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Brief Report

Genome Assemblies of Two Ormosia Species: Gene Duplication Related to Their Evolutionary Adaptation

by
Pan-Pan Liu
1,
En-Ping Yu
2,3,4,
Zong-Jian Tan
1,
Hong-Mei Sun
1,
Wei-Guang Zhu
2,3,
Zheng-Feng Wang
2,3,* and
Hong-Lin Cao
2,3,*
1
Zhongshan Management Centre of the Natural Protected Area, Zhongshan 528400, China
2
Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
3
South China National Botanical Garden, Guangzhou 510650, China
4
University of Chinese Academy of Sciences, Beijing 100049, China
*
Authors to whom correspondence should be addressed.
Agronomy 2023, 13(7), 1757; https://doi.org/10.3390/agronomy13071757
Submission received: 25 April 2023 / Revised: 24 June 2023 / Accepted: 26 June 2023 / Published: 29 June 2023
(This article belongs to the Section Crop Breeding and Genetics)
Browse Figures
Versions Notes

Abstract

:
Ormosia is a genus of the Fabaceae family that shows a distinct evolutionary history due to its typical Asian-American tropical disjunction distribution pattern. However, both its phylogeny and biogeographic mechanisms have not been fully resolved. In addition, Ormosia species have great economic and ecological potential in the wood and handicraft (using their attractive seeds) industries, reforestation, and folk medicine (due to their flavonoids, alkaloids, and terpenoids), making them highly valuable in research, especially from a genomic perspective. We report the genome assemblies of two common Ormosia species, Ormosia emarginata and Ormosia semicastrata, in South China, using both long and short sequencing reads. The genome assemblies of O. emarginata and O. semicastrata comprised 90 contigs with a total length of 1,420,917,605 bp and 63 contigs with a total length of 1,511,766,959 bp, respectively. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment revealed 97.0% and 98.3% completeness of the O. emarginata and O. semicastrata assemblies, respectively. The assemblies contain 48,599 and 52,067 protein-coding genes, respectively. Phylogenetic analyses using 1032 single-copy genes with 19 species indicated that they are closely related to Lupinus albus. We investigated genes related to plant hormones, signaling, the circadian rhythm, transcription factors, and secondary metabolites derived from the whole genome and tandem and proximal duplications, indicating that these duplications should play important roles in the growth, development, and defense of Ormosia species. To our knowledge, our study is the first report on Ormosia genome assemblies. This information will facilitate phylogenetic and biogeographic analyses and species breeding in the future.

1. Introduction

The genus Ormosia within the family Fabaceae contains about 150 species [1]. These species are mostly distributed in tropical regions, mainly in Southeast Asia, northern Australia, Papua New Guinea, Brazil, and the Caribbean [1,2]. Phylogenetic analysis using ITS, matK, and trnL-F markers indicate the Ormosia species are clustered into three clades: the Old World Ormosia clade 1, the Old World Ormosia clade 2, and the New World Ormosia clade [1]. Species of the Old World Ormosia clades are distributed from east-central China to southern India, the Solomon Islands, and northeastern Australia. Species of the New World Ormosia clade are mainly present on the mainland from southern Mexico to Bolivia and southernmost Brazil. Continental Asia is the origin of Ormosia, and the New World distribution might have occurred around the Oligocene or early Miocene [1]. In China, fossil analysis indicates that southern China was the Ormosia distribution center, and it extended northwards during the Miocene due to drastic climate change in East Asia [3]. However, due to complicated morphological variations, the phylogeny and biogeography of Ormosia have not yet been fully resolved [1,2,4].
Many Ormosia species are high-quality timber species that have great economic benefits in production, and some species are valuable garden or medical trees [5,6]. The other distinct characteristics of Ormosia species are their attractive, brightly colored seeds (red or black) that are often used for jewelry and ornamental items.
Ormosia emarginata and Ormosia semicastrata are naturally distributed in southern China, but O. emarginata extends to Vietnam. O. semicastrata can be found in high latitudes to 27°, while the highest latitude for O. emarginata is 23° [3]. Both Ormosia species are evergreen trees, and O. emarginata sometimes occurs as a shrub. Phylogenetic analysis indicates that these two species are in different clades, with O. emarginata in the Old World Ormosia clade 1 and O. semicastrata in the Old World Ormosia clade 2 [1]. Ormosia emarginata is different from the other Ormosia species because its leaf tip forms a clear notch, a feature that underlies its species name (emarginata).
In this study, we obtained the whole genome assemblies for O. emarginata and O. semicastrata. To our acknowledge, this is the first report of the genome assemblies of Oromia species. The reported assemblies will provide a valuable resource for future evolutionary and ecological research.

