Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the Lauraceae

Abstract

Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.

Keywords: Lauraceae; Lindera megaphylla; gene microsynteny; tandem and proximal duplications (TD/PD); wood decay resistance (WDR).

Figure 1

Phylogenomic analysis of three major angiosperm groups. (A) Phylogenetic tree of 18 plant species generated by the concatenation-based method. Pie charts indicate the predicted expansion (red) and contraction (blue) of the gene family. The numbers represent divergence time of each node (Mya, million years ago), and values in brackets are 95% confidence intervals for the time of divergence. The yellow circle shows the WGD events identified in Lauraceae species. (B) Comparison of phylogenetic trees produced by the concatenation- and multi-species coalescent (MSC)-based methods. (C) Comparison of phylogenetic trees generated using concatenation- and microsynteny-based methods. (D) Comparison of phylogenetic trees produced using the microsynteny- and MSC-based methods.

Figure 2

Analysis of gene microsyntenic clusters. (A) Heatmap of the number of microsyntenic clusters shared among Magnoliid, eudicot, and monocot species. (B) Venn diagram showing the microsyntenic clusters shared among Magnoliids, eudicots, and monocots. (C) The black solid circle on the left surrounds microsyntenic clusters shared by eudicots and monocots, where blue dots represent eudicots, and red dots represent monocots. The black dotted rectangle on the right highlights an example of a cluster (in a subnetwork) shared between eudicots and monocots. (D) The black solid circle on the right surrounds microsyntenic clusters shared by Magnoliids and monocots, where yellow dots represent Magnoliids and red dots represent monocots. The black dotted rectangle on the left highlights an example of a cluster (in a subnetwork) shared between Magnoliids and monocots. (E) The black solid circle on the left surrounds microsyntenic clusters shared by Magnoliids and eudicots, where yellow dots represent Magnoliids and blue dots represent eudicots. The black dotted rectangle on the right highlights an example of a cluster (in a subnetwork) shared between Magnoliids and eudicots.

Figure 3

The expansion of duplicated genes. (A) The stacked bar chart shows the proportion of genes derived from five duplication types (WGD whole-genome duplication, TD tandem duplication, PD proximal duplication, TRD transposed duplication and DSD dispersed duplication). (B) GO and KEGG functional enrichment analysis of expanded genes arising from tandem and proximal duplicates (TD/PD) in Lauraceae. The red line represents GO enrichment and the blue line represents KEGG enrichment. Blue letters indicate terms related to wood decay resistance.

Figure 4

Characteristics of benzylisoquinoline alkaloid genes in Lauraceae. (A) The biosynthesis pathway of isoquinoline alkaloids. TyrAT, tyrosine aminotransferase; PDC, 4-hydroxyphenylpyruvate decarboxylase; NCS, (S)-norcoclaurine synthase; 6OMT, (RS)-norcoclaurine 6-O-methyltransferase; CNMT, (S)-coclaurine-N-methyltransferase; CYP80B, N-methylcoclaurine 3′-hydroxylase; 4OMT, 3′-hydroxy-N-methyl-(S)-coclaurine 4′-O-methyltransferase; CYP80G, (S)-corytuberine synthase; RNMT, reticuline N-methyltransferase; BBE, berberine bridge enzyme; SMT, (S)-scoulerine 9-O-methyltransferase; CYP719A, (S)-canadine synthase; THBO, tetrahydroberberine oxidase; CoOMT, columbamine O-methyltransferase. (B) Number of annotated genes in each enzyme gene family (4OMT, 6OMT, SOMT, CoOMT, CYP80G, CYP80B, CYP719A, BBE, NMT, NCS, and TyrAT) for each species. (C) Proportion of tandem (TD) and proximal (PD) duplication genes in each enzyme gene family (4OMT, 6OMT, SOMT, CoOMT, CYP80G, CYP80B, CYP719A, BBE, NMT, NCS, and TyrAT) for each species. (D) Microsyntenic gene clusters associated with subfamilies of the OMT gene family (here, 4OMT, 6OMT, and CoOMT). Circles in dashed red line denote the syntenic clusters (here, C4, C5, C7, C10 and C12) unique to Lauraceae species. (E) Heatmap of 12 microsyntenic clusters in (D), five of which are Lauraceae-specific and highlighted by a red square. The color in the heatmap represents the gene number in each cluster for each species. (F) Phylogenetic analysis of OMT gene families. The red stars represent genes within Lauraceae-specific gene clusters identified in (D).

