Pan-Genomics in Fruit Crops: Current Progress, Challenges and Future Directions
85 / 48
Authors
-
Anupama Roy
The Graduate School, ICAR-Indian Agricultural Research Institute, New Delhi
-
Sarika
ICAR-Indian Agricultural Statistics Research Institute, New Delhi
-
Mir Asif Iquebal
ICAR-Indian Agricultural Statistics Research Institute, New Delhi
Keywords:
Pan-genomics; Tropical and subtropical fruit crops; Structural variation; Presence–absence variation (PAV); Graph-based genomes; Crop wild relatives; Molecular breeding; Genomic diversity; Long-read sequencing; Climate-resilient horticulture.Abstract
Pan-genomics captures the full spectrum of genetic diversity within plant species and overcomes the limitations of single reference genomes. By
integrating core, dispensable, and unique genomic components, pan-genomic approaches enable comprehensive detection of structural variants,
presence–absence variations, and lineage-specific genes that underpin phenotypic diversity, domestication, and environmental adaptation. In plant and
horticultural crops, particularly tropical and subtropical fruit species characterized by high heterozygosity, polyploidy, and clonal propagation, pan
genomics has revealed extensive hidden variation influencing fruit quality, disease resistance, and stress tolerance that was previously inaccessible
using traditional genomics.
This review synthesizes the concepts, methodological advances, computational tools, and recent progress in plant pan-genomics, with a focused
emphasis on tropical and subtropical fruit crops. We discuss pan-genome construction strategies, graph-based representations, and emerging
resources, alongside key applications in trait discovery, evolutionary analysis, and molecular breeding. Current challenges, including limited accession
diversity, incomplete functional annotation, and computational complexity, are critically examined. Finally, we highlight future directions toward
population-scale, graph-based, and multi-omics–integrated pan-genomes, underscoring their potential to accelerate precision breeding and support
the development of climate-resilient, high-quality fruit crop varieties.
Downloads
References
Afsharyan, N.P., Golicz, A.A., and Snowdon, R.J. (2025). Pangenomic
structural variant patterns reflect evolutionary diversification
in Brassica napus. Genome Biology, 26(1), 381. https://doi.
org/10.1186/s13059-025-03833-x
Ahmad, B., Su, Y., Hao, Y., Razzaq, T., Arshad, R., Zhang, Y., Zhang,
Y., Wang, X., Huang, G., Su, X., Hou, T., Li, C., Yang, X., Li, C.,
Chu, Z., Wang, Q., Zhang, Y., Jin, Z., Xu, Q., … and Garrison
Tian, X. (2025). Mango pangenome reveals dramatic impacts
of reference bias on population genomic analyses. Horticulture
Research, 12(9), uhaf166.https://doi.org/10.1093/hr/uhaf166
Andreace, F., Lechat, P., Dufresne, Y., and Chikhi, R. (2023). Comparing
methods for constructing and representing human pangenome
graphs. Genome Biology, 24(1), 274. https://doi.org/10.1186/
s13059-023-03098-2
Bu, C., Zhang, H., Zhang, F., Liang, W., Gao, H., Zhao, J., Lv, F., Xue,
R., Liu, Q., Zhang, Z., Jin, Z., and Xiao, J. (2025). PGAP2: A
comprehensive toolkit for prokaryotic pan-genome analysis based
on fine-grained feature networks. Nature Communications, 16(1),
9865. https://doi.org/10.1038/s41467-025-64846-5
Campbell, M.S., Law, M., Holt, C., Stein, J.C., Moghe, G.D., Hufnagel,
D.E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C.J., Ware,
D., Shiu, S.-H., Childs, K.L., Sun, Y., Jiang, N., and Yandell,
M. (2014). MAKER-P: A Tool Kit for the Rapid Creation,
Management, and Quality Control of Plant Genome Annotations.
Plant Physiology, 164(2), 513-524. https://doi.org/10.1104/
pp.113.230144
Chen, W., Xie, Q., Fu, J., Li, S., Shi, Y., Lu, J., Zhang, Y., Zhao, Y., Ma,
R., Li, B., Zhang, B., Grierson, D., Yu, M., Fei, Z., and Chen, K.
