Recent Advances in Assembly of Complex Plant Genomes

Abstract

Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.

A haplotype-resolved reference genome ofQuercus albasheds light on the evolutionary history of oaks

“…We confirmed the completeness and accuracy of both genome assembly haplotypes with BUSCO and LAI scores as well as a new genetic linkage map. The haplotypes have contig N50s of 8.3 Mb and 8.9 Mb, commensurate with the highest quality recent plant genome assemblies (Kong et al ., 2023), with 97% of bases scaffolded into chromosomes ( Table 1 ). Similar to other Quercus genomes (Sork et al ., 2022; Ai et al ., 2022), each haplotype has 12 chromosomes and is approximately 793 Mb in length, in agreement with cytology (Friesner, 1930) and C-value estimates (Bai et al ., 2012).…”

“…Mb, commensurate with the highest quality recent plant genome assemblies (Kong et al, 2023), with 97% of bases scaffolded into chromosomes (Table 1). Similar to other Quercus genomes (Sork et al, 2022;Ai et al, 2022), each haplotype has 12 chromosomes and is approximately 793 Mb in length, in agreement with cytology (Friesner, 1930) and C-value estimates (Bai et al, 2012).…”

Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant

“…However, our assembly displayed a completeness comparable to the previously reported B. schreberi assembly [8], which showed 89.0 and 95.9% completeness using BUSCO in the Eudicots and Embryphyta databases, respectively, and 91.3% and 97.0% completeness using compleasm in the Eudicots and Embryphyta databases, respectively. Nevertheless, because this previous assembly did not remove duplications from the assembly [43], some assembly errors may exist for gene prediction. For the completed BUSCOs, our assembly revealed 39.7% and 46.8% higher complete and single-copy BUSCOs using BUSCO in the Eudicots and Embryphyta database, while it was 37.4 and 44.0% complete and single-copy BUSCOs in Eudicots and Embryphyta for the previously reported assembly.…”

Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant

“…schreberi assembly [ 8 ], which showed 89.0 and 95.9% completeness using BUSCO in the Eudicots and Embryphyta databases, respectively, and 91.3% and 97.0% completeness using compleasm in the Eudicots and Embryphyta databases, respectively. Nevertheless, because this previous assembly did not remove duplications from the assembly [ 43 ], some assembly errors may exist for gene prediction. For the completed BUSCOs, our assembly revealed 39.7% and 46.8% higher complete and single-copy BUSCOs using BUSCO in the Eudicots and Embryphyta database, while it was 37.4 and 44.0% complete and single-copy BUSCOs in Eudicots and Embryphyta for the previously reported assembly.…”