Pantranscriptomics

* Entities refer to the biological units represented in the assembled pantranscriptome, such as species, accessions, cultivars, lines, genotypes, or combinations thereof.

No.	Species	Total entities* in the pantranscriptome dataset	Reference
1	Pinus spp.	6	(Choi et al., 2026)
2	Pseudotsuga menziesii	19	(Cronn et al., 2017)
3	Liriodendron spp.	81	(Wu et al., 2024)
4	Zea mays	368	(Jin et al., 2016)
5	Zea mays	503	(Hirsch et al., 2014)
6	Oryza spp.	250	(Zhang et al., 2024)
7	Oryza sativa	11	(Zhong et al., 2024)
8	Poaceae spp.	3	(Guillotin et al., 2023)
9	Avena spp.	23	(Avni et al., 2026)
10	Hordeum vulgare	63	(Ma et al., 2019)
11	Hordeum vulgare	20	(Guo et al., 2025)
12	Triticum spp.	9	(White et al., 2025)
13	Triticum aestivum	200	(Chen et al., 2025)
14	Triticum aestivum	328	(Zhang et al., 2025)
15	Sorghum bicolor	10	(Nnamdi et al., 2025)
16	Saccharum spp.	44	(Chen et al., 2025)
17	Saccharum spp.	4	(Huang et al., 2026)
18	Cicer spp.	32	(Rajkumar et al., 2026)
19	Medicago sativa	3	(Medina et al., 2021)
20	Medicago sativa	8	(Zhang et al., 2022)
21	Lens spp.	8	(Gutierrez-Gonzalez et al., 2022)
22	Pyrus pyrifolia	389	(Sun et al., 2025)
23	Salix spp.	16	(Yan et al., 2023)
24	Gossypium hirsutum	4	(Grover et al., 2025)
25	Brassica juncea	204	(Harper et al., 2020)
26	Bougainvillea glabra	18	(Huang et al., 2022)
27	Camellia sinensis	15	(Kong et al., 2022)
28	Camellia spp.	116	(Wu et al., 2022)
29	Solanum lycopersicum	399	(Liu et al., 2020)
30	Solanum tuberosum	4	(Petek et al., 2020)
31	Solanum section petota spp.	68	(Zhang et al., 2026)

References

Choi, B.Y., Lee, D., Jung, J., Kim, Y.-G., Park, Y.-I., Kang, K.-S. and Shim, D. (2026) Pan-transcriptome analysis of pine wilt disease-resistant and susceptible Pinus species and a hybrid. Front. Genet., 17, 1743952.

Cronn, R., Dolan, P.C., Jogdeo, S., Wegrzyn, J.L., Neale, D.B., St. Clair, J.B. and Denver, D.R. (2017) Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. BMC Genomics, 18, 558.

Wu, H., Liu, X., Zong, Y., Yang, L., Wang, J., Tong, C. and Li, H. (2024) Leaf morphology related genes revealed by integrating Pan‐transcriptome, GWAS and eQTL analyses in a Liriodendron population. Physiologia Plantarum, 176, e14392.

Jin, M., Liu, H., He, C., Fu, J., Xiao, Y., Wang, Y., Xie, W., Wang, G. and Yan, J. (2016) Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep, 6, 18936.

Hirsch, C.N., Foerster, J.M., Johnson, J.M., et al. (2014) Insights into the Maize Pan-Genome and Pan-Transcriptome. The Plant Cell, 26, 121–135.

Zhang, H., Chen, W., Zhu, D., et al. (2024) Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice. The Plant Cell, 36, 4372–4387.

Zhong, Y., Luo, Y., Sun, J., et al. (2024) Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice. The Plant Cell, 36, 2117–2139.

Guillotin, B., Rahni, R., Passalacqua, M., et al. (2023) A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature, 617, 785–791.

Avni, R., Kamal, N., Bitz, L., et al. (2026) A pangenome and pantranscriptome of hexaploid oat. Nature, 649, 131–139.

Ma, Y., Liu, M., Stiller, J. and Liu, C. (2019) A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. BMC Genomics, 20, 12.

Guo, W., Schreiber, M., Marosi, V.B., et al. (2025) A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity. Nat Genet, 57, 441–450.

White, B., Lux, T., Rusholme-Pilcher, R., et al. (2025) De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome. Nat Commun, 16, 8538.

