All Publications-Laboratory of Genetics & Evolution of Molluscs

Widespread presence of bone marrow–like hematopoietic stem cell niche in invertebrate skeletons (ScienceAdviser Highlight: Hematopoietic stem cells on the half shell)

Lian S#, Hu N#, Chen X#, Dai X#, Zhu X, Qiao R, Liu S, Lu Y, Zhang F, Sun F, Pu Z, Yang Z, Xu R, Wang H, Zhao L, Xing Q, Li S, Wang W, Dong B, Zhang L, Hu J, Wang J*, Bao Z*, Wang S*

Science Advances. 2025，11: eadw0958.

Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions

Lv J#, Ma S#, Ma C#, Liu F#, Duan X, Geng Q, Liu F, Li G, Li Y, Wang J, Li C, Zheng H, Zhang Y, Sun Z, Wang J, Fan G, Huang S, Zhang L*, Bao Z*, Wang S*

Nucleic Acids Research (In press)

MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species

Liu F#, Cai B#, Lian S#, Chang X, Chen D, Pu Z, Bao L, Wang J, Lv J, Zheng H, Bao Z, Zhang L*, Wang S*, Li Y*

Nucleic Acids Research 53：D1075-D1086

Marine evo-devo: New frontiers from Lophotrochozoa

Lian S#, Lv J#, Li Y, Zhang L, Bao Z, Wang S*

The Innovation 6(6): 100869

Molluscan systematics historical perspectives and the way ahead

Xu B, Kong L, Sun J, Zhang J, Zhang Y, Song H, Li Q, Uribe JE, Halanych KM, Cai C, Dong Y, Wang S, Li Y*

Biological Reviews 100: 672-697

Chromosome-level genome assembly of Eden’s whale clarifies the taxonomy and speciation of Bryde’s whale complex

Lin YT, Hui F, Han W, Li YX, Heung BYW, Hou CM, Wang S, Qiu JW*

Molecular Biology and Evolution 42: 1-9

100 dinoflagellate genome project

Wang DZ*, You YC, Zhang WP, Liu JQ, Bao LS, Han WT, Teng ZJ, Qin QL, Zheng Y, Zhao LS, Gu HF, Li YL, Li X, Zhen HK, Chen HJ, Wang S, Lin Q*, Zhang Y*

The Innovation 7: 101120

Diversity of reverse-transcriptase-containing viruses through global metagenomics

Zheng K, Liang Y*, Zhang Y, Paez-Espino D, Shao H, Sung YY, Mok WJ, Wong LL, Wang S, McMinn A*, Wang M*

hLife 3:52–56

High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

Chen X#, Han W#, Chang X, Tang C, Chen K, Bao L, Zhang L, Hu J, Wang S*, Bao Z*.

Scientific Data 12: 507

Single-cell RNA sequencing reveals cellular heterogeneity and gonadal niche interactions in the hermaphroditic scallop Argopecten irradians

Shu Y#, Li Y#, Wei H*, Liu L, Liu T, Zhang L, Ma X, Yang Y, Li G, Zhang X, Wang S, Bao Z, Zhang L*

Water Biology and Security. 100405.

Optimizing genotype imputation strategies for low coverage whole genome and 2b-RAD sequencing in bivalve molluscs

Huang X, Duan X, Ma S, Sun X, Geng Q, Sun X, Xing Q, Zhang L, Wang S, Lv J*

Aquaculture. 608: 742713.

Systematic screening and dynamic profiling of germline regulatory pathways and spermatogonial surface markers in a bivalve mollusc

Liu L#, Shu Y#, Liu T, Wei H, Yang Y, Zhang L, Ma X, Li G, Li Y, Wang S, Zhang L*

Computational and Structural Biotechnology Journal 27: 519-530

Core histone families of mollusca: systematic identification, evolutionary insights, and functional analysis

Guan Y, Chen X, Zhu X, Liu F, Ma Y, Han W, Yang R, Li Y, Bao L, Wang S, Bao Z, Wang J*

BMC Genomics 26：594

Insights from the single-cell level lineage trajectory and somatic-germline interactions during spermatogenesis in dwarf surfclam Mulinia lateralis

Li Y, Wei H*, Dai X, Zhang L, Liu L, Chen X, Liu T, Shu Y, Yang Y, Wang S, Bao Z, Zhang L*