Figure 5

Specificity of 6OMT and 4OMT genes in Lauraceae. (A) The different panels illustrate the phylogenetic tree of the 6OMT gene family (left), the distribution of motifs in the promoter sequences and the predicted transcription factor binding sites (TFBS) (middle), and the distribution of motifs in protein sequences (right). Thick squares represent motifs and thin ones represent TFBSs. Dashed boxes highlight genes and promoter motifs unique to Lauraceae species. (B) The syntenic block containing the 6OMT gene family within the Lauraceae-specific microsynteny gene cluster (C5), which was identified in Figures 4D, E . This syntenic block was compared among P. bournei, C. kanehirae, L. cubeba, and L. megaphylla. Chartreuse squares represent the 6OMT genes and aquamarine squares represent other genes on the syntenic block. (C) The syntenic block containing the 6OMT gene family within the Lauraceae-specific microsynteny gene cluster (C10), which was identified in Figures 4D, E . This syntenic block was compared among P. bournei, C. kanehirae, L. cubeba, and L. megaphylla. Blue squares represent 6OMT genes and aquamarine squares represent other genes on the syntenic block. (D) The syntenic block containing the 4OMT gene family within the Lauraceae-specific microsynteny gene cluster (C7), which was identified in Figures 4D , E . This syntenic block was compared among P. bournei, C. kanehirae, L. cubeba, and L. megaphylla. Red squares represent 4OMT genes and aquamarine squares represent other genes on the syntenic block. (E) The different panels show the phylogenetic tree of the 4OMT gene family (left),the distribution of motifs in the promoter sequences and the predicted transcription factor binding sites (TFBS) (middle), and the distribution of motifs in protein sequences (right). Thick squares represent motifs and thin ones represent TFBSs. Dashed boxes highlight genes and promoter motifs unique to Lauraceae species.

Figure 6

Characteristics of flavonoid and lignin genes in Lauraceae. (A) Biosynthesis pathways of general phenylpropanoids, flavonoids, and lignin. PAL, phenylalanine ammonia-lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumarate CoA ligase 4; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3-hydroxylase; FLS, flavonol synthase; F3′H, flavonoid 3′-hydroxylase; F3′5′H, flavonoid 3′,5′-hydroxylase; DFR, dihydroflavonol 4-reductase; ANS, anthocyanidin synthase; C3′H, p-coumaroyl shikimate 3′-hydroxylase; CCR, cinnamoyl-CoA reductase; CAD, (hydroxy)cinnamyl alcohol dehydrogenase; HCT, hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase; CCoAOMT, caffeoyl-CoAO methyltransferase; F5H, coniferaldehyde/ferulate 5-hydroxylase; COMT, caffeicacid/5-hydroxyferulic acid O-methyltransferase. (B) Proportion of tandem and proximal duplication genes in 4CL, C4H, F3H, F3′5′H, C3′H, CAD, CCoAOMT, COMT, F5H and HCT gene families in each species. (C) Heatmap of 13 microsyntenic clusters of C4H gene families in 18 species. The Lauraceae-specific cluster is highlighted by a red square. Colors in the heatmap indicate gene number in each cluster for each species. (D) Phylogenetic analysis of C4H gene families. The gene names of Lauraceae species are shown in red, and red stars represent Lauraceae-specific gene clusters identified in (C). Yellow stars show the tandem and proximal duplication (TD/PD) genes. (E) The phylogenetic tree of the C4H gene family (left), the distribution of motifs in the promoter sequences and the predicted transcription factor binding sites (TFBS) (middle), and the distribution of motifs in protein sequences (right) are shown. Thick squares represent motifs and thin ones represent TFBSs. Dashed boxes highlight genes and promoter motifs unique to Lauraceae species. (F) The syntenic block containing the C4H gene family within the Lauraceae-specific microsynteny gene cluster (C4) identified in (C). Here, this syntenic block was compared among L. chinense, P. bournei, C. kanehirae, L. cubeba, and L. megaphylla. Chartreuse squares represent C4H genes and blue squares represent other genes on the syntenic block.

Figure 7

Characterization of PAL and 4CL genes in Lauraceae species. (A) Different panels represent of the phylogenetic tree of the PAL gene family (the left), the distribution of motifs in the promoter sequence and the predicated transcription factor binding sites (TFBS) (the right). Fat squares represent the motifs and thin ones the TFBSs. Red boxes highlight the promoter motifs uniquely found among the Lauraceae species. (B) Different panels represent of the phylogenetic tree of the 4CL gene family (the left), the distribution of motifs in the promoter sequence and the predicated transcription factor binding sites (TFBS) (the right). Fat squares represent the motifs and thin ones the TFBSs. Purple boxes highlight the promoter motifs uniquely found among the Lauraceae species.

Figure 8

Lauraceae-specific CCR and HCT genes in lignin biosynthesis pathway. (A) Heatmap of 26 microsynteny clusters identified to be related with CCR gene family, one of which specific to Lauraceae were highlighted in a red square. Color in the heatmap was determined by the gene number found in each cluster for each species. (B) The syntenic block containing of CCR gene family within the Lauraceae-specific microsynteny gene cluster (C9) identified in (A). Here this syntenic block was compared among P. bournei, C. kanehirae, L. cubeba and L. megaphylla. Yellow squares represent the CCR genes and blue ones represent other genes on the syntenic block. (C) Heatmap of 27 microsynteny clusters identified to be related with HCT gene familiy, one of which specific to Lauraceae were highlighted in a red square. Color in the heatmap was determined by the gene number found in each cluster for each species. (D) The syntenic block containing of HCT gene family inside the Lauraceae-specific microsynteny gene cluster (C24) in (C). Here this syntenic block was compared among P. bournei, C. kanehirae, L. cubeba and L. megaphylla. Red squares represents the HCT genes and blue ones represents other genes on the syntenic block.