2. Materials and Methods

2.1. Sample Collection and Sequencing

One O. emarginata and one O. semicastrata individual were collected from Wuguishan, Zhongshan City, China. Their genomic DNA and total RNA were isolated from leaf tissues. Next, long- and short-read whole-genome sequencing (WGS) and short-read RNA sequencing (RNA-seq) libraries were constructed. Long-read WGS sequencing was performed by using the Nanopore PromethION sequencer, while both short-read WGS and RNA-seq were performed by using the MGI DNBSEQ-T7 sequencer under the 150 base pair (bp) paired-end (insert size 300 bp) sequencing strategies. GrandOmics Biosciences (GB, Wuhan, China) completed the sequencing and library construction.

2.2. Data Pre-Processing

Most modern sequencing technologies produce different kinds of errors in the raw sequences, which influence the accuracy of downstream bioinformatics analyses. These low-quality reads then need to be trimmed and/or corrected. After sequencing, short WGS reads of O. emarginata and O. semicastrata were quality-trimmed using Sickle v1.33 [7], an efficient quality-trimming tool via a sliding window, by removing the reads with a base quality value of <30 and a length of <80 bp. The reads were further error corrected by using RECKONER v1.1 [8], an efficient error corrector using a k-spectrum-based algorithm. Using the error-corrected reads, the genome size of O. emarginata and O. semicastrata was estimated with KmerGenie v1.7044 [9], GenomeScope 2.0 [10], and findGSE [11]. All these programs are k-mer-based genome size estimators. The adapters for Nanopore long reads were removed using Porchop 0.2.4 [12].

2.3. Genome Assembly

The genomes of O. emarginata and O. semicastrata were assembled based on their Nanopore long reads with nextDenovo 2.3.1 [13]. NextDenovo is a string graph-based de novo assembler for noisy long reads. It applies a “correction then assembly” strategy and promises continuous assemblies containing fewer misassemblies. After assembly, Pseudohaploid [14] and Purge_Dups v1.2.6 [15] were applied to examine and remove duplications caused by heterozygosity in the assemblies. Considering the initial assembly still contained many errors, the assembles were then polished by racon v1.5.0 [16], hapo-G v1.3.2 [17], and polypolish v0.5.0 [18], and possible misassemblies were further corrected using Depthcharge v0.2.0 [19]. Racon and Depthcharge were performed using the Nanopore long reads of two species, and hapo-G and polypolish were performed using their error-corrected short WGS reads. Benchmarking Universal Single-Copy Orthologs (BUSCO) v5.4.4 [20] with the database eudicots_odb10.2020-09-10 was used to evaluate the quality of each assembly. BUSCO assessments are based on matching the regions in the genome assembly to the lineage-specific sets of near-universal single-copy orthologous genes. Regions that contain potential matches to the orthologue set are classified as “complete” if they are full-length matches, “single-copy” if they are complete matches and only appear once, “fragmented” if 90% matches, and “missing” if there are no matches.

2.4. Repeat Annotation

Repeat sequences (Repeats) are DNA fragments with multiple copies in the genome and are important genetic material in the genomes of almost all species [21,22]. Repeats generally include tandem repeats (TRs, including satellites, minisatellites, and microsatellites) and transposable elements (TEs). TEs are categorized as retrotransposons and DNA transposons. Long-terminal repeat (LTR) retrotransposons and terminal inverted repeat (TIR) are two major components of retrotransposons and DNA transposons, respectively. Repeat sequences of O. emarginata and O. semicastrata assemblies were identified with EDTA v2.1.0 [21] and RED v2.0 [22], respectively, and their results were then combined by using the “merge” command in bedtools v2.29.2 [23]. Based on the combined repeated sequences, O. emarginata and O. semicastrata genome assemblies were masked using the “maskfasta” command in bedtools. EDTA is a precise and efficient TE detector, and RED is rapid and accurate in both TRs and TEs identifications.

