{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T03:32:42Z","timestamp":1788838362418,"version":"build-2803163510"},"reference-count":53,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T00:00:00Z","timestamp":1778112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province","doi-asserted-by":"publisher","award":["PL2024C030"],"award-info":[{"award-number":["PL2024C030"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province","doi-asserted-by":"publisher","award":["PL2025C091"],"award-info":[{"award-number":["PL2025C091"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Agricultural Science and Technology Innovation Leapfrog Project of Heilongjiang Province","award":["CX25JC66"],"award-info":[{"award-number":["CX25JC66"]}]},{"name":"Agricultural Science and Technology Innovation Leapfrog Project of Heilongjiang Province","award":["CX23ZD04"],"award-info":[{"award-number":["CX23ZD04"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFD1200704-2"],"award-info":[{"award-number":["2022YFD1200704-2"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Major Special Task on Agricultural Biological Breeding","award":["2024ZD040780303"],"award-info":[{"award-number":["2024ZD040780303"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Soybean (Glycine max L.) yield is critically influenced by the number of nodes on the main stem (MSN), which serves as the primary site for pods and seeds. To elucidate the genetic mechanisms underlying MSN, we conducted a multi-omics analysis integrating bulk segregant analysis sequencing (BSA-seq), phytohormone, and transcriptome profilings in a soybean mutant, LSD914, which exhibits a significantly increased MSN number compared to its wild-type parent, HN48. BSA-seq of an F2 population identified 27 candidate genomic regions spanning 2.92 Mb, primarily on chromosome 18. Within these regions, 149 genes harbored non-synonymous SNPs and 26 genes contained frameshift InDels, with functional enrichment pointing to pathways in plant hormone signal transduction and developmental regulation. Phytohormone profiling revealed a distinct shift in LSD914, characterized by down-regulation of jasmonates, salicylates, and auxins, alongside specific accumulation of cis-zeatin. Integrative transcriptome analysis identified Glyma.18G259400, a gene encoding a gibberellin-regulated protein (GmGASA32), which was consistently and significantly down-regulated in LSD914 across all developmental stages and tissues. This finding contrasts with previous reports of its overexpression promoting plant height, suggesting a nuanced, context-dependent regulatory role. Our integrated approach identifies a key set of candidate genes and highlights GmGASA32 as a pivotal node in a hormone signaling network that orchestrates soybean node number, providing valuable targets for breeding high-yield soybean varieties with optimized plant architecture.<\/jats:p>","DOI":"10.3390\/plants15101418","type":"journal-article","created":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T08:01:39Z","timestamp":1778140899000},"page":"1418","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Multi-Omics Integration Unravels the Genetic and Hormonal Regulatory Mechanisms Underlying Increased Main Stem Node Number in Soybean"],"prefix":"10.3390","volume":"15","author":[{"given":"Jinbo","family":"Zhang","sequence":"first","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongbin","family":"Wang","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Tan","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bixian","family":"Zhang","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunxu","family":"Leng","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Peng","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Licheng","family":"Wu","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanhang","family":"Zhou","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aoran","family":"Song","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaojun","family":"Liu","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China"},{"name":"Heilongjiang Laboratory of Crop and Livestock Molecular Breeding, Harbin 150028, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.molp.2025.01.004","article-title":"Soybean2035: A Decadal Vision for Soybean Functional Genomics and Breeding","volume":"18","author":"Tian","year":"2025","journal-title":"Mol. Plant"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"106502","DOI":"10.1016\/j.still.2025.106502","article-title":"Legume-Based Rotation Benefits Crop Productivity and Agricultural Sustainability in the North China Plain","volume":"250","author":"Zhang","year":"2025","journal-title":"Soil Tillage Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.2135\/cropsci2012.11.0663","article-title":"The Relationship between the Number of Nodes and Pods in Soybean Communities","volume":"53","author":"Egli","year":"2013","journal-title":"Crop Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1016\/j.molp.2020.03.002","article-title":"Toward a \u201cGreen Revolution\u201d for Soybean","volume":"13","author":"Liu","year":"2020","journal-title":"Mol. Plant"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.2134\/agronj2004.1372","article-title":"Response of Soybean Yield Components to Management System and Planting Date","volume":"96","author":"Pedersen","year":"2004","journal-title":"Agron. J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1126\/science.aax5482","article-title":"Teosinte Ligule Allele Narrows Plant Architecture and Enhances High-Density Maize Yields","volume":"365","author":"Tian","year":"2019","journal-title":"Science"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"7939","DOI":"10.1038\/s41467-023-42991-z","article-title":"Soybean Reduced Internode 1 Determines