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. 2022 Feb 15:20:1002-1011.
doi: 10.1016/j.csbj.2022.02.009. eCollection 2022.

A chromosome-level genome assembly of Amorphophallus konjac provides insights into konjac glucomannan biosynthesis

Yong Gao  1 , Yanan Zhang  1 , Chen Feng  2 , Honglong Chu  1 , Chao Feng  3 , Haibo Wang  1 , Lifang Wu  1 , Si Yin  1 , Chao Liu  1 , Huanhuan Chen  1 , Zhumei Li  1 , Zhengrong Zou  4 , Lizhou Tang  4
Affiliations

A chromosome-level genome assembly of Amorphophallus konjac provides insights into konjac glucomannan biosynthesis

Yong Gao et al. Comput Struct Biotechnol J. .

Abstract

Amorphophallus konjac, a perennial herb in the Araceae family, is a cash crop that can produce a large amount of konjac glucomannan. To explore mechanisms underlying such large genomes in the genus Amorphophallus as well as the gene regulation of glucomannan biosynthesis, we present a chromosome-level genome assembly of A. konjac with a total genome size of 5.60 Gb and a contig N50 of 1.20 Mb. Comparative genomic analysis reveals that A. konjac has undergone two whole-genome duplication (WGD) events in quick succession. Two recent bursts of transposable elements are identified in the A. konjac genome, which contribute greatly to the large genome size. Our transcriptomic analysis of the developmental corms characterizes key genes involved in the biosynthesis of glucomannan and related starches. High expression of cellulose synthase-like A, Cellulose synthase-like D, mannan-synthesis related 1, GDP-mannose pyrophosphorylase and phosphomannomutase fructokinase contributes to glucomannan synthesis during the corm expansion period while high expression of starch synthase, starch branching enzyme and phosphoglucomutase is responsible for starch synthesis in the late corm development stage. In conclusion, we generate a high-quality genome of A. konjac with different sequencing technologies. The expansion of transposable elements has caused the large genome of this species. And the identified key genes in the glucomannan biosynthesis provide valuable candidates for molecular breeding of this crop in the future.

Keywords: Amorphophallus konjac; Genome evolution; Glucomannan biosynthesis; Whole-genome duplication.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

None
Graphical abstract
Fig. 1
Fig. 1
Leaf, flower, fruit and corm morphology, and the genome landscape of A. konjac. (A-D) The leaf, flower, fruit and corm morphology of A. konjac; (E) The genome landscape of A. konjac, (a) Length of each chromosome in megabases (Mb), (b) Gene density, (c) Repeat density, (d) Tandem repeat density, (e) GC content, (f) Intragenomic synteny information.
Fig. 2
Fig. 2
Phylogenetic tree of 12 plant species and evolution of gene families. Left, the phylogeny of 12 species. Black numerical value beside each node shows the estimated divergence time (million years ago), and red circle indicates the node age calibration point. Right, the distribution of single-copy, multiple-copy, unique and unclustered genes for each species.
Fig. 3
Fig. 3
Distribution of synonymous substitution levels (Ks) of syntenic orthologous (A) and collinearity patterns between paralogous genes of S. polyrhiza, A. konjac and C. esculenta (B).
Fig. 4
Fig. 4
LTR analysis for genomes of S. polyrhiza, A. konjac and C. esculenta. (A) The LTR content in genomes of S. polyrhiza, A. konjac and C. esculenta. (B) The estimated insertion times of LTR in genomes of the three species. (C) Distribution of insertion times of Gypsy and Copia retrotransposons in A. konjac genome.
Fig. 5
Fig. 5
Transcriptome and RT-qPCR analyses for KGM biosynthesis. (A) Principal component analysis (PCA) of 15 A. konjac corm samples. (B) RT-qPCR and measurement of KGM content. Values represent means ± SD. Asterisks indicate statistical significance using student’s t-test (P < 0.05, n = 3) and one-way ANOVA with post hoc Tukey HSD test is applied to compare KGM content of four stages (P < 0.01, n = 4). (C) Heatmap of KGM biosynthesis-related genes that are highly expressed in stage 2 and/or stage 3. The threshold is Log2 FC (stageN/stage1) > 2 (N = 2 or 3, P < 0.05).
Fig. 6
Fig. 6
Maximum likelihood (ML) tree of CSLA family of enzymes. Different colors represented different species, and only the FPKM values of CSLA genes at stage 2 were shown by colored circles.
Fig. 7
Fig. 7
Chromosome positions of KGM synthesis-related genes and putative biosynthetic pathway of KGM. (A) Positions of KGM synthesis-related genes distributed on chromosomes 5 and 11. (B) Putative biosynthetic pathway of KGM. Group 1, group 2 and group 3 are highlighted in green, orange and red, respectively. Dash lines represent speculative pathways. Sucrose synthase (SuS), invertase (INV), phosphoglucose isomerase (PGI), phosphoglucomutase (PGM), phosphomannose isomerase (PMI), phosphomannomutase (PMM), starch synthase (SS), GDP-mannose pyrophosphorylase (GMPP), UDP-glucose pyrophosphorylase (UGP), ADP-glucose pyrophosphorylase (AGP), fructokinase (FRK), hexokinase (HXK), starch branching enzyme (SBE), cellulose synthase-like A (CSLA), Cellulose synthase-like D (CSLD), mannan-synthesis related 1 (MSR1).
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