(2025). Graph pangenome reveals the regulation of malate content
in blood-fleshed peach by NAC transcription factors. Genome
Biology, 26(1), 7. https://doi.org/10.1186/s13059-024-03470-w
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., and Li, H. (2021).
Haplotype-resolved de novo assembly using phased assembly
graphs with hifiasm. Nature Methods, 18(2), 170-175. https://doi.
org/10.1038/s41592-020-01056-5
De Oliveira, R., Rimbert, H., Balfourier, F., Kitt, J., Dynomant, E.,
Vrána, J., Doležel, J., Cattonaro, F., Paux, E., and Choulet, F.
(2020). Structural Variations Affecting Genes and Transposable
Elements of Chromosome 3B in Wheats. Frontiers in Genetics,
11, 891.https://doi.org/10.3389/fgene.2020.00891
184
Anupama Roy et al. / Journal of the Indian Society of Agricultural Statistics 175–186
Diesh, C., Stevens, G.J., Xie, P., De Jesus Martinez, T., Hershberg, E.A.,
Leung, A., Guo, E., Dider, S., Zhang, J., Bridge, C., Hogue, G.,
Duncan, A., Morgan, M., Flores, T., Bimber, B.N., Haw, R., Cain,
S., Buels, R.M., Stein, L.D., and Holmes, I.H. (2023). JBrowse 2:
a modular genome browser with views of synteny and structural
variation. Genome Biology, 24(1), 74. https://doi.org/10.1186/
s13059-023-02914-z
Droc, G., Larivière, D., Guignon, V., Yahiaoui, N., This, D., Garsmeur,
O., Dereeper, A., Hamelin, C., Argout, X., Dufayard, J.-F.,
Lengelle, J., Baurens, F.-C., Cenci, A., Pitollat, B., D’Hont, A.,
Ruiz, M., Rouard, M., and Bocs, S. (2013). The Banana Genome
Hub. Database, 2013, bat035. https://doi.org/10.1093/database/
bat035
Du, Z.-Z., He, J.-B., and Jiao, W.-B. (2025). Plant graph-based
pangenomics:
techniques,
applications,
and
challenges.
ABIOTECH, 6(2), 361-376. https://doi.org/10.1007/s42994-025
00206-7
Dutilh, B.E., and C.P.-G. Consortium. (2016). Computational
pan-genomics: status, promises and challenges. Briefings in
Bioinformatics, 19(1), 118-135. https://doi.org/10.1093/bib/
bbw089
Fuentes, R.R., Chebotarov, D., Duitama, J., Smith, S., De la Hoz, J.F.,
Mohiyuddin, M., Wing, R. A., McNally, K. L., Tatarinova, T.,
Grigoriev, A., Mauleon, R., and Alexandrov, N. (2019). Structural
variants in 3000 rice genomes. Genome Research, 29(5), 870-880.
https://doi.org/10.1101/gr.241240.118
Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D.M.,
Burzynski-Chang, E.A., Fish, T. L., Stromberg, K.A., Sacks,
G.L., Thannhauser, T.W., Foolad, M.R., Diez, M.J., Blanca, J.,
Canizares, J., Xu, Y., van der Knaap, E., Huang, S., Klee, H.J., …
and Fei, Z. (2019). The tomato pan-genome uncovers new genes
and a rare allele regulating fruit flavor. Nature Genetics, 51(6),
1044-1051. https://doi.org/10.1038/s41588-019-0410-2
Garrison, E., Guarracino, A., Heumos, S., Villani, F., Bao, Z., Tattini,
L., ... and Prins, P. (2024). Building pangenome graphs. Nature
Methods, 21(11), 2008-2012.
Glick, L., and Mayrose, I. (2023). The Effect of Methodological
Considerations on the Construction of Gene-Based Plant Pan
genomes. Genome Biology and Evolution, 15(7), evad121.https://
doi.org/10.1093/gbe/evad121
Guarracino, A., Heumos, S., Nahnsen, S., Prins, P., and Garrison, E.