BMC Genomics 26: 69

Development and evaluation of high-throughput HD-Marker arrays in pacific white shrimp (Litopenaeus vannamei)

Liu M#, Yang Z#, Huang X#, Zeng Q, Mu Q, Xu Z, Li Z, Liu P*, Wang S, Hu J, Bao Z

Aquaculture 599: 742119

Transcriptome analysis reveals the lncRNA-mRNA co-expression network regulating the aestivation of sea cucumber

Chen X, Han W, Yang R, Zhu X, Li S, Wang Y, Sun X, Li Y, Bao L, Zhang L, Wang S, Wang J*

Marine Biotechnology 27: 15

A draft genome assembly of the mushroom coral Podabacia crustacea (Pallas, 1766)

Tang C#, Chen X#, Ke S#, Han W, Chang X, Li X, Wang Z, Chen K, Bao L, Hu J, Wang S, Bao Z*

Scientific Data 12: 1677

Re-annotation improved large-scale assembly of the reef-building coral Acropora intermedia

Chang X#, Han W#, Chen X, Tang C, Wang D, Huang H, Li Y, Chen K, Hu J, Bao Z, Chen H*, Wang S*

Scientific Data 12: 1504

An improved chromosome-level genome assembly of a deep-sea limpet (Bathyacmaea lactea)

Chen D#, Ma Y#, Liu Y, Wang M, Wang J, Wang S, Li Y*

Scientific Data (In press)

Complete mitochondrial genome of the brain coral Platygyra daedalea (Ellis & Solander, 1786)

Chang X, Chen X*, Ke S, Li X, Chen K, Li Y, Bao L, Hu J, Wang S, Bao Z

Mitochondrial DNA Part B 10(6): 414-419

Complete mitochondrial genome and phylogenetic analysis of Podabacia crustacea (Pallas, 1766)

Tang C, Han W*, Ke S, Wang D, Chen K, Bao L, Guan L, Hu J, Wang S, Bao Z

Mitochondrial DNA Part B 10(7):537-542

Complete mitochondrial genome and phylogenetic analysis of Podabacia elegans (Pallas, 1766)

20.Tang C, Han W*, Ke S, Wang D, Chen K, Bao L, Guan L, Hu J, Wang S, Bao Z

Mitochondrial DNA Part B 10: 537-542

Pan-evolutionary and regulatory genome architecture delineated by integrated macro- and microsynteny approach

Yu H#, Li Y #*, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S*

Nature Protocols. 2024, 19: 1623–1678.

Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids

Wei J#, Zhang W#, Jiang A#, Peng H#, Zhang Q#, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L*, Chen K*, Dong B*.

Nature Communications. 2024, 15: 2395.

Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs

Jiang A#, Han K#, Wei J#, Su X#, Wang R, Zhang W, Liu X, Qiao J, Liu P, Liu Q, Zhang J, Zhang N, Ge Y, Zhuang Y, Yu H, Wang S, Chen K, Lu W, Xu X, Yang H, Fan G*, Dong B*

Science Advances. 2024, 10(13): eadi9035.

Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach

Ma C#, Xu C#, Zhang T#, Mu Q, Lv J, Xing Q, Yang Z, Guan Y, Chen C, Ni K, Dai X, Ding W, Hu J, Bao Z, Wang S, Liu P*.

Communications Biology. 2024, 7: 827.

Deqformer: High-definition and scalable deep learning probe design method

Cai Y#, Lv J#, Li R#, Huang X., Wang S, Bao Z, Zeng Q*.

Briefings in Bioinformatics. 2024, 25(2): 1–9.

Genome-wide association study reveals the underlying regulatory mechanisms of red blood traits in Anadara granosa

He X, Liao Y, Yu G, Wang S, Bao, Y*

BMC Genomics 25: 931

Tracking organic matrix in the seashell by elemental mapping under laser-induced breakdown spectroscopy

Ren L, Li S, Ye W, Lv Q, Sun Y, Zhou X, Lian S, Lv J, Wang S, Guo J, Tian Y, Zheng R, Lu Y*.

Talanta. 2024, 271: 125658.

A genome-wide association study to identify the genes associated with growth-related traits in Tegillarca granosa

He X, Liao Y, Yang Z, Liu H, Wang S, Bao Y*.

Aquaculture. 2024, 578: 740127.

