AUTHOR=Bao Yuting , He Miaohua , Zhang Chenji , Jiang Sirong , Zhao Long , Ye Zhengwen , Sun Qian , Xia Zhiqiang , Zou Meiling 

TITLE=Advancing understanding of Ficus carica: a comprehensive genomic analysis reveals evolutionary patterns and metabolic pathway insights

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1298417

DOI=10.3389/fpls.2023.1298417

ISSN=1664-462X

ABSTRACT=<p><italic>Ficus carica</italic> L. (dioecious), the most significant commercial species in the genus <italic>Ficus</italic>, which has been cultivated for more than 11,000 years and was one of the first species to be domesticated. Herein, we reported the most comprehensive <italic>F. carica</italic> genome currently. The contig N50 of the Orphan <italic>fig</italic> was 9.78 Mb, and genome size was 366.34 Mb with 13 chromosomes. Based on the high-quality genome, we discovered that <italic>F. carica</italic> diverged from <italic>Ficus microcarpa</italic> ~34 MYA, and a WGD event took place about 2─3 MYA. Throughout the evolutionary history of <italic>F. carica</italic>, chromosomes 2, 8, and 10 had experienced chromosome recombination, while chromosome 3 saw a fusion and fission. It is worth proposing that the chromosome 9 experienced both inversion and translocation, which facilitated the emergence of the <italic>F. carica</italic> as a new species. And the selections of <italic>F. carica</italic> for the genes of recombination chromosomal fragment are compatible with their goal of domestication. In addition, we found that the <italic>F. carica</italic> has the <italic>FhAG2</italic> gene, but there are structural deletions and positional jumps. This gene is thought to replace the one needed for female common type <italic>F. carica</italic> to be pollinated. Subsequently, we conducted genomic, transcriptomic, and metabolomic analysis to demonstrate significant differences in the expression of <italic>CHS</italic> among different varieties of <italic>F. carica</italic>. The <italic>CHS</italic> playing an important role in the anthocyanin metabolism pathway of <italic>F. carica</italic>. Moreover, the <italic>CHS</italic> gene of <italic>F. carica</italic> has a different evolutionary trend compared to other <italic>Ficus</italic> species. These high-quality genome assembly, transcriptomic, and metabolomic resources further enrich <italic>F. carica</italic> genomics and provide insights for studying the chromosomes evolution, sexual system, and color characteristics of <italic>Ficus</italic>.</p>