(2022). ODGI: understanding pangenome graphs. Bioinformatics,
38(13), 3319-3326. https://doi.org/10.1093/bioinformatics/
btac308
Hall, N., Montgomery, J., Chen, J., Saski, C., Matzrafi, M., Westra, P.,
Gaines, T., and Patterson, E. (2025). FHY3/FAR1 transposable
elements generate adaptive genetic variation in the Bassia
scoparia genome. Pest Management Science, 81(8), 4393-4402.
https://doi.org/10.1002/ps.8798
Hassan, A.H., Mokhtar, M.M., and El Allali, A. (2024). Transposable
elements: multifunctional players in the plant genome.
Frontiers in Plant Science, 14, 1330127.https://doi.org/10.3389/
fpls.2023.1330127
He, Q., Tang, S., Zhi, H., Chen, J., Zhang, J., Liang, H., Alam, O., Li,
H., Zhang, H., Xing, L., Li, X., Zhang, W., Wang, H., Shi, J., Du,
H., Wu, H., Wang, L., Yang, P., Xing, L., and Diao, X. (2023).
A graph-based genome and pan-genome variation of the model
plant Setaria. Nature Genetics, 55(7), 1232-1242. https://doi.
org/10.1038/s41588-023-01423-w
Hickey, G., Monlong, J., Ebler, J., Novak, A.M., Eizenga, J.M., Gao, Y.,
Human Pangenome Reference Consortium, Marschall, T., Li, H.,
and Paten, B. (2024). Pangenome graph construction from genome
alignments with Minigraph-Cactus. Nature Biotechnology, 42(4),
663-673. https://doi.org/10.1038/s41587-023-01793-w
Hu, G., Cheng, L., Cheng, Y., Mao, W., Qiao, Y., and Lan, Y. (2022).
Pan-genome analysis of three main Chinese chestnut varieties.
Frontiers in Plant Science, 13, 916550.https://doi.org/10.3389/
fpls.2022.916550
Hu, H., Li, R., Zhao, J., Batley, J., and Edwards, D. (2024). Technological
Development and Advances for Constructing and Analyzing Plant
Pangenomes. Genome Biology and Evolution, 16(4). https://doi.
org/10.1093/gbe/evae081
Hu, H., Zhao, J., Thomas, W.J.W., Batley, J., and Edwards, D. (2025).
The role of pangenomics in orphan crop improvement. Nature
Communications, 16(1), 118. https://doi.org/10.1038/s41467-024
55260-4
Hu, Z., Sun, C., Lu, K., Chu, X., Zhao, Y., Lu, J., Shi, J., and Wei, C.
(2017). EUPAN enables pan-genome studies of a large number of
eukaryotic genomes. Bioinformatics, 33(15), 2408-2409. https://
doi.org/10.1093/bioinformatics/btx170
Jayakodi, M., Schreiber, M., Stein, N. and Mascher, M. (2021).
Building pan-genome infrastructures for crop plants and their use
in association genetics. DNA Research, 28(1), dsaa030.https://doi.
org/10.1093/dnares/dsaa030
Jiang, M., Chen, M., Zeng, J., Du, Z., and Xiao, J. (2024). A
comprehensive evaluation of the potential of three next-generation
short-read-based plant pan-genome construction strategies for the
identification of novel non-reference sequence. Frontiers in Plant
Science, 15, 1371222.https://doi.org/10.3389/fpls.2024.1371222
Jiang, M., Qian, Q., Lu, M., Chen, M., Fan, Z., Shang, Y., Bu, C., Du, Z.,
Song, S., Zeng, J., and Xiao, J. (2025). PlantPan: A comprehensive
multi‐species plant pan‐genome database. The Plant Journal,
122(1). https://doi.org/10.1111/tpj.70144
Jonkheer, E.M., van Workum, D.-J.M., Sheikhizadeh Anari, S.,
Brankovics, B., de Haan, J. R., Berke, L., van der Lee, T. A.
J., de Ridder, D., and Smit, S. (2022). PanTools v3: functional
annotation, classification and phylogenomics. Bioinformatics,
38(18), 4403-4405. https://doi.org/10.1093/bioinformatics/
btac506
Kolmogorov, M., Yuan, J., Lin, Y., and Pevzner, P. A. (2019).
