{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T19:41:55Z","timestamp":1757706115345,"version":"3.41.2"},"reference-count":58,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Physiol."],"abstract":"<jats:p>Medical leeches are widely been used in biochemical and clinical medical studies, helping to restore blood circulation to grafted or severely injured tissue. Mostly, adult leeches are being used in the traditional pharmacopeia, but the gene expression profiling of leeches in different growth periods is not well-reported. So, in this study, we used transcriptome analysis to analyze the comparative gene expression patterns of <jats:italic>Hirudinaria manillensis<\/jats:italic> (<jats:italic>H. manillensis<\/jats:italic>) in different growth periods, including larval, young, and adult stages. We constructed 24 cDNA libraries from <jats:italic>H. manillensis<\/jats:italic> larval, young, and adult stages, and about 54,639,118 sequences were generated, 18,106 mRNA transcripts of which 958 novel mRNAs and 491 lncRNAs were also assembled as well. Furthermore, the results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the differentially upregulated genes from the larval to adult stages were enriched in pathways such as cilium, myofibril, contractile fiber, cytoskeleton proteins, dilated cardiomyopathy, adrenergic signaling in cardiomyocytes, etc. Moreover, in the adult stages, a significant increase in the expression of the Hirudin-HM (<jats:italic>HIRM2<\/jats:italic>) genes was detected. In addition, our comparative transcriptome profiling data from different growth stages of <jats:italic>H. manillensis<\/jats:italic> also identified a large number of DEGs and DElncRNAs which were tentatively found to be associated with the growth of <jats:italic>H. manillensis<\/jats:italic>; as it grew, the muscle-related gene expression increased, while the lipid metabolism and need for stimulation and nutrition-related genes decreased. Similarly, the higher expression of <jats:italic>HIRM2<\/jats:italic> might attribute to the high expression of protein disulfide isomerase gene family (PDI) family genes in adulthood, which provides an important clue that why adult leeches rather than young leeches are widely used in clinical therapeutics and traditional Chinese medicine.<\/jats:p>","DOI":"10.3389\/fphys.2022.897458","type":"journal-article","created":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T08:12:01Z","timestamp":1653466321000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Comprehensive Transcriptome Sequencing Analysis of Hirudinaria manillensis in Different Growth Periods"],"prefix":"10.3389","volume":"13","author":[{"given":"Huiquan","family":"Shan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Ren","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiasheng","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saif ur","family":"Rehman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiuying","family":"Yan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaocong","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yalin","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tong","family":"Feng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaobo","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhipeng","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weiguan","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Chuang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingkun","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinghui","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingyou","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,5,25]]},"reference":[{"key":"B2","doi-asserted-by":"publisher","first-page":"12147","DOI":"10.1038\/s41598-019-47506-9","article-title":"Systematic Identification and Characterization of aedes Aegypti Long Noncoding Rnas (Lncrnas)","volume":"9","author":"Azlan","year":"2019","journal-title":"Sci. Rep."},{"key":"B3","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1186\/s12864-020-6748-0","article-title":"Draft Genome Sequences of Hirudo Medicinalis and Salivary Transcriptome of Three Closely Related Medicinal Leeches","volume":"21","author":"Babenko","year":"2020","journal-title":"BMC Genomics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an Ultra-fast All-In-One Fastq Preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinforma. Oxf. Engl."},{"key":"B5","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1046\/j.1432-1327.1998.2580662.x","article-title":"Amino-acid-sequence Determination and Biological Activity of Tessulin, a Naturally Occurring Trypsin-Chymotrypsin Inhibitor Isolated from the Leech Theromyzon Tessulatum","volume":"258","author":"Chopin","year":"1998","journal-title":"Eur. J. Biochem."