1. Govindaraj, M., Vetriventhan, M. & Srinivasan, M. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genetics research international 2015, 431487 (2015).
2. Thudi, M. et al. Genomic resources in plant breeding for sustainable agriculture. Journal of Plant Physiology 257, 153351 (2021).
3. Wang, P. et al. The genome evolution and domestication of tropical fruit mango. Genome Biology 21, 1–17 (2020).
4. Xia, E. et al. The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation. Molecular Plant 13, 1013–1026 (2020).
5. Gordon, S. P. et al. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications 8, 1–13 (2017).
6. Hübner, S. et al. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Nature Plants 5, 54–62 (2019).
7. Gao, L. et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics 51, 1044–1051 (2019).
8. Lei, L. et al. Plant Pan-Genomics Comes of Age. Annual Review of Plant Biology 72, 411–435 (2021).
9. Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J. & Edwards, D. Plant pan-genomes are the new reference. Nature plants 6, 914–920 (2020).
10. Ou, L. et al. Pan-genome of cultivated pepper (Capsicum) and its use in gene presence–absence variation analyses. New Phytologist 220, 360–363 (2018).
11. Golicz, A. A., Batley, J. & Edwards, D. Towards plant pangenomics. Plant Biotechnology Journal 14, 1099–1105 (2016).
12. della Coletta, R., Qiu, Y., Ou, S., Hufford, M. B. & Hirsch, C. N. How the pan-genome is changing crop genomics and improvement. Genome Biology 22, 1–19 (2021).
13. Golicz, A. A., Batley, J. & Edwards, D. Towards plant pangenomics. Plant Biotechnology Journal 14, 1099–1105 (2016).
14. Danilevicz, M. F., Tay Fernandez, C. G., Marsh, J. I., Bayer, P. E. & Edwards, D. Plant pangenomics: approaches, applications and advancements. Current Opinion in Plant Biology 54, 18–25 (2020).
15. Liu, Y. et al. Pan-Genome of Wild and Cultivated Soybeans. Cell 182, 162–176 (2020).
16. Torkamaneh, D., Lemay, M. A. & Belzile, F. The pan‐genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content. Plant Biotechnology Journal 19, 1852 (2021).
17. Sun, C. et al. RPAN: rice pan-genome browser for ∼3000 rice genomes. Nucleic Acids Research 45, 597–605 (2017).
18. Zhao, Q. et al. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nature Genetics 50, 278–284 (2018).
19. Qin, P. et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell 184, 3542–3558 (2021).
20. Glick, L. & Mayrose, I. Panoramic: A package for constructing eukaryotic pan-genomes. Molecular Ecology Resources 21, 1393–1403 (2021).
21. Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular biology and evolution 35, 543–548 (2018).
22. Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639–1643 (2021).
23. Scalzitti, N., Jeannin-Girardon, A., Collet, P., Poch, O. & Thompson, J. D. A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms. BMC Genomics 21, 1–20 (2020).
24. Stephens, Z. D. et al. Simulating next-generation sequencing datasets from empirical mutation and sequencing models. PLOS ONE 11, 1–18 (2016).
25. Ferrés, I., Fresia, P. & Iraola, G. simurg: simulate bacterial pangenomes in R. Bioinformatics 36, 1273–1274 (2020).
26. Rakocevic, G. et al. Fast and accurate genomic analyses using genome graphs. Nature Genetics 51, 354–362 (2019).
27. Marschall, T. et al. Computational pan-genomics: Status, promises and challenges. Briefings in Bioinformatics 19, 118–135 (2018).
28. Tao, Y., Jordan, D. R. & Mace, E. S. A Graph-Based Pan-Genome Guides Biological Discovery. Molecular Plant 13, 1247–1249 (2020).
29. Jiao, W. B. & Schneeberger, K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nature Communications 11, 1–10 (2020).
30. Gan, X. et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477, 419–423 (2011).
31. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
32. Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
33. Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology 19, 455–477 (2012).
34. Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).
35. Alonge, M. et al. RaGOO: Fast and accurate reference-guided scaffolding of draft genomes. Genome Biology 20, 224 (2019).
36. Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
37. Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology 20, 1–18 (2019).
38. Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, ii215–ii225 (2003).
39. Korf, I. Gene finding in novel genomes. BMC Bioinformatics 5, 1–9 (2004).
40. Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004).
41. Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9, 1–22 (2008).
42. Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology 35, 1026–1028 (2017).
43. Gremme, G., Brendel, V., Sparks, M. E. & Kurtz, S. Engineering a software tool for gene structure prediction in higher organisms. Information and Software Technology 47, 965–978 (2005).
44. Emms, D. M. & Kelly, S. OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biology 20, 1–14 (2019).
45. Zheng, C., Swenson, K., Lyons, E. & Sankoff, D. OMG! Orthologs in Multiple Genomes - Competing graph-theoretical formulations. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) vol. 6833 LNBI 364–375 (Springer Verlag, 2011).
46. Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
47. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows--Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
48. Camacho, C. et al. BLAST+: Architecture and applications. BMC Bioinformatics 10, 1–9 (2009).
49. Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16, 1–14 (2015).
50. Hagberg, A., Chult, D. & Swart, P. Exploring network structure, dynamics, and function using NetworkX. Proceedings of the 7th Python in Science conference 2008, 11–15 (2008).
51. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
52. Song, J. M. et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants 6, 34–45 (2020).
53. Hurgobin, B. et al. Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnology Journal 16, 1265–1274 (2018).
54. Zhao, Q. et al. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nature Genetics 2018 50:2 50, 278–284 (2018).
55. Wang, W. et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557, 43–49 (2018).
56. Li, H. et al. Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nature Communications 2022 13:1 13, 1–14 (2022).
57. Zhou, P. et al. Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. BMC Genomics 18, 1–14 (2017).
58. Hufford, M. B. et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373, 655–662 (2021).
59. Sun, X. et al. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nature Genetics 2020 52:12 52, 1423–1432 (2020).
60. Golicz, A. A. et al. The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications 7, 1–8 (2016).
61. Barchi, L. et al. Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. The Plant Journal 107, 579–596 (2021).
62. Zhao, J. et al. Trait associations in the pangenome of pigeon pea ( Cajanus cajan ). Plant Biotechnology Journal 18, 1946–1954 (2020).