Assembly of long, error-prone reads using repeat graphs. Nature
Biotechnology, 37(5), 540-546. https://doi.org/10.1038/s41587
019-0072-8
Koren, S., Walenz, B.P., Berlin, K., Miller, J.R., Bergman, N.H., and
Phillippy, A.M. (2017). Canu: scalable and accurate long-read
assembly via adaptive k -mer weighting and repeat separation.
Genome Research, 27(5), 722-736. https://doi.org/10.1101/
gr.215087.116
Li, B., Li, X., Wang, Y., Liu, X., Li, K., Li, R., Faiz, M.U., Darlington,
U.T., Rao, Z., Wu, Q., Yue, Y., Wang, S., Fei, Z., Liu, Y., Zheng,
Y., and Yue, J. (2025). KPGD: A kiwifruit pangenome database for
comprehensive mining of genetic diversity in the genus Actinidia.
Plant Communications, 6(8), 101373. https://doi.org/10.1016/j.
xplc.2025.101373
Li, J., Yuan, D., Wang, P., Wang, Q., Sun, M., Liu, Z., Si, H., Xu, Z.,
Ma, Y., Zhang, B., Pei, L., Tu, L., Zhu, L., Chen, L.-L., Lindsey,
K., Zhang, X., Jin, S., and Wang, M. (2021). Cotton pan-genome
Anupama Roy et al. / Journal of the Indian Society of Agricultural Statistics 175–186
retrieves the lost sequences and genes during domestication and
selection. Genome Biology, 22(1), 119. https://doi.org/10.1186/
s13059-021-02351-w
185
differences between genera and genomes. The Plant Genome,
15(1), e20100.https://doi.org/10.1002/tpg2.20100
Roy, A., Chandra, T., Mondal, R., Molla, J., Jaiswal, S., Srivastava,
Li, Q., Qiao, X., Li, L., Gu, C., Yin, H., Qi, K., Xie, Z., Yang, S.,
Zhao, Q., Wang, Z., Yang, Y., Pan, J., Li, H., Wang, J., Wang,
C., Rieseberg, L. H., Zhang, S., and Tao, S. (2024). Haplotype
resolved T2T genome assemblies and pangenome graph of pear
reveal diverse patterns of allele-specific expression and the
genomic basis of fruit quality traits. Plant Communications, 5(10),
101000. https://doi.org/10.1016/j.xplc.2024.101000
Liu, H., Wang, X., Liu, S., Huang, Y., Guo, Y.-X., Xie, W.-Z., Liu, H.,
Tahir ul Qamar, M., Xu, Q., and Chen, L.-L. (2022). Citrus Pan
Genome to Breeding Database (CPBD): A comprehensive genome
database for citrus breeding. Molecular Plant, 15(10), 1503-1505.
https://doi.org/10.1016/j.molp.2022.08.006
Liu, Z., Wang, N., Su, Y., Long, Q., Peng, Y., Shangguan, L., Zhang,
F., Cao, S., Wang, X., Ge, M., Xue, H., Ma, Z., Liu, W., Xu, X.,
Li, C., Cao, X., Ahmad, B., Su, X., Liu, Y., and Zhou, Y. (2024).
Grapevine pangenome facilitates trait genetics and genomic
breeding. Nature Genetics, 56(12), 2804-2814. https://doi.
org/10.1038/s41588-024-01967-5
Loegler, V., Friedrich, A., and Schacherer, J. (2025). Dynamics
of genome evolution in the era of pangenome analysis. Cell
Genomics, 5, 101067. https://doi.org/10.1016/j.xgen.2025.101067
Matthews, C. A., Watson-Haigh, N.S., Burton, R.A., and Sheppard,
A.E. (2024). A gentle introduction to pangenomics. Briefings
in Bioinformatics, 25(6), bbae588.https://doi.org/10.1093/bib/
bbae588
Montenegro, J.D., Golicz, A.A., Bayer, P.E., Hurgobin, B., Lee, H.,
Chan, C.K.K., and Edwards, D. (2017). The pan-genome of
hexaploid bread wheat. The Plant Journal, 90(5), 1007-1013.
https://doi.org/10.1111/tpj.13515
Munir, F., Saba, N.U., Arveen, M., Siddiqa, A., Ahmad, J., and Amir,
R. (2020). Pan-genomics of plants and its applications. In Pan
genomics: Applications, Challenges, and Future Prospects (pp.