},{"key":"B6","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1097\/00006534-200201000-00034","article-title":"Evaluation of Performance Characteristics of the Medicinal Leech (Hirudo Medicinalis) for the Treatment of Venous Congestion","volume":"109","author":"Conforti","year":"2002","journal-title":"Plastic Reconstr. Surg."},{"key":"B7","doi-asserted-by":"publisher","first-page":"9552","DOI":"10.1021\/bi00029a032","article-title":"Core Domain of Hirudin from the Leech Hirudinaria Manillensis: Chemical Synthesis, Purification, and Characterization of a Trp3 Analog of Fragment 1-47","volume":"34","author":"De Filippis","year":"1995","journal-title":"Biochemistry"},{"key":"B8","doi-asserted-by":"publisher","first-page":"3585","DOI":"10.1242\/dev.129.15.3585","article-title":"Elbow and Noc Define a Family of Zinc Finger Proteins Controlling Morphogenesis of Specific Tracheal Branches","volume":"129","author":"Dorfman","year":"2002","journal-title":"Dev. Camb. Engl."},{"key":"B9","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1608\/frj-4.1.417","article-title":"Medicinal Leeches: Historical Use, Ecology, Genetics and Conservation","volume":"4","author":"Elliott","year":"2011","journal-title":"Freshw. Rev."},{"key":"B10","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.yjmcc.2017.11.013","article-title":"Acetylation of Tbx5 by Kat2b and Kat2a Regulates Heart and Limb Development","volume":"114","author":"Ghosh","year":"2018","journal-title":"J. Mol. Cell. Cardiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"2331","DOI":"10.1210\/en.2009-1255","article-title":"Glioma Pathogenesis-Related 1-like 1 Is Testis Enriched, Dynamically Modified, and Redistributed during Male Germ Cell Maturation and Has a Potential Role in Sperm-Oocyte Binding","volume":"151","author":"Gibbs","year":"2010","journal-title":"Endocrinology"},{"key":"B12","first-page":"31","volume-title":"Hirudotherapy","author":"Gileva","year":"2013"},{"key":"B13","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1186\/s12864-018-4937-x","article-title":"Analysis of Codon Usage Patterns in Hirudinaria Manillensis Reveals a Preference for Gc-Ending Codons Caused by Dominant Selection Constraints","volume":"19","author":"Guan","year":"2018","journal-title":"BMC Genomics"},{"key":"B14","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.3389\/fgene.2019.01321","article-title":"Draft Genome of the Asian Buffalo Leech Hirudinaria Manillensis","volume":"10","author":"Guan","year":"2019","journal-title":"Front. Genet."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1152\/physrev.00001.2007","article-title":"Tropomyosin-based Regulation of the Actin Cytoskeleton in Time and Space","volume":"88","author":"Gunning","year":"2008","journal-title":"Physiol. Rev."},{"key":"B16","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1186\/s12864-018-5209-5","article-title":"Intramuscular Preadipocytes Impede Differentiation and Promote Lipid Deposition of Muscle Satellite Cells in Chickens","volume":"19","author":"Guo","year":"2018","journal-title":"BMC Genomics"},{"key":"B17","first-page":"25","volume-title":"Leech Therapy: A History","author":"Hyson","year":"2005"},{"key":"B18","doi-asserted-by":"publisher","first-page":"660757","DOI":"10.3389\/fphar.2021.660757","article-title":"Pharmacological Activities and Mechanisms of Hirudin and its Derivatives - a Review","volume":"12","author":"Junren","year":"2021","journal-title":"Front. Pharmacol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"2159","DOI":"10.3390\/toxins7062159","article-title":"Bioinformatics-aided Venomics","volume":"7","author":"Kaas","year":"2015","journal-title":"Toxins"},{"key":"B20","doi-asserted-by":"publisher","first-page":"1676","DOI":"10.1134\/s000629791613006x","article-title":"Myosin Light Chain Kinase Mylk1: Anatomy, Interactions, Functions, and Regulation","volume":"81","author":"Khapchaev","year":"2016","journal-title":"Biochem. Mosc."},{"key":"B21","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"Hisat: a Fast Spliced Aligner with Low Memory Requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods."},{"key":"B22","doi-asserted-by":"publisher","first-page":"20153025","DOI":"10.1098\/rspb.2015.3025","article-title":"Molecular Assessment of the Effect of Light and Heterotrophy in the Scleractinian Coral Stylophora Pistillata","volume":"283","author":"Levy","year":"2016","journal-title":"Proc. R. Soc. B"},{"key":"B23","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.gene.2015.12.055","article-title":"Genetic Variation in Whitmania Pigra, Hirudo Nipponica and Poecilobdella Manillensis, Three Endemic and Endangered Species in china Using Ssr and Trap Markers","volume":"579","author":"Liu","year":"2016","journal-title":"Gene"},{"key":"B24","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/j.jprot.2019.03.009","article-title":"In-depth Profiles of Bioactive Large Molecules in Saliva Secretions of Leeches Determined by Combining Salivary Gland Proteome and