Transcriptomic analysis of mRNA and miRNA reveals new insights into the regulatory mechanisms of Anadara granosa responses to heat stress.

He X, Liao Y, Shen Y, Shao J, Wang S, Bao Y*.

Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. 2024, 52: 101311.

EDomics: a comprehensive and comparative multi-omics database for animal evo-devo

Wei J#, Liu P#, Liu F#, Jiang A, Qiao J, Pu Z, Wang B, Zhang J, Jia D, Li Y*, Wang S*, Dong B*.

Nucleic Acids Research. 2023, 51: D913-D923.

Cardiac performance and heart gene network provide dynamic responses of bay scallop Argopecten irradians irradians exposure to marine heatwaves

Zhu X, Zhang J, Li M, Hou X, Liu A, Dong X, Wang W, Xing Q*

Science of The Total Environment. 2023, 882: 163594.

Hemoglobin wonders: A fascinating gas transporter diving into molluscs

Zhang W, Zhang Y, Shi X, Wang S, Bao Y*.

Critical Reviews in Biochemistry and Molecular Biology. 2023, 58(2–6): 132–157.

K252a inhibition of sperm viability for efficient crossbreeding of hermaphroditic bivalves

Liu T, Wei H, Zhang L, Liu L, Li Y, Shu Y, Yang Y, Zhao B, Xing Q, Zeng Q, Wang C, Wang S, Bao Z, Zhang L*

Aquaculture. 2023, 577: 739930.

Comparative analysis of the cardiac structure and transcriptome of scallop and snail, perspectives on heart chamber evolution

Lu M#, Hayat R#, Zhang X#, Jiao Y, Huang J, Huangfu Y, Jiang M, Fu J, Jiang Q, Gu Y, Wang S, Akerberg A A, Su Y*, Zhao L*.

Marine Life Science & Technology. 2023, 5(4): 478–491.

Preliminary study of laser-induced breakdown spectroscopy for Mg/Ca investigation in cultured scallop shells

Li Y, Wang Y, Wang S, Zheng R, Bao Z, Lu Y*.

Journal of Laser Applications. 2023, 35: 022018.

Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation

Han W#, Liu L#, Wang J#, Wei H#, Li Y#, Zhang L#, Guo Z, Li Y, Liu T, Zeng Q, Xing Q, Shu Y, Wang T, Yang Y, Zhang M, Li R, Yu J, Pu Z, Lv J, Lian S, Hu J, Hu X, Bao Z, Bao L*, Zhang L*, Wang S*.

Nature Ecology & Evolution. 2022, 6: 1891-1906.

Biosynthesis of saponin defensive compounds in sea cucumbers

Thimmappa R*, Wang S#, Zheng M#, Misra RC, Huang AC, Saalbach G, Chang Y, Zhou Z, Hinman V, Bao Z, Osbourn A*.

Nature Chemical Biology. 2022, 18: 774-781.

Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

Sun Z#, Huang S#,*, Zhu P, Tzehau L, Zhao H, Lv J, Zhang R, Zhou L, Niu Q, Wang X, Zhang M, Jing G, Bao Z, Liu J, Wang S*, Xu J*.

Genome Biology. 2022, 23: 36.

Targeted genotyping of a whole-gene repertoire by an ultrahigh-multiplex and flexible HD-Marker approach

Liu P#, Lv J#,*, Ma C, Zhang T, Huang X, Yang Z, Zhang L, Hu J, Wang S, Bao Z*.

Engineering. 2022, 13: 186-196.

Adaptive bird-like genome miniaturization during the evolution of scallop swimming lifestyle

Li Y#, Liu Y#, Yu H, Liu F, Han W, Zeng Q, Zhang Y, Zhang L, Hu J, Bao Z, Wang S*.

Genomics Proteomics & Bioinformatics. 2022, 20: 1066-1077.

Dynamic transcriptome analysis reveals the gene network of gonadal development from the early history life stages in dwarf surfclam Mulinia lateralis

Li Y, Liu L, Zhang L, Wei H, Wu S, Liu T, Shu Y, Yang Y, Yang Z, Wang S, Bao Z, Zhang L*.

Biology of Sex Differences. 2022, 13: 69.

Development of a high-throughput SNP array for sea cucumber (Apostichopus japonicus) and its application in genomic selection with MCP regularized deep neural networks

Lv J#, Wang Y#,*, Ni P, Lin P, Hou H, Ding J*, Chang Y*, Hu J*, Wang S, Bao Z.

