Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis

Hui Huang,Huilin Huang,Caihong Zhong,Qi Tan,Songquan Song,Juan Liang,Xianjin Wu,Ian Max Møller,Linfeng Ou,Xiaolin Li

doi:10.1038/s41438-020-00458-y

Hui Huang, Huilin Huang + Show 8 more

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https://doi.org/10.1038/s41438-020-00458-y

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Akebia trifoliata subsp. australis is a well-known medicinal and potential woody oil plant in China. The limited genetic information available for A. trifoliata subsp. australis has hindered its exploitation. Here, a high-quality chromosome-level genome sequence of A. trifoliata subsp. australis is reported. The de novo genome assembly of 682.14 Mb was generated with a scaffold N50 of 43.11 Mb. The genome includes 25,598 protein-coding genes, and 71.18% (485.55 Mb) of the assembled sequences were identified as repetitive sequences. An ongoing massive burst of long terminal repeat (LTR) insertions, which occurred ~1.0 million years ago, has contributed a large proportion of LTRs in the genome of A. trifoliata subsp. australis. Phylogenetic analysis shows that A. trifoliata subsp. australis is closely related to Aquilegia coerulea and forms a clade with Papaver somniferum and Nelumbo nucifera, which supports the well-established hypothesis of a close relationship between basal eudicot species. The expansion of UDP-glucoronosyl and UDP-glucosyl transferase gene families and β-amyrin synthase-like genes and the exclusive contraction of terpene synthase gene families may be responsible for the abundant oleanane-type triterpenoids in A. trifoliata subsp. australis. Furthermore, the acyl-ACP desaturase gene family, including 12 stearoyl-acyl-carrier protein desaturase (SAD) genes, has expanded exclusively. A combined transcriptome and fatty-acid analysis of seeds at five developmental stages revealed that homologs of SADs, acyl-lipid desaturase omega fatty acid desaturases (FADs), and oleosins were highly expressed, consistent with the rapid increase in the content of fatty acids, especially unsaturated fatty acids. The genomic sequences of A. trifoliata subsp. australis will be a valuable resource for comparative genomic analyses and molecular breeding.

Highlights

Akebia trifoliata (Thumb.) Koidz. subsp. australis is a perennial woody plant that belongs to the genus Akebia (Lardizabalaceae) and is mainly distributed in East Asia[1]
We identified key genes involved in triterpene synthesis and the accumulation of UFAs
The genome of A. trifoliata was initially sequenced and assembled using the HiSeq X Ten sequencing platform from Illumina and PacBio single-molecule real-time (SMRT) sequencing technology, and the assembled contigs were anchored to pseudochromosomes using the HiC technique

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Introduction

Akebia trifoliata (Thumb.) Koidz. subsp. australis is a perennial woody plant that belongs to the genus Akebia (Lardizabalaceae) and is mainly distributed in East Asia[1]. We identified key genes involved in triterpene synthesis and the accumulation of UFAs. The availability of this genomic information will be helpful for comparative genomic analysis and the molecular breeding and engineering of A. trifoliata. K-mer analysis revealed that the estimated genome size of A. trifoliata was 669.76 Mb with a heterozygosity of 0.89% (Fig. S1).

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