Transcriptome Data","volume":"200","author":"Liu","year":"2019","journal-title":"J. Proteomics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated Estimation of Fold Change and Dispersion for Rna-Seq Data with Deseq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"1444","DOI":"10.3389\/fphys.2019.01444","article-title":"Non-synaptic Plasticity in Leech Touch Cells","volume":"10","author":"Meiser","year":"2019","journal-title":"Front. Physiol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"31668","DOI":"10.1038\/srep31668","article-title":"Kremen1 Regulates Mechanosensory Hair Cell Development in the Mammalian Cochlea and the Zebrafish Lateral Line","volume":"6","author":"Mulvaney","year":"2016","journal-title":"Sci. Rep."},{"key":"B28","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1159\/000067831","article-title":"Sf1 in the Development of the Adrenal Gland and Gonads","author":"Ozisik","year":"2003","journal-title":"Horm. Res."},{"volume-title":"Mechanosensitive Cation Channels of Leech Neurons","year":"2005","author":"Pellegrino","key":"B29"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.23297.2","article-title":"Gff Utilities: Gffread and Gffcompare","volume":"9","author":"Pertea","year":"2020","journal-title":"F1000Research"},{"key":"B31","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"Stringtie Enables Improved Reconstruction of a Transcriptome from Rna-Seq Reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1016\/j.ijppaw.2020.09.003","article-title":"Leeches in the Extreme: Morphological, Physiological, and Behavioral Adaptations to Inhospitable Habitats","volume":"12","author":"Phillips","year":"2020","journal-title":"Int. J. Parasitol. Parasites Wildl."},{"key":"B33","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1006\/dbio.1999.9505","article-title":"Hepatocyte Growth Factor (Hgf) Receptor Expression and Role of Hgf during Embryonic Mouse Testis Development","volume":"216","author":"Ricci","year":"1999","journal-title":"Dev. Biol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1111\/j.1610-0387.2010.07473.x","article-title":"Medicinal Leeches for the Treatment of Venous Congestion and Hematoma after Plastic Reconstructive Surgery","volume":"8","author":"Riede","year":"2010","journal-title":"J. der Deutschen Dermatologischen Gesellschaft = J. Ger. Soc. Dermatology JDDG"},{"key":"B35","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1016\/s1097-2765(00)80081-7","article-title":"The Tec29 Tyrosine Kinase Is Required during drosophila Embryogenesis and Interacts with Src64 in Ring Canal Development","volume":"1","author":"Roulier","year":"1998","journal-title":"Mol. Cell."},{"key":"B36","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1007\/978-1-59745-528-2_2","article-title":"Oligo 7 Primer Analysis Software","volume":"402","author":"Rychlik","year":"2007","journal-title":"Methods Mol. Biol. Clift. N.J.)."},{"key":"B37","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1111\/j.1432-1033.1993.tb17924.x","article-title":"Novel Hirudin Variants from the Leech Hirudinaria Manillensis","author":"Scacheri","year":"1993","journal-title":"Amino acid sequence, cDNA cloning genomic Organ. Eur. J. Biochem."},{"key":"B38","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1038\/nprot.2008.73","article-title":"Analyzing Real-Time Pcr Data by the Comparative C(t) Method","volume":"3","author":"Schmittgen","year":"2008","journal-title":"Nat. Protoc."},{"key":"B39","doi-asserted-by":"publisher","first-page":"4955","DOI":"10.1021\/bi4005254","article-title":"Organization of F-Actin by Fesselin (Avian Smooth Muscle Synaptopodin 2)","volume":"52","author":"Schroeter","year":"2013","journal-title":"Biochemistry"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.3390\/jdb6040027","article-title":"Kat2a and Kat2b Acetyltransferase Activity Regulates Craniofacial Cartilage and Bone Differentiation in Zebrafish and Mice","volume":"6","author":"Sen","year":"2018","journal-title":"J. Dev. Biol."},{"key":"B1","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1016\/j.jaim.2018.11.006","article-title":"Scientometric Analysis of Medicinal Leech Therapy","volume":"11","author":"\u015eenel","year":"2020","journal-title":"J. Ayurveda Integr. Med."