Genomics. 2022, 114: 110426.

Decoding the byssus fabrication by spatiotemporal secretome analysis of scallop foot

Dai X#, Zhu X#, Bao L#, Chen X, Miao Y, Li Y, Li Y, Lv J, Zhang L, Huang X, Bao Z, Wang S*, Wang J*.

Computational and Structural Biotechnology Journal. 2022, 20: 2713-2722.

The effect of temperature on gonadal sex differentiation of Yesso scallop Patinopecten yessoensis

Liu T, Li R, Liu L, Wu S, Zhang L, Li Y, Wei H, Shu Y, Yang Y, Wang S, Xing Q, Zhang L*, Bao Z.

Frontiers in Cell and Developmental Biology. 2022, 9: 803046.

Functional characterization of Cfap206 for bivalve ciliogenesis by RNAi and CRISPR/Cas9 technologies

Wang Y#, Zhu X#, Lian S*, Li Y, Hu N, Hu X, Bao Z, Wang S.

Frontiers in Marine Science. 2022, 9: 864037.

Discovery of Nanos1 and Nanos2/3 as germ cell markers during scallop gonadal development

Liu L, Liu T, Wu S, Li Y, Wei H, Zhang L, Shu Y, Yang Y, Xing Q, Wang S, Zhang L*.

Marine Biotechnology. 2022, 24: 408-416.

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

Liu F, Li Y*, Yu H, Zhang L, Hu J, Bao Z, Wang S*.

Nucleic Acids Research. 2021, 49: D988-D997.

Genomic insights into the origin and evolution of molluscan red-bloodedness in the blood clam Tegillarca granosa

Bao Y#, Zeng Q#, Wang J#, Zhang Z#, Zhang Y#, Wang S#, Wong N#, Yuan W, Huang Y, Zhang W, Liu J, Lv L, Xue Q, Zha S, Peng Z, Yao H, Bao Z, Wang S*, Lin Z*.

Molecular Biology and Evolution. 2021, 38: 2351-2365.

High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance

Zeng Q#, Liu J#, Wang C#, Wang H, Zhang L, Hu J, Bao L* & Wang S*.

Computational and Structural Biotechnology Journal. 2021, 19: 4954-4960.

Sexual development of the hermaphroditic scallop Argopecten irradians revealed by morphological, endocrine and molecular analysis

Wei H, Li W, Liu T, Li Y, Liu L, Shu Y, Zhang L, Wang S, Xing Q, Zhang L*, Bao Z.

Frontiers in Cell and Developmental Biology. 2021, 9: 646754.

An efficient integrated approach for nonlethal DNA sampling and genome-wide genotyping in bivalve molluscs

Liu P#, Zhang T#, Lv J*, Ma C, Yang Z, Huang X, Zhang L, Bao Z, Wang S*.

Aquaculture. 2021, 536: 736489.

Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae

Wang J#, Zhang L#, Lian S#, Qin Z#, Zhu X#, Dai X, Huang Z, Ke C, Zhou Z, Wei J, Liu P, Hu N, Zeng Q, Dong B, Dong Y, Kong D, Zhang Z, Liu S, Xia Y, Li Y, Zhao L, Xing Q, Huang X, Hu X, Bao Z, Wang S*.

Nature Ecology & Evolution. 2020, 4: 725-736.

The evo-devo of molluscs: insights from a genomic perspective

Yang Z, Zhang L, Hu J, Wang J, Bao Z, Wang S*. Evolution & Development. 2020, 22: 409-424.

Evolution & Development. 2020, 22: 409-424.

Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology

Wang J#, Yu H#, Yao L#, Li Y*, Liu F, Han W, Cui C, Hu J, Bao Z, Wang S*.

Computational and Structural Biotechnology Journal. 2020, 18: 2744-2756.

The chromosomal-level genome assembly and comprehensive transcriptomes of the razor clam (Sinonovacula constricta)

Dong Y#, Zeng Q#, Ren J#, Yao H, Lv L, He L, Ruan W, Xue Q, Bao Z, Wang S*, Lin Z*.

Frontiers in Genetics. 2020, 11: 664.

Potential GnRH and steroidogenesis pathways in the scallop

Zhang M#, Wei H#, Liu T, Li W, Li Y, Wang S, Xing Q, Hu X, Zhang L*, Bao Z.