Internode Length and Improves Grain Yield at Dense Planting","volume":"14","author":"Li","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1007\/s00122-003-1527-2","article-title":"QTL Mapping of Ten Agronomic Traits on the Soybean (Glycine max L. Merr.) Genetic Map and Their Association with EST Markers","volume":"108","author":"Zhang","year":"2004","journal-title":"Theor. Appl. Genet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11703-007-0001-3","article-title":"A Comparative Study on Segregation Analysis and QTL Mapping of Quantitative Traits in Plants\u2014With a Case in Soybean","volume":"1","author":"Gai","year":"2007","journal-title":"Front. Agric. China"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/S1671-2927(07)60062-5","article-title":"QTL Analysis of Major Agronomic Traits in Soybean","volume":"6","author":"Chen","year":"2007","journal-title":"Agric. Sci. China"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Li, R., Jiang, H., Zhang, Z., Zhao, Y., Xie, J., Wang, Q., Zheng, H., Hou, L., Xiong, X., and Xin, D. (2020). Combined Linkage Mapping and BSA to Identify QTL and Candidate Genes for Plant Height and the Number of Nodes on the Main Stem in Soybean. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21010042"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Zha, B., Zhang, C., Yuan, R., Zhao, K., Sun, J., Liu, X., Wang, X., Zhang, F., Zhang, B., and Lamlom, S.F. (2025). Integrative QTL Mapping and Candidate Gene Analysis for Main Stem Node Number in Soybean. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06457-2"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1007\/s11032-021-01235-y","article-title":"Natural Variation of the Dt2 Promoter Controls Plant Height and Node Number in Semi-Determinant Soybean","volume":"41","author":"Kou","year":"2021","journal-title":"Mol. Breed."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1642","DOI":"10.1016\/j.cj.2023.08.002","article-title":"Regulation of Soybean Stem Growth Habit: A Ten-Year Progress Report","volume":"11","author":"Xiong","year":"2023","journal-title":"Crop J."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Zhang, C., Zha, B., Yuan, R., Zhao, K., Sun, J., Liu, X., Wang, X., Zhang, F., Zhang, B., and Lamlom, S.F. (2025). Identification of Quantitative Trait Loci for Node Number, Pod Number, and Seed Number in Soybean. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26052300"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Wang, J., Yang, Q., Chen, Y., Liu, K., Zhang, Z., Xiong, Y., Yu, H., Yu, Y., Wang, J., and Song, J. (2024). QTL Mapping and Genomic Selection of Stem and Branch Diameter in Soybean (Glycine max L.). Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1388365"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e18539","DOI":"10.7717\/peerj.18539","article-title":"Multi-Environment QTL Mapping Identifies Major Genetic Loci Influencing Soybean Main Stem Node Architecture","volume":"12","author":"Ren","year":"2024","journal-title":"PeerJ"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"5247","DOI":"10.1093\/jxb\/erw283","article-title":"A Soybean Quantitative Trait Locus That Promotes Flowering under Long Days Is Identified as FT5a, a FLOWERING LOCUS T Ortholog","volume":"67","author":"Takeshima","year":"2016","journal-title":"J. Exp. Bot."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1111\/jipb.13070","article-title":"FT5a Interferes with the Dt1-AP1 Feedback Loop to Control Flowering Time and Shoot Determinacy in Soybean","volume":"63","author":"Yue","year":"2021","journal-title":"J. Integr. Plant Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1111\/jipb.12988","article-title":"Soybean AP1 Homologs Control Flowering Time and Plant Height","volume":"62","author":"Chen","year":"2020","journal-title":"J. Integr. Plant Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1016\/j.cub.2022.02.046","article-title":"A Functionally Divergent SOC1 Homolog Improves Soybean Yield and Latitudinal Adaptation","volume":"32","author":"Kou","year":"2022","journal-title":"Curr. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"6429","DOI":"10.1038\/s41467-022-34153-4","article-title":"Natural Variation of Dt2 Determines Branching in Soybean","volume":"13","author":"Liang","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/jxb\/erv475","article-title":"Soybean Fruit Development and Set at the Node Level under Combined Photoperiod and Radiation Conditions","volume":"67","author":"Nico","year":"2016","journal-title":"J. Exp. Bot."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1111\/jipb.13021","article-title":"Molecular Mechanisms for the Photoperiodic Regulation of Flowering in Soybean","volume":"63","author":"Lin","year":"2021","journal-title":"J. Integr. Plant Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.cj.2017.10.005","article-title":"Elevated Temperature Intensity, Timing, and Duration of Exposure Affect Soybean Internode Elongation, Mainstem Node Number, and Pod Number per Plant","volume":"6","author":"Allen","year":"2018","journal-title":"Crop J."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"uhac189","DOI":"10.1093\/hr\/uhac189","article-title":"Comparative Transcriptome and Metabolome Analysis Reveal Key Regulatory Defense Networks and Genes Involved in Enhanced Salt Tolerance of Actinidia (Kiwifruit)","volume":"9","author":"Abid","year":"2022","journal-title":"Hortic. Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1016\/S2095-3119(19)62676-6","article-title":"Concentration Difference of Auxin Involved in Stem Development in Soybean","volume":"19","author":"Jiang","year":"2020","journal-title":"J. Integr. Agric."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Wang, C., Huang, S., Yu, B., Shan, F., Lyu, X., Yan, C., Ma, C., and Jiang, B. (2025). Hormone Regulation Effect of Blue Light on Soybean Stem Internode Growth Based on the Grey Correlation Analysis Model. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26094411"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.gene.2014.01.024","article-title":"A Novel MYB Transcription Factor, GmMYBJ1, from Soybean Confers Drought and Cold Tolerance in Arabidopsis thaliana","volume":"538","author":"Su","year":"2014","journal-title":"Gene"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1603","DOI":"10.1111\/jipb.13682","article-title":"The MADS-Box Transcription Factor GmFULc Promotes GmZTL4 Gene Transcription to Modulate Maturity in Soybean","volume":"66","author":"Sun","year":"2024","journal-title":"J. Integr. Plant Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"113039","DOI":"10.1016\/j.celrep.2023.113039","article-title":"Next-Generation Bulked Segregant Analysis for Breeding 4.0","volume":"42","author":"Wang","year":"2023","journal-title":"Cell Rep."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Majeed, A., Johar, P., Raina, A., Salgotra, R.K., Feng, X., and Bhat, J.A. (2022). Harnessing the Potential of Bulk Segregant Analysis Sequencing and Its Related Approaches in Crop Breeding. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.944501"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"uhae191","DOI":"10.1093\/hr\/uhae191","article-title":"Association Analysis of BSA-Seq, BSR-Seq, and RNA-Seq Reveals Key Genes Involved in Purple Leaf Formation in a Tea Population (Camellia sinensis)","volume":"11","author":"Wang","year":"2024","journal-title":"Hortic. Res."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Geng, X., Yang, F., Tang, W., Wang, Y., Fu, S., Yu, Z., Cheng, W., Chen, L., and Xue, X. (2025). Combined BSA-Seq and RNA-Seq Approaches Reveal Candidate Genes Associated with Seed Weight in Brassica napus. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1678464"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Ma, Y., Mackon, E., Jeazet Dongho Epse Mackon, G.C., Zhao, Y., Li, Q., Dai, X., Yao, Y., Xia, X., Nong, B., and Liu, P. (2022). Combined Analysis of BSA-Seq Based Mapping, RNA-Seq, and Metabolomic Unraveled Candidate Genes Associated with Panicle Grain Number in Rice (Oryza sativa L.). Biomolecules, 12.","DOI":"10.3390\/biom12070918"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"127771","DOI":"10.1016\/j.ijbiomac.2023.127771","article-title":"Integrated BSA-Seq and RNA-Seq Analysis to Identify Candidate Genes Associated with Nitrogen Utilization Efficiency (NUtE) in Rapeseed (Brassica napus L.)","volume":"254","author":"Nan","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1855017","DOI":"10.1080\/15592324.2020.1855017","article-title":"Overexpression of GmGASA32 Promoted Soybean Height by Interacting with GmCDC25","volume":"16","author":"Chen","year":"2021","journal-title":"Plant Signal. Behav."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1111\/j.1365-313X.2010.04390.x","article-title":"The Arabidopsis Cysteine-Rich Protein GASA4 Promotes GA Responses and Exhibits Redox Activity in Bacteria and in Planta","volume":"64","author":"Rubinovich","year":"2010","journal-title":"Plant J."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e70165","DOI":"10.1111\/ppl.70165","article-title":"Auxin Biodynamics and Its Integral Role in Enhancing Plant Resilience to Environmental Cues","volume":"177","author":"Ali","year":"2025","journal-title":"Physiol. Plant."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Ali, M., Wang, Z., Guo, Q., Wang, Y., Cai, Y., Du, J., Pi, E., Ding, P., and Shen, J. (2026). Mapping Plant Cell-Type-Specific Responses to Environmental Stresses. Trends Plant Sci., in press.","DOI":"10.1016\/j.tplants.2026.03.003"},{"key":"ref_41","doi-asserted-by":"crossref","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":"Bioinformatics"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and Accurate Short Read Alignment with Burrows\u2013Wheeler Transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"1000 Genome Project Data Processing Subgroup. The Sequence Alignment\/Map Format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce Framework for Analyzing next-Generation DNA Sequencing Data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A Program for Annotating and Predicting the Effects of Single Nucleotide Polymorphisms, SnpEff: SNPs in the Genome of Drosophila melanogaster Strain w1118; Iso-2; Iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast Universal RNA-Seq Aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s13059-019-1910-1","article-title":"Transcriptome Assembly from Long-Read RNA-Seq Alignments with StringTie2","volume":"20","author":"Kovaka","year":"2019","journal-title":"Genome Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and Sensitive Protein Alignment Using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-Mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-Scale Protein Function Classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_52","doi-asserted-by":"crossref","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":"ref_53","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R Package for Comparing Biological Themes Among Gene Clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS J. Integr. Biol."}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/10\/1418\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T08:47:44Z","timestamp":1778143664000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/10\/1418"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,7]]},"references-count":53,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["plants15101418"],"URL":"https:\/\/doi.org\/10.3390\/plants15101418","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,7]]}}}