2.5. Gene Prediction and Annotation

The primary gene sets of O. emarginata and O. semicastrata were obtained using de novo transcriptome assemblies with TransPi 1.1.0-Rc [24] using their RNA-seq reads. TransPi applies different transcriptome assemblers to produce a combined transcriptome assembly, which greatly improves the representation of the assembly. The over-assembled transcriptome is then reduced to output the results with fewer biases, duplication, and misassemblies using a consensus approach. The TransPi results and protein sequences from Abrus precatorius, Aeschynomene evenia, Cicer arietinum, Glycine max, Lupinus albus, and Senna tora (Table S1, used as protein evidence-based prediction) were then input into the funannotate pipeline v1.8.13 [25] to obtain the final integrated and consensus gene sets, using the commands “funannotate train”, “funannotate predict”, and “funannotate update”. For the “predict” and “update” steps, the parameters “-max_intronlen 100,000”, “-busco_db embryophyte”, and “-organism other” were applied. Funannotate is a user-friendly genome prediction, annotation, and comparison software package. It takes into account repeated elements and includes different evidence (ab-initio predictions, transcript, and protein sequences) to improve the gene predictions.
After gene prediction, the command “funannotate annotate” was used for functional annotation of the genes. The annotation databases used included dbCAN v10.0 [26], eggnog-mapper v5.0.2 [27], Gene Ontology (GO) [28,29], Kyoto Encyclopedia of Genes and Genomes (KEGG) [30], InterPro v5.60-92.0 [31], MEROPS v12.0 [32], Pfam v35.0 [33], and UniProt v2022_05 [34].

2.6. Gene Families and Comparative Genomics

A gene family is a group of functionally related genes formed by duplication of a single original gene. The gene families for O. emarginata and O. semicastrata and 17 other species (Table S2) were identified with OrthoFinder 3.0.0 [35,36] by comparing their predicted protein-coding gene sequences. In this process, only the longest transcript for each gene in each species was used in the subsequent analyses unless otherwise mentioned. The orthologous groups generated by OrthoFinder were regarded as distinct gene families. After the identification of orthologous groups, 1032 single-copy orthologs were selected to generate the species trees by using STAG [37] and STRIDE [38] embedded in OrthoFinder.
Based on the inferred phylogenetic tree, MCMCTree [39] was used to obtain the dated tree, in which 13 species pairs were used as calibration points, and their estimated divergence time was derived from http://timetree.org/ (accessed on 31 March 2023) (Table S3). In the MCMCTree run, the burn-in period, the sample frequency, and the sample number were 2,000,000, 10, and 4,000,000, respectively. Using the dated tree, CAFE v5 [40] was applied to identify the gene family (i.e., the orthologous gene group) that had potentially undergone expansion or contraction. CAFE is a tool for the statistical analysis of changes in gene family size among species along a phylogenetic tree using a stochastic birth and death process. For significantly expanded and contracted gene families, their corresponding enrichment analysis according to the GO and KEGG databases was conducted by using TBtools v1.115 [41].

2.7. Gene Duplications

Whole Genome Duplications (WGDs) are characterized by large-scale genomic duplication in an organism. Ancient WGD events in O. emarginata and O. semicastrata were detected using wgd v1.1.2 [42]. Doubletrouble v0.99.1 [43] was further used to examine how many duplications were derived from WGD or other duplications, including tandem duplications (TD), proximal duplications (PD), transposed duplications (TRD), and dispersed duplications (DD) [44]. Lupinus albus was used as outgroup species in the doubletrouble analysis. For WGD, TD, and PD genes, enrichment analysis according to the GO and KEGG databases was conducted using TBtools.

3. Results and Discussion

3.1. Genome Sequencing

Sequencing yielded approximately 150.7 Gb of long-WGS reads, 145.7 of Gb short-WGS reads, 32.5 Gb transcriptome reads for O. emarginata, and 132.8 Gb of long-WGS reads, 150.7 Gb of short-WGS reads, and 36.7 Gb transcriptome reads for O. semicastrata.