},{"key":"B41","doi-asserted-by":"publisher","first-page":"E880","DOI":"10.1152\/ajpendo.00503.2018","article-title":"Liver-specific Knockdown of Long-Chain Acyl-Coa Synthetase 4 Reveals its Key Role in Vldl-Tg Metabolism and Phospholipid Synthesis in Mice Fed a High-Fat Diet","volume":"316","author":"Singh","year":"","journal-title":"Am. J. Physiology-Endocrinology Metabolism"},{"key":"B42","doi-asserted-by":"publisher","first-page":"E880","DOI":"10.1152\/ajpendo.00503.2018","article-title":"Liver-specific Knockdown of Long-Chain Acyl-Coa Synthetase 4 Reveals its Key Role in Vldl-Tg Metabolism and Phospholipid Synthesis in Mice Fed a High-Fat Diet","volume":"316","author":"Singh","year":"","journal-title":"Am. J. Physiology-Endocrinology Metabolism"},{"key":"B43","unstructured":"The Spssau Project2017"},{"key":"B44","article-title":"A New Species of Mammalian Trypanosome, Trypanosoma (Megatrypanum) Bubalisi Sp. Nov., Found in the Freshwater Leech Hirudinaria Manillensis","author":"Su","year":"2021","journal-title":"Int. J. Parasitol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"1903","DOI":"10.1016\/j.celrep.2016.07.029","article-title":"Increased 4e-Bp1 Expression Protects against Diet-Induced Obesity and Insulin Resistance in Male Mice","volume":"16","author":"Tsai","year":"2016","journal-title":"Cell. Rep."},{"key":"B46","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1016\/s1097-2765(02)00696-2","article-title":"The FAD- and O2-dependent Reaction Cycle of Ero1-Mediated Oxidative Protein Folding in the Endoplasmic Reticulum","volume":"10","author":"Tu","year":"2002","journal-title":"Mol. Cell."},{"key":"B47","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1111\/j.1432-1033.1994.tb20056.x","article-title":"Probing the Structure of Hirudin from Hirudinaria Manillensis by Limited Proteolysis. Isolation, Characterization and Thrombin-Inhibitory Properties of N-Terminal Fragments","volume":"226","author":"Vindigni","year":"1994","journal-title":"Eur. J. Biochem."},{"key":"B48","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1016\/j.bbrc.2019.10.029","article-title":"Protein Composition of Thick Filaments from Molluscan Catch Muscle and the Role of Twitchin in the Catch-State Formation","volume":"520","author":"Vyatchin","year":"2019","journal-title":"Biochem. Biophysical Res. Commun."},{"key":"B49","doi-asserted-by":"publisher","first-page":"3795","DOI":"10.1242\/dev.00570","article-title":"Zag-1, a Zn-Finger Homeodomain Transcription Factor Controlling Neuronal Differentiation and Axon Outgrowth in c. Elegans","volume":"130","author":"Wacker","year":"2003","journal-title":"Dev. Camb. Engl."},{"key":"B50","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.cbi.2006.08.005","article-title":"Neuroprotective Effects of Arachidonic Acid against Oxidative Stress on Rat Hippocampal Slices","volume":"163","author":"Wang","year":"2006","journal-title":"Chemico-Biological Interact."},{"key":"B51","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1016\/0305-0491(90)90207-a","article-title":"Paramyosin and the Catch Mechanism","volume":"96","author":"Watabe","year":"1990","journal-title":"Comp. Biochem. Physiology Part B Comp. Biochem."},{"key":"B52","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1016\/j.abb.2010.10.013","article-title":"Troponin T Isoforms and Posttranscriptional Modifications: Evolution, Regulation and Function","volume":"505","author":"Wei","year":"2011","journal-title":"Archives Biochem. Biophysics"},{"key":"B53","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"Ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"volume-title":"Tcseq: Time Course Sequencing Data Analysis","year":"2021","author":"Wu","key":"B54"},{"key":"B55","doi-asserted-by":"publisher","first-page":"104258","DOI":"10.1016\/j.jprot.2021.104258","article-title":"Proteomic Analysis of Liver Tissues in Chicken Embryo at Day 16 and Day 20 Reveals Antioxidant Mechanisms","volume":"243","author":"Yang","year":"","journal-title":"J. Proteomics"},{"key":"B56","doi-asserted-by":"publisher","first-page":"104258","DOI":"10.1016\/j.jprot.2021.104258","article-title":"Proteomic Analysis of Liver Tissues in Chicken Embryo at Day 16 and Day 20 Reveals Antioxidant Mechanisms","volume":"243","author":"Yang","year":"","journal-title":"J. Proteomics"},{"key":"B57","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1016\/j.ijbiomac.2020.06.097","article-title":"Hirudin Protects against Isoproternol-Induced Myocardial Infraction by Alleviating Oxidative via an Nrf2 Dependent Manner","volume":"162","author":"Zhang","year":"2020","journal-title":"Int. J. Biol. Macromol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"914","DOI":"10.4268\/cjcmm20130629","article-title":"Species Study on Chinese Medicine Leech and Discussion on its Resource Sustainable Utilization","author":"Zhang","year":"2013","journal-title":"China J. Chin. Materia Medica"}],"container-title":["Frontiers in Physiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphys.2022.897458\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T08:12:11Z","timestamp":1653466331000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphys.2022.897458\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,25]]},"references-count":58,"alternative-id":["10.3389\/fphys.2022.897458"],"URL":"https:\/\/doi.org\/10.3389\/fphys.2022.897458","relation":{},"ISSN":["1664-042X"],"issn-type":[{"type":"electronic","value":"1664-042X"}],"subject":[],"published":{"date-parts":[[2022,5,25]]},"article-number":"897458"}}