732, China
    Sci China Life Sci 55:312-20. 2012
    ..9 Mya). The speciation of glyptosternoid fishes is hypothesized to be closely related with the uplift of the Qinghai-Tibet Plateau...
  31. doi request reprint Hox genes of the Japanese eel Anguilla japonica and Hox cluster evolution in teleosts
    Baocheng Guo
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P R China
    J Exp Zool B Mol Dev Evol 314:135-47. 2010
    ..Based on current teleostean phylogeny, the HoxDb cluster was lost independently in the teleost lineages Otocephala and Euteleostei...
  32. ncbi request reprint Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences
    Xianguang Guo
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
    Mol Phylogenet Evol 35:344-62. 2005
    ....
  33. doi request reprint The complete mitochondrial genome of Glyptothorax fukiensis fukiensis (Teleostei, Siluriformes: Sisoridae)
    Chuanjiang Zhou
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
    Mitochondrial DNA 23:414-6. 2012
    ..The complete mitochondrial genome sequence of G. fukiensis fukiensis is the first report for Sisoridae, it would contribute to better understand population genetics, biogeography, and evolution of this lineage...
  34. ncbi request reprint Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences
    Zuogang Peng
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
    Mol Phylogenet Evol 31:979-87. 2004
    ..Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi...
  35. pmc Evolutionary patterns of RNA-based gene duplicates in Caenorhabditis nematodes coincide with their genomic features
    Ming Zou
    The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
    BMC Res Notes 5:398. 2012
    ..However, studies about this kind of duplication in Caenorhabditis nematodes have not been reported...
  36. ncbi request reprint The complete mitochondrial genome of Leiocassis crassilabris (Teleostei, Siluriformes: Bagridae)
    Chuanjiang Zhou
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    Mitochondrial DNA 25:183-4. 2014
    ..The complete mitochondrial genome sequence of L. crassilabris would contribute to better understand population genetics, conservation, biogeography, evolution of this lineage...
  37. doi request reprint Olfactory receptor gene family evolution in stickleback and medaka fishes
    Ming Chen
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
    Sci China Life Sci 53:257-66. 2010
    ..Further analysis showed that many PTSs overlap, or are adjacent to previously deduced binding sites in mammals. These results support the hypothesis that binding sites of fish OR genes may evolved under positive selection...
  38. ncbi request reprint Cloning and sequencing of the growth hormone gene of large yellow croaker and its phylogenetic significance
    Yun Chen
    State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, People s Republic of China
    Biochem Genet 42:365-75. 2004
    ..In general, this analysis does not support the monophyll of the families Centropomidae and Carangidae. But our GH gene tree indicates that the representative species of the families Sparidae and Sciaenidae are a monophyletic group...
  39. doi request reprint A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)
    Liandong Yang
    The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, PR China University of Chinese Academy of Sciences, Beijing 100049, PR China Electronic address
    Gene 533:261-9. 2014
    ..This study has provided an update on rainbow trout miRNAs and their targets, which represents a foundation for future studies. ..
  40. pmc The roles and evolutionary patterns of intronless genes in deuterostomes
    Ming Zou
    The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Comp Funct Genomics 2011:680673. 2011
    ..These genes are good candidates for subsequent functional and evolutionary analyses specifically...