3.2. Genome Assembly

The estimated genome sizes varied from 1,049,123,288 to 1,676,161,399 bp for O. emarginata and from 1,117,552,851 to 1,436,238,535 bp for O. semicastrata under different K-mer sizes (Table S4). The genome assembly based on Nonopore long reads was 1,420,917,605 bp with 90 contigs and N50 of 28,195,512 bp for O. emarginata, and 1,511,766,959 bp with 63 contigs and N50 of 48,976,089 bp for O. semicastrata (Table 1).
BUSCO assessment of the assembled O. emarginata genome produced a 97.0% completeness score for the eudicot dataset (2326 core genes), including 2075 (89.2%) complete and single-copy genes, 182 (7.8%) complete and duplicated genes, 9 (0.4%) fragmented genes, and 60 (2.6%) missing genes. Assessment of the O. semicastrata genome yielded a 98.3% completeness score, including 90.3% complete and single-copy genes, 8.0% complete and duplicated genes, 0.2% fragmented genes, and 1.5% missing genes.

3.3. Repeat Annotation

Based on the EDTA and RED results, 69.87% (992,753,897 bp) and 62.47% (887,588,204 bp), respectively, of the O. emarginata genome assembly were repetitive regions and 71.54% (1,081,509,223) and 64.11% (969,217,860 bp) of the O. semicastrata genome assembly were repetitive regions. According to EDTA, the most repetitive sequences were long terminal repeats (LTRs) in both Ormosia species. In O. emarginata, they accounted for 60.99% (866,687,265 bp) of the genome size, and Gypsy-like LTRS were the most abundant, with 497,532,853 bp (35.01%). In O. semicastrata, LTRs accounted for 60.42% (913,370,786 bp) of the genome size, and again Gypsy-like LTRs in it were the most abundant, with 417,795,386 bp (27.64%) (Table S5). By combining the EDTA and RED results, a total of 1,053,199,477 bp (74.12%) of the assembled O. emarginata genome and 1,137,510,135 bp (75.24%) of the assembled O. semicastrata genome were annotated as repetitive components.

3.4. Gene Prediction and Annotation

Gene predictions via the Funannotate pipeline yielded a total of 46,117 genes coding 48,599 proteins in the O. emarginata genome and 49,301 genes coding 52,067 proteins in the O. semicastrata genome. Functional annotation of these genes showed that 35,339 (72.71%) and 37,533 (72.09%) of the genes, respectively, were annotated to at least one database from these two species (Table S6).

