{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T15:54:06Z","timestamp":1782921246169,"version":"3.54.5"},"reference-count":39,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100004386","name":"Universiti Malaya","doi-asserted-by":"publisher","award":["S\/18042019\/26112018\u201004\/R"],"award-info":[{"award-number":["S\/18042019\/26112018\u201004\/R"]}],"id":[{"id":"10.13039\/501100004386","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["anatomypubs.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Developmental Dynamics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Testicular development is a highly orchestrated process essential for male fertility, but its temporal genetic regulation remains incompletely resolved in many mammalian models. This study re\u2010analyses rat testis transcriptomes across 15 stages from embryonic day 12 to postnatal week 16 using bulk RNA\u2010sequencing data from a multispecies organ development atlas, generating a continuous, testis\u2010focused temporal framework, and pinpointing key developmental transition windows and regulatory modules.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Of 23,748 annotated genes, 17,717 were differentially expressed (DEGs), and hierarchical plus co\u2010expression analyses identified four principal expression modules and five clusters capturing spermatogenic, morphogenetic, immune, and neurone\u2010like programs. Four major transcriptional transition windows, embryonic day 14, embryonic day 19, postnatal week 2, and postnatal week 6, were defined, with the largest remodeling between 2 and 6\u2009weeks coinciding with the onset of robust spermatogenesis and marking a particularly vulnerable window for environmental or toxicant\u2010induced perturbation. Stage\u2010specific spermatogenesis\u2010associated gene sets at embryonic day 19 (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200928), postnatal week 2 (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200961), and week 6 (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009735) showed minimal overlap, supporting sequential regulatory waves driving germ cell commitment, early meiosis, and terminal differentiation. Target enrichment analyses highlighted five conserved microRNAs (rno\u2010miR\u2010151\u20105p, rno\u2010miR\u201029b\u20103p, rno\u2010miR\u2010384\u20105p, rno\u2010miR\u2010500\u20105p, rno\u2010miR\u2010672\u20105p) whose predicted and validated targets form modules related to extracellular matrix remodeling, apoptosis and cell\u2010cycle control, ion\u2010channel signaling, and neuronal\u2010like pathways, with high sequence conservation to human homologs. Immune\u2010related genes and blood\u2013testis barrier components displayed coordinated expression dynamics, and a conserved core of 487 spermatogenesis genes showed strong cross\u2010mammalian orthology, indicating a deeply shared transcriptional backbone on which species\u2010specific regulatory nuances are layered.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This multistage transcriptomic analysis delineates major developmental transitions, co\u2010expression modules, and regulatory miRNA\u2013mRNA networks that orchestrate rat testis maturation and highlight a critical P2W\u2013P6W transition window. The resource complements existing multiorgan and single\u2010cell datasets by providing a testis\u2010focused temporal framework and identifies conserved gene sets and regulatory candidates of direct relevance to male infertility, toxicology, and cross\u2010species translational studies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/dvdy.70166","type":"journal-article","created":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T15:40:27Z","timestamp":1782920427000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi\u2010stage transcriptome analysis reveals genetic orchestration of rat testis development"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2698-5250","authenticated-orcid":false,"given":"Chew Chin","family":"Chan","sequence":"first","affiliation":[{"name":"Animal Genetics and Genome Evolutionary Laboratory (AGAGEL), Department of Genetics and Microbiology Institute of Biological Sciences, Faculty of Science, Universiti Malaya  Kuala Lumpur Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajad","family":"Jamalpour","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology Faculty of Medicine, Universiti Malaya  Kuala Lumpur Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chandramathi","family":"Samudi","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology Faculty of Medicine, Universiti Malaya  Kuala Lumpur Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hasmahzaiti","family":"Omar","sequence":"additional","affiliation":[{"name":"Animal Genetics and Genome Evolutionary Laboratory (AGAGEL), Department of Genetics and Microbiology Institute of Biological Sciences, Faculty of Science, Universiti Malaya  Kuala Lumpur Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subha","family":"Bhassu","sequence":"additional","affiliation":[{"name":"Animal Genetics and Genome Evolutionary Laboratory (AGAGEL), Department of Genetics and Microbiology Institute of Biological Sciences, Faculty of Science, Universiti Malaya  Kuala Lumpur Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,1]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev\u2010genet\u2010020821\u2010013934"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41422\u2010018\u20100099\u20102"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2019.12.004"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.4103\/jhrs.JHRS_154_21"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12967\u2010023\u201004657\u20103"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.202201711"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms25136925"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061558"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2022.146405"},{"key":"e_1_2_9_11_1","first-page":"155","article-title":"Morphometric aspects of rat testis development","volume":"145","author":"Gaytan F","year":"1986","journal-title":"J Anat"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1095\/biolreprod59.1.84"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1210\/endocr\/bqab046"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2023.1114769"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2015.03.010"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.12.015"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.3390\/toxics13090712"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s43587\u2010025\u201000824\u20102"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/toxsci\/kfaf089"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010019\u20101338\u20105"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u20107\u2010191"},{"key":"e_1_2_9_22_1","volume-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews S","year":"2010"},{"key":"e_1_2_9_23_1","unstructured":"Broad Institute.Picard toolkit. 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