The genome of Magnolia hypoleuca provides a new insight into cold tolerance and the evolutionary position of magnoliids

Abstract

Magnolia hypoleuca Sieb. & Zucc, a member of the Magnoliaceae of magnoliids, is one of the most economically valuable, phylogenetic and ornamental tree species in Eastern China. Here, the 1.64 Gb chromosome-level assembly covers 96.64% of the genome which is anchored to 19 chromosomes, with a contig N50 value of 1.71 Mb and 33,873 protein-coding genes was predicted. Phylogenetic analyses between M. hypoleuca and other 10 representative angiosperms suggested that magnoliids were placed as a sister group to the eudicots, rather than sister to monocots or both monocots and eudicots. In addition, the relative timing of the whole-genome duplication (WGD) events about 115.32 Mya for magnoliid plants. M. hypoleuca was found to have a common ancestor with M. officinalis approximately 23.4 MYA, and the climate change of OMT (Oligocene-Miocene transition) is the main reason for the divergence of M. hypoleuca and M. officinalis, which was along with the division of Japanese islands. Moreover, the TPS gene expansion observed in M. hypoleuca might contribute to the enhancement of flower fragrance. Tandem and proximal duplicates of younger age that have been preserved have experienced more rapid sequence divergence and a more clustered distribution on chromosomes contributing to fragrance accumulation, especially phenylpropanoid, monoterpenes and sesquiterpenes and cold tolerance. The stronger selective pressure drived the evolution of tandem and proximal duplicates toward plant self-defense and adaptation. The reference M. hypoleuca genome will provide insights into the evolutionary process of M. hypoleuca and the relationships between the magnoliids with monocots and eudicots, and enable us to delve into the fragrance and cold tolerance produced by M. hypoleuca and provide more robust and deep insight of how the Magnoliales evolved and diversified.

The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP)

“…45 Mb). This is superior to the data available from L. chinense (1.74 Gb with contigs N50 of ∼1.43 Mb) [ 38 ], M. officinalis (1.68 Gb, with contigs N50 of 0.22 Mb) [ 40 ], M. obovata (1.64 Gb, with contigs N50 of 1.71 Mb) [ 41 ], and M. biondii (2.22 Gb with contigs N50 of 0.27 Mb) [ 39 ].…”

A high-quality haplotype genome of Michelia alba DC reveals differences in methylation patterns and flower characteristics

“…The position of Magnoliaceae in plant evolution has been extensively studied, but there have been no accurate conclusions. We selected 2 dicot plant species ( Vitis vinifera, Arabidopsis thaliana ), 3 monocot plant species Elaeis guineensis (Yang et al 2023 ), Zea mays (Gui et al 2020 ), Oryza sativa (Sakai et al 2013 ), 10 Magnoliids species ( M. montana, M. champaca, Magnolia biondii , Chimonanthus praecox (Shang et al 2020b ), Cinnamomum kanehirae (Chaw et al 2019a ), Amborella trichopoda (Qin et al 2021 ), L. chinense , Piper nigrum (Hu et al 2019 ), Magnolia hypoleuca (Zhou et al 2023 ) and Magnolia officinalis (Yin et al 2021 ), an early angiosperm species ( Nymphaea tetragona ), an ancient Pteridophyta species ( Selaginella tamariscina ), and an ancient gymnosperm ( Picea abies ) for homologous gene analysis to more accurately depict the phylogenetic relationships. After thorough evaluation and selection, we utilized single-copy gene familys to construct the phylogenetic tree.…”

Evidence for the Use of Karst Tiankengs as Shelters: The Effect of Karst Tiankengs on Genetic Diversity and Population Differentiation in Manglietia aromatica

“…A Trimmomatic v0.36 (default parameters) [20] was used to extract adapter sequences, cleavage sites (first 6 base pairs of reads) and low-quality reads (Q20 < 20, length < 36 bp) from raw sequence data [20]. The clean reads were then aligned with the Magnolia hypoleuca (Magnoliaceae) reference genome [21] using BWA v0.7.12 [22]. The Stacks v.2.59 software's rm-pcr-duplicates parameter was utilized to eliminate PCR repeats and conduct SNP calling [23].…”