285-306). Academic Press.
Naithani, S., Deng, C.H., Sahu, S.K., and Jaiswal, P. (2023). Exploring
Pan-Genomes: An Overview of Resources and Tools for
Unraveling Structure, Function, and Evolution of Crop Genes
and Genomes. Biomolecules, 13(9), 1403.https://doi.org/10.3390/
biom13091403
Oshkin, I. Y., Miroshnikov, K.K., Grouzdev, D.S., and Dedysh,
S.N. (2020). Pan-Genome-Based Analysis as a Framework
for Demarcating Two Closely Related Methanotroph Genera
Methylocystis and Methylosinus. Microorganisms, 8(5), 768.
https://doi.org/10.3390/microorganisms8050768
Qiao, Q., Edger, P.P., Xue, L., Qiong, L., Lu, J., Zhang, Y., Cao, Q.,
Yocca, A. E., Platts, A. E., Knapp, S. J., Van Montagu, M., Van
de Peer, Y., Lei, J., and Zhang, T. (2021). Evolutionary history
and pan-genome dynamics of strawberry (Fragaria spp.).
Proceedings of the National Academy of Sciences, 118(45).
https://doi.org/10.1073/pnas.2105431118
Raza, A., Bohra, A., and Varshney, R.K. (2023). Pan-genome for pearl
millet that beats the heat. Trends in Plant Science, 28(8), 857-860.
https://doi.org/10.1016/j.tplants.2023.04.016
Rijzaani, H., Bayer, P. E., Rouard, M., Doležel, J., Batley, J., and
M., Kumar, D., Molla, K. A., and Iquebal, M.A. (2025). Genomic
resources and genetic improvement of vital tropical and subtropical
fruit crops: current status and prospects. AoB PLANTS, 17(6),
plaf059.https://doi.org/10.1093/aobpla/plaf059
Ruperao, P., Thirunavukkarasu, N., Gandham, P., Selvanayagam,
S., Govindaraj, M., Nebie, B., Manyasa, E., Gupta, R., Das,
R.R., Odeny, D.A., Gandhi, H., Edwards, D., Deshpande, S.P.,
and Rathore, A. (2021). Sorghum Pan-Genome Explores the
Functional Utility for Genomic-Assisted Breeding to Accelerate
the Genetic Gain. Frontiers in Plant Science, 12, 666342.https://
doi.org/10.3389/fpls.2021.666342
Sabety, J., Svara, A., Tegtmeier, R., Feulner, H., Cho, P., Sakina, A.,
Hickok, D., and Khan, A. (2024). Unlocking diversity from wild
relatives of perennial fruit crops in the pan-genomics era. Current
Opinion in Plant Biology, 82, 102652. https://doi.org/10.1016/j.
pbi.2024.102652
Sarawad, A., Hosagoudar, S., and Parvatikar, P. (2025). Pan-genomics:
Insight into the Functional Genome, Applications, Advancements,
and Challenges. Current Genomics, 26(1), 2-14. https://doi.org/10
.2174/0113892029311541240627111506
Schatz, M.C., Maron, L.G., Stein, J.C., Wences, A.H., Gurtowski, J.,
Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright,
M. H., Chia, J., Ware, D., McCouch, S. R., and McCombie, W.
R. (2014). Whole genome de novo assemblies of three divergent
strains of rice, Oryza sativa, document novel gene space of aus
and indica. Genome Biology, 15(11), 506. https://doi.org/10.1186/
s13059-014-0506-z
She, H., Liu, Z., Xu, Z., Zhang, H., Wu, J., Cheng, F., Wang, X., and
Qian, W. (2024). Pan‐genome analysis of 13 Spinacia accessions
reveals structural variations associated with sex chromosome
evolution and domestication traits in spinach. Plant Biotechnology
Journal, 22(11), 3102-3117. https://doi.org/10.1111/pbi.14433
Sheikhizadeh, S., Schranz, M. E., Akdel, M., de Ridder, D., and Smit,
S. (2016). PanTools: representation, storage and exploration of
pan-genomic data. Bioinformatics, 32(17), i487–i493. https://doi.
