Here, we summarise the latest developments in the fast progressing field of plant genome sequencing, identify current challenges, highlight opportunities and postulate future directions. Long-read sequencing is currently the method of choice to generate highly contiguous plant genome assemblies. Many application cases require a genome sequence that represents all haplophases of the investigated species.

A sequence representing this combination of neighbouring alleles is called a haplophase. Therefore, it becomes useful to investigate specific allele combinations of neighbouring genes which are forming a haplotype. Extreme examples are biosynthetic gene clusters that can reach sizes of several hundred kb or even multiple megabases (Mbp) (Nützmann et al., Reference Nützmann, Huang and Osbourn2016 Zheng et al., Reference Zheng, Meinhardt, Goenaga, Zhang and Yin2021). Loci responsible for a certain trait might involve multiple genes and span hundreds or even thousands of kilobasepairs (kb). Plant genomics is often applied to unlock the agronomic potential of plants through identification of genetic loci underlying agronomical traits. This technological advancement facilitated major discoveries in numerous fields of life science, such as the discovery of biosynthetic gene clusters in crops (Ma, Vaistij, et al., Reference Ma, Vaistij, Li, Jansen van Rensburg, Harvey, Bairu, Venter, Mavengahama, Ning, Graham, Van Deynze, Van de Peer and Denby2021), insights into the genomic diversity of crops (Jayakodi et al., Reference Jayakodi, Padmarasu, Haberer, Bonthala, Gundlach, Monat, Lux, Kamal, Lang, Himmelbach, Ens, Zhang, Angessa, Zhou, Tan, Hill, Wang, Schreiber, Boston and Stein2020 Walkowiak et al., Reference Walkowiak, Gao, Monat, Haberer, Kassa, Brinton, Ramirez-Gonzalez, Kolodziej, Delorean, Thambugala, Klymiuk, Byrns, Gundlach, Bandi, Siri, Nilsen, Aquino, Himmelbach, Copetti and Pozniak2020 Zhou, Chebotarov, et al., Reference Zhou, Chebotarov, Kudrna, Llaca, Lee, Rajasekar, Mohammed, Al-Bader, Sobel-Sorenson, Parakkal, Arbelaez, Franco, Alexandrov, Hamilton, Leung, Mauleon, Lorieux, Zuccolo, McNally and Wing2020), and generally a better understanding of land plant genome evolution (Carta et al., Reference Carta, Bedini and Peruzzi2020 Liu et al., Reference Liu, Wang, Wang, Cui, Wu, Ai, Hu, Li, He, Shao, Wu, Feng, Chang, Mu, Hou, Dai, Yin, Ruan and Cao2021). The increase in sequencing capacity is frequently displayed outpacing Moore’s law. Enormous progress has been made in the sequencing fields over the last decades. As a biochemically homogeneous molecule, DNA can be analysed at high throughput.

Resolving the genome structure of plants is the key to unlock the complex chassis of genetic factors determining phenotypic traits.

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