Chen, B., Liu, Y., Yang, Y., et al. (2025) A system genetics analysis uncovers the regulatory variants controlling drought response in wheat. Plant Biotechnology Journal, 23, 1565–1584.

Zhang, Z., Ma, S., Yin, M., et al. (2025) Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement. Nat Commun, 16, 11133.

Nnamdi, C.D., Songsomboon, K., Zarasvand, A.A., Voelker, W.G. and Cooper, E.A. (2025) Utilizing a pan-transcriptome reveals genotype-specific responses to iron deficiency in Sorghum bicolor. Available at: http://biorxiv.org/lookup/doi/10.1101/2024.12.17.626333 [Accessed September 16, 2026].

Chen, M., Liu, P., An, R., He, X., Zhao, P., Huang, D. and Yang, X. (2025) Sugarcane Pan-Transcriptome Identifying a Master Gene ScHCT Regulating Lignin and Sugar Traits. J. Agric. Food Chem., 73, 1739–1755.

Huang, Y., Zhang, Y., Zhang, Q., et al. (2026) Multiscale pangenome graphs empower the genomic dissection of mixed-ploidy sugarcane species. Science, 391, eadx1616.

Rajkumar, M.S., Banerjee, A.K., Bansal, J., Jain, M. and Garg, R. (2026) Pan-transcriptome analysis of diverse chickpea accessions reveals specific expression patterns and genetic variations associated with agronomic traits. Plant Mol Biol, 116, 41.

Medina, C.A., Samac, D.A. and Yu, L.-X. (2021) Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.). Sci Rep, 11, 17203.

Zhang, X., Yang, H., Li, M., Bai, Y., Chen, C., Guo, D., Guo, C. and Shu, Y. (2022) A Pan-Transcriptome Analysis Indicates Efficient Downregulation of the FIB Genes Plays a Critical Role in the Response of Alfalfa to Cold Stress. Plants, 11, 3148.

Gutierrez-Gonzalez, J.J., García, P., Polanco, C., González, A.I., Vaquero, F., Vences, F.J., Pérez De La Vega, M. and Sáenz De Miera, L.E. (2022) Multi-Species Transcriptome Assemblies of Cultivated and Wild Lentils (Lens sp.) Provide a First Glimpse at the Lentil Pangenome. Agronomy, 12, 1619.

Sun, C., Wang, R., Li, J., Li, X., Song, B., Edwards, D. and Wu, J. (2025) Pan-transcriptome analysis provides insights into resistance and fruit quality breeding of pear (Pyrus pyrifolia). Journal of Integrative Agriculture, 24, 1813–1830.

Yan, Z., Chen, L., Guo, Y., Dai, X., Yin, T. and Xue, L. (2023) Pan-Transcriptome Analysis of Willow Species from Diverse Geographic Distributions. Forests, 14, 1182.

Grover, C.E., Jareczek, J.J., Swaminathan, S., et al. (2025) A high-resolution model of gene expression during Gossypium hirsutum (cotton) fiber development. BMC Genomics, 26, 221.

Harper, A.L., He, Z., Langer, S., Havlickova, L., Wang, L., Fellgett, A., Gupta, V., Kumar Pradhan, A. and Bancroft, I. (2020) Validation of an Associative Transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits. The Plant Journal, 103, 1885–1893.

Huang, H., Ji, H., Ju, S., et al. (2022) Pantranscriptome combined with phenotypic quantification reveals germplasm kinship and regulation network of bract color variation in Bougainvillea. Front. Plant Sci., 13, 1018846.

Kong, W., Jiang, M., Wang, Y., et al. (2022) Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis. Horticulture Research, 9, uhac100.

Wu, Q., Tong, W., Zhao, H., et al. (2022) Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. The Plant Journal, 111, 406–421.

Liu, D., Yang, L., Zhang, J., et al. (2020) Domestication and breeding changed tomato fruit transcriptome. Journal of Integrative Agriculture, 19, 120–132.

Petek, M., Zagorščak, M., Ramšak, Ž., Sanders, S., Tomaž, Š., Tseng, E., Zouine, M., Coll, A. and Gruden, K. (2020) Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato. Sci Data, 7, 249.

Zhang, Z., Wu, Y., Long, J., et al. (2026) Multiomics dissection of the structural and biosynthetic diversity of steroidal glycoalkaloids in wild potatoes. Plant Physiology, 200, kiaf652.