org/10.1093/bioinformatics/btw455
Song, J.-M., Guan, Z., Hu, J., Guo, C., Yang, Z., Wang, S., Liu, D.,
Wang, B., Lu, S., Zhou, R., Xie, W.-Z., Cheng, Y., Zhang, Y., Liu,
K., Yang, Q.-Y., Chen, L.-L., and Guo, L. (2020). Eight high
quality genomes reveal pan-genome architecture and ecotype
differentiation of Brassica napus. Nature Plants, 6(1), 34-45.
https://doi.org/10.1038/s41477-019-0577-7
Springer, N. M., Ying, K., Fu, Y., Ji, T., Yeh, C.-T., Jia, Y., Wu, W.,
Richmond, T., Kitzman, J., Rosenbaum, H., Iniguez, A. L.,
Barbazuk, W. B., Jeddeloh, J. A., Nettleton, D., and Schnable, P.
S. (2009). Maize Inbreds Exhibit High Levels of Copy Number
Variation (CNV) and Presence/Absence Variation (PAV) in
Genome Content. PLoS Genetics, 5(11), e1000734. https://doi.
org/10.1371/journal.pgen.1000734
Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., and
Morgenstern, B. (2006). AUGUSTUS: ab initio prediction of
alternative transcripts. Nucleic Acids Research, 34(Web Server),
W435–W439. https://doi.org/10.1093/nar/gkl200
Sun, X., Jiao, C., Schwaninger, H., Chao, C.T., Ma, Y., Duan, N., Khan,
A., Ban, S., Xu, K., Cheng, L., Zhong, G.-Y., and Fei, Z. (2020).
Edwards, D. (2022). The pangenome of banana highlights
Phased diploid genome assemblies and pan-genomes provide
186
Anupama Roy et al. / Journal of the Indian Society of Agricultural Statistics 175–186
insights into the genetic history of apple domestication. Nature
Genetics, 52(12), 1423-1432. https://doi.org/10.1038/s41588
020-00723-9
Sun, Y., Wang, J., Li, Y., Jiang, B., Wang, X., Xu, W.-H., Wang, Y.-Q.,
Zhang, P.-T., Zhang, Y.-J., and Kong, X.-D. (2022). Pan-Genome
Analysis Reveals the Abundant Gene Presence/Absence Variations
Among Different Varieties of Melon and Their Influence on Traits.
Frontiers in plant science, 13, 835496.https://doi.org/10.3389/
fpls.2022.835496
Tahir ul Qamar, M., Fatima, K., Rao, M. J., Tang, Q., Sadaqat, M.,
Ding, B., Chen, L.-L., and Zhu, X.-T. (2025). Comparative
genomics profiling of Citrus species reveals the diversity and
disease responsiveness of the GLP pangenes family. BMC Plant
Biology, 25(1), 388. https://doi.org/10.1186/s12870-025-06397-x
Tettelin, H., Masignani, V., Cieslewicz, M.J., Donati, C., Medini, D.,
Ward, N.L., Angiuoli, S. V., Crabtree, J., Jones, A.L., Durkin,
A. S., DeBoy, R. T., Davidsen, T.M., Mora, M., Scarselli, M.,
Margarit y Ros, I., Peterson, J. D., Hauser, C. R., Sundaram, J.P.,
Nelson, W. C., … and Fraser, C.M. (2005). Genome analysis
of multiple pathogenic isolates of Streptococcus agalactiae:
Implications for the microbial “pan-genome.” Proceedings of the
National Academy of Sciences, 102(39), 13950-13955. https://doi.
org/10.1073/pnas.0506758102
Tong, C., Jia, Y., Hu, H., Zeng, Z., Chapman, B., and Li, C. (2025).
Pangenome and pantranscriptome as the new reference for gene
family characterization: A case study of basic helix-loop-helix
(bHLH) genes in barley. Plant Communications, 6(1), 101190.
https://doi.org/10.1016/j.xplc.2024.101190
Tonkin-Hill, G., MacAlasdair, N., Ruis, C., Weimann, A., Horesh, G.,
Lees, J.A., Gladstone, R.A., Lo, S., Beaudoin, C., Floto, R. A.,
Frost, S.D.W., Corander, J., Bentley, S.D., and Parkhill, J. (2020).
