The Phoebe genome sheds light on the evolution of magnoliids

Abstract

Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46-and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids.

Genome-Wide Identification of the YABBY Gene Family in Seven Species of Magnoliids and Expression Analysis in Litsea

“…Previous work provided evidence that YAB2 -like genes function to promote laminar outgrowth and stamen morphologic evolution [ 17 ]. Apart from conserved YAB2 regulation, the dynamic regulation and biological function of INO -like and CRC -like genes should be conserved in angiosperm plants as consistent as that in the previous findings that INO and CRC genes were involved in the seed formation and differentiation of the nectary in basal taxa, respectively [ 14 , 16 , 22 , 28 , 29 ].…”

“…The flowering plants are the most diverse group of plants, and the basal flowering plant lineages were diverged at a very early stage in angiosperms’ evolution, followed by rapid diversification among the magnoliids, eudicots, and monocots [ 26 , 27 ]. Gene family comparisons in whole genomes across plant lineages would contribute to identifying critical events in the evolution of major flowering plants [ 27 , 28 ]. The magnoliids constitute a significant group of flowering plants but are much smaller than the monocots and eudicots.…”

“…Moreover, the relationships among magnoliids, eudicots, and monocots have not been conclusively resolved. Recently, several whole genomes of magnoliids species, including three Lauracea species, Cinnamomum micranthum , Litsea cubeba , and Phoebe bournei , two Calycanthaceae species, C. praecox and Chimonanthus salicifolius ; Piper nigrum (Piperaceae), as well as Liriodendron chinense (Magnoliaceae), have been sequenced [ 27 , 28 , 31 , 32 , 33 , 34 , 35 ]. The completed assembly of the whole genome of these magnoliids would provide a new opportunity for a systematic exploration of the YABBY gene family.…”

Research Progress in Plant Molecular Systematics of Lauraceae

“…The whole genome sequencing has nowadays been completed for Persea americana , Cinnamomum kanehirae , Phoebe bournei and Litsea cubeba in the Lauraceae [ 32 , 76 , 77 , 78 ]. Although there have been some studies on the whole genome of Lauraceae other than the phylogeny, this review here focuses on the systematics of Lauraceae.…”

SPDE: A Multi-functional Software for Sequence Processing and Data Extraction

“…Extracting and organizing valid information from biological big data are the two foundations of bioinformatics analyses. In recent years, the rapid accumulation of genome data 1,2 indicates that more efficient and reliable tools are needed to extract and organize the resultant biological big data. Although a lot of bioinformatic software 3,4 have been developed, many are distributed in Linux systems or require users to have a knowledge of programming language.…”