Journal of Steroid Biochemistry and Molecular Biology. 2020, 204: 105756.

Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)

Wei J, Zhang J, Lu Q, Ren P, Guo X, Wang J, Li X, Chang Y, Duan S, Wang S, Yu H, Zhang X, Yang X, Gao H, Dong B*.

Molecular Ecology Resources. 2020, 20: 1414-1431.

Integration of biochemical, cellular and genic indicators for understanding the ageing process in a bivalve mollusc Chlamys farreri.

Lian S#, Wang J#, Zhang L, Xing Q, Hu N, Liu S, Dai X, Zhang F, Hu X, Bao Z & Wang S*.

Marine Biotechnology. 2019, 21: 718-730.

HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay

Lv J#, Jiao W#, Guo H#, Liu P, Wang R, Zhang L, Zeng Q, Hu X, Bao Z, Wang S*.

Genome Research. 2018, 28: 1919-1930.

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation

Li Y#, Wang R#, Xun X#, Wang J#, Bao L#, Thimmappa R#, Ding J#, Jiang J#, Zhang L, Li T, Lv J, Mu C, Hu X, Zhang L, Liu J, Li Y, Yao L, Jiao W, Wang Y, Lian S, Zhao Z, Zhan Y, Huang X, Liao H, Wang J, Sun H, Mi X, Xia Y, Xing Q, Lu W, Osbourn A, Zhou Z*, Chang Y*, Bao Z*, Wang S*.

Cell Discovery. 2018, 4: 29.

FOXL2 and DMRT1L are Yin and Yang genes for determining timing of sex differentiation in a bivalve mollusc Patinopecten yessoensis

Li R#, Zhang L#,*, Li W, Zhang Y, Li Y, Zhang M, Zhao L, Hu X, Wang S, Bao Z.

Frontiers in Physiology. 2018, 9: 1166.

Identification and characterization of neuropeptides by transcriptome and proteome analyses in a bivalve mollusc Patinopecten yessoensis

Zhang M, Wang Y, Li Y, Li W, Li R, Xie X, Wang S, Hu X, Zhang L*, Bao Z.

Frontiers in Genetics. 2018, 9: 197.

Population genetic structure of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific

Xu T, Sun J, Watanabe HK, Chen C, Nakamura M, Ji R, Feng D, Lv J, Wang S, Bao Z, Qian PY, Qiu JW*.

Evolutionary Applications. 2018, 11: 1915-1930.

The discovered chimeric protein plays the cohesive role to maintain scallop byssal root structural integrity

Xu P#, Dai X#, Wang D, Miao Y, Zhang X, Wang S, Teng L, Dong B, Bao Z, Wang S, Lyu Q*, Liu W*.

Scientific Reports. 2018, 8: 17082.

Scallop genome provides insights into evolution of bilaterian karyotype and development

Wang S#, Zhang J#, Jiao W#, Li J#, Xun X#, Sun Y#, Guo X#, Huan P#, Dong B, Zhang L, Hu X, Sun X, Wang J, Zhao C, Wang Y, Wang D, Huang X, Wang R, Lv J, Li Y, Zhang Z, Liu B, Lu W, Hui Y, Liang J, Zhou Z, Hou R, Li X, Liu Y, Li H, Ning X, Lin Y, Zhao L, Xing Q, Dou J, Li Y, Mao J, Guo H, Dou H, Li T, Mu C, Jiang W, Fu Q, Fu X, Miao Y, Liu J, Yu Q, Li R, Liao H, Li X, Kong Y, Jiang Z, Chourrout D*, Li R*, Bao Z*.

Nature Ecology & Evolution. 2017, 1: 0120.

Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins

Li Y#, Sun X#, Hu X#, Xun X#, Zhang J#, Guo X#, Jiao W, Zhang L, Liu W, Wang J, Li J, Sun Y, Miao Y, Zhang X, Cheng T, Xu G, Fu X, Wang Y, Yu X, Huang X, Lu W, Lv J, Mu C, Wang D, Li X, Xia Y, Li Y, Yang Z, Wang F, Zhang L, Xing Q, Dou H, Ning X, Dou J, Li Y, Kong D, Liu Y, Jiang Z, Li R, Wang S*, Bao Z*.

Nature Communications. 2017, 8: 1721.