Producing polished prokaryotic pangenomes with the Panaroo
pipeline. Genome Biology, 21(1), 180. https://doi.org/10.1186/
s13059-020-02090-4
Torkamaneh, D., Lemay, M., and Belzile, F. (2021). The pan‐genome
of the cultivated soybean (PanSoy) reveals an extraordinarily
conserved gene content. Plant Biotechnology Journal, 19(9),
1852-1862. https://doi.org/10.1111/pbi.13600
Urhan, A., and Abeel, T. (2021). A comparative study of pan-genome
methods for microbial organisms: Acinetobacter baumannii pan
genome reveals structural variation in antimicrobial resistance
carrying plasmids. Microbial Genomics, 7(11). https://doi.
org/10.1099/mgen.0.000690
Wang, Y., Li, P., Zhu, Y., Zhang, F., Zhang, S., He, Y., Wu, Y., Lin,
Y., Wang, H., Ren, W., Wang, L., Yang, Y., Wang, R., Zheng, P.,
Liu, Y., Wang, S., and Yue, J. (2024). Graph‐Based Pangenome of
Actinidia chinensis Reveals Structural Variations Mediating Fruit
Degreening. Advanced Science, 11(28), e2400322.https://doi.
org/10.1002/advs.202400322
Weiss-Schneeweiss, H., Emadzade, K., Jang, T.-S., and Schneeweiss,
G.M. (2013). Evolutionary consequences, constraints and
potential of polyploidy in plants. Cytogenetic and Genome
Research, 140(2-4), 137-150. https://doi.org/10.1159/000351727
Yang, S., Cai, J., Wang, M., Liu, W., Yan, J., Jiang, B., and Xie, D. (2023).
The construction and analysis of wax gourd pangenome uncover
fruit quality-related and resistance genes. Scientia Horticulturae,
318, 112084. https://doi.org/10.1016/j.scienta.2023.112084
Yocca, A.E., Platts, A., Alger, E., Teresi, S., Mengist, M.F., Benevenuto,
J., Ferrão, L.F.V, Jacobs, M., Babinski, M., Magallanes-Lundback,
M., Bayer, P., Golicz, A., Humann, J. L., Main, D., Espley, R. V,
Chagné, D., Albert, N. W., Montanari, S., Vorsa, N., and Edger, P.
P. (2023). Blueberry and cranberry pangenomes as a resource for
future genetic studies and breeding efforts. Horticulture Research,
10(11), uhad202.https://doi.org/10.1093/hr/uhad202
Yuan, Y., Bayer, P.E., Batley, J., and Edwards, D. (2021). Current status
of structural variation studies in plants. Plant Biotechnology
Journal, 19(11), 2153-2163. https://doi.org/10.1111/pbi.13646
Zhang, X., Chen, X., Liang, P., and Tang, H. (2018). Cataloging Plant
Genome Structural Variations. Current Issues in Molecular
Biology, 181-194. https://doi.org/10.21775/cimb.027.181
Zhang, Y., Yang, Z., He, Y., Liu, D., Liu, Y., Liang, C., Xie, M., Jia, Y.,
Ke, Q., Zhou, Y., Cheng, X., Huang, J., Liu, L., Xiang, Y., Raman,
H., Kliebenstein, D. J., Liu, S., and Yang, Q.-Y. (2024). Structural
variation reshapes population gene expression and trait variation
in 2,105 Brassica napus accessions. Nature Genetics, 56(11),
2538-2550. https://doi.org/10.1038/s41588-024-01957-7
Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., Wu, Y., Cheng,
L., Fang, Y., Wu, K., Zhang, J., Lyu, H., Lin, T., Gao, Q., Saha, S.,
Mueller, L., Fei, Z., Städler, T., Xu, S., … and Huang, S. (2022).
Graph pangenome captures missing heritability and empowers
tomato breeding. Nature, 606(7914), 527-534. https://doi.
org/10.1038/s41586-022-04808-9
Zimin, A.V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S.L.,
and Yorke, J.A. (2013). The MaSuRCA genome assembler.
Bioinformatics, 29(21), 2669-2677. https://doi.org/10.1093/
bioinformatics/btt476
Downloads
Submitted
Published
Issue
Section
How to Cite
