Medicinal Plant Research 2025, Vol.15, No.3, 142-150 http://hortherbpublisher.com/index.php/mpr 144 Figure 1 Circos plot illustrating the genome of AM genome. The plot includes the following components, arranged from inside to outside: (I) Collinear regions within AM assembly; (II) GC content in non-overlapping 1 Mb windows; (III) Percentage of repeats in 1-Mb sliding windows; (IV) Gene density in 1-Mb sliding windows; (V) Length of pseudo-chromosome in megabases (Mb) (Adopted from Fan et al., 2024) 3 Advances in Pan-genome Construction: Sequencing, Assembly, and Alignment 3.1 Concept of the pan-genome Pan-genome is the totality of the genes of a species, comprising the core genome (genes shared by all individuals) and accessory or dispensable genome (genes present in some but not all individuals). The term encompasses genetic variation as well as structural variation and helps to explain adaptation and diversity of traits (Jayakodi et al., 2021). 3.2 Technical approaches for pan-genome construction Pan-genome assembly typically involves sequencing several samples through the use of high-throughput techniques. Short-read and long-read sequencing are utilized, but long-read platforms such as PacBio and Oxford Nanopore now enable more contiguous and completed assemblies, especially in repeat or complex regions (Jayakodi et al., 2021). Assembly methods include de novo assembly of every genome and subsequent whole-genome alignment for identifying common and specific sequences (Zhang et al., 2022). Reference-assisted scaffolding tools, such as RaGOO, can even facilitate assembly contiguity and identify structural variants (Alonge et al., 2019). Assembly quality and depth of sequencing are also crucial as they directly affect the gene presence/absence calling accuracy and also the structure of the pan-genome.
RkJQdWJsaXNoZXIy MjQ4ODYzNA==