3.5. Gene Families

Orthofinder identified a total of 37,260 gene families among 641,470 genes from O. emarginata, O. semicastrata, and the other species (Table S2). For O. emarginata, 88.5% (40,829/46,117) of its genes were assigned to 56.6% (21,075/37,260) of the gene families, and 970 gene families composed of 2872 genes were specific to O. emarginata (Table S7). Enrichment analysis indicated that these specific genes are mainly functionally related to serine, trehalose, and disaccharide biosynthetic/metabolic processes in the GO biological process category (Table S8) and related to aminoacyl-tRNA biosynthesis, prenyltransferases, and mismatch repair in KEGG (Table S9).
For O. semicastrata, 87.2% (42,987/49,301) of its genes were assigned to 58.0% (21,605/37,260) of the gene families, and 1063 gene families composed of 3276 genes were specific to O. semicastrata (Table S7). Enrichment analysis indicated that these specific genes in O. emarginata are mainly functionally related to vesicle targeting/localization in the GO biological process category (Table S10) and related to terpenoid backbone biosynthesis and membrane trafficking in KEGG (Table S11).
The phylogenetic tree (Figure 1) shows that O. emarginata and O. semicastrata cluster together and are sisters to L. albus. The estimated divergence time between the two species is about 10.42 (95% confidence interval [CI] 3.73511–18.5831) million years ago, and the two species diverged from L. albus about 44.46 (95% CI 35.1582–52.6539) million years ago.
For O. emarginata, there were 1565 expanded families and 1152 contracted families, of which 24 were significantly expanded and 30 were significantly contracted (p < 0.05). Based on GO enrichment analysis, the significantly expanded gene families are related to terpenoid and glutathione biosynthetic/metabolic process, the defense response, and transcription (Table S12); KEGG annotation further indicated their major functions are flavone and flavonol biosynthesis (Table S13). The significantly contracted gene families are related to proteolysis and pyruvate metabolism (Tables S14 and S15).
For O. semicastrata, there were 2011 expanded families and 778 contracted families, of which 53 were significantly expanded and 18 were significantly contracted (p < 0.05). Based on GO enrichment, the significantly expanded gene families are related to DNA integration, cell recognition, the defense response, and recognition of pollen (Table S16); KEGG annotation further indicated that their major functions are biosynthesis of various alkaloids, monoterpenoid biosynthesis, tyrosine metabolism, and fatty acid degradation (Table S17). The significantly contracted gene families are related to oxidoreductase activity and alpha-linolenic acid metabolism (Tables S18 and S19).
Specific and expanded gene enrichment analysis indicated that terpenoids play an important role in the metabolism of O. emarginata and O. semicastrata. Terpenoids represent a highly diverse class of natural products [45,46,47]. They are involved in various stages of plant growth and development, but more basically, they serve as a chemical defense in the stressful abiotic and biotic environment of plants [46,48]. Although less studied in O. emarginata and O. semicastrata, it has been reported that Ormosia species are rich in terpenoids as well as alkaloids and flavonoids [49]. We found that the genes related to the latter two components were significantly expanded in O. semicastrata and O. emarginata, respectively.
The analysis identified 283 gene families that were specific to Fabaceae. In O. emarginata and O. semicastrata, these families contained a total of 521 and 535 genes, respectively. Enrichment analyses indicated these genes are associated with the regulation of response to alcohol and lipid, zeatin biosynthesis, tryptophan metabolism, ascorbate and aldarate metabolism, porphyrin metabolism, phenylpropanoid biosynthesis, and pentose and glucuronate interconversions in two species (Tables S20–S23). In legumes, alcohol and lipid metabolism play essential roles in nodule formation and development [50,51]. Similarly, by studying 13 legume species, Garg et al. [52] found legume-specific gene families were enriched in genes involved in nodulation and nitrogen fixation, and the others included defense response, TOR signaling, flavonol biosynthesis, calcium ion homeostasis, response to symbiotic bacterium, arbuscular mycorrhizal association, and gravitropism. Our results, therefore, improve the understanding of legume species evolution.

3.6. Gene Duplications

Both O. emarginata and O. semicastrata underwent the same ancient WGD events (Figure 2), which was consistent with the WGD shared by other legume species [53,54,55]. Gene duplications using the doubletrouble program revealed 12,489 WGD-type genes, 2410 TD-type genes, 2645 PD-type genes, 35 TRD-type genes, and 16,850 DD-type genes in O. emarginata, and 13,063 WGD-type genes, 2521 TD-type genes, 3027 PD-type genes, 49 TRD-type genes, and 17,803 DD-type genes in O. semicastrata.
WGD, TD, and PD are central duplication processes related to the biotic and abiotic environmental adaptions of plant species [44]. Enrichment analysis indicated duplicated genes due to WGD in O. emarginata and O. semicastrata are mainly related to multiple aspects of development, growth, and defense—for example, glycosylphosphatidylinositol (GPI)-anchored proteins, plant hormone signal transduction, GTP-binding proteins, signal transduction, the circadian rhythm in plants, and transcription factors (Tables S24–S27). GPI-anchored proteins are important surface proteins that are anchored to the membrane or cell wall. These proteins can take part in many processes, including signaling, immune response, and cell wall development, which are essential for pathogen resistance in plants [56,57,58]. Plant hormones are messengers and signaling agents that control plant growth, development, and environmental stress responses [59]. They are classified into five major types: abscisic acid, auxins, cytokinins, ethylene, and gibberellins, while salicylic acid, jasmonates, polyamines, strigolactones, brassinosteroids, and nitric oxide (NO) are signaling molecules involved in hormonal responses. These molecules interact [60], and signal transductions among them are often carried out via GTP-binding proteins (G-proteins) [61]. Hormone signaling is also involved in many other processes in plants, such as photo-morphogenesis and carbon metabolism, which are linked to the circadian clock [62,63]. Transcription factors function as transcriptional regulation of gene expression, which is crucial to the plant’s response to various abiotic and biotic stresses [64,65]. In Astragalus sinicus, functional insight of WGD retained genes showed they were also related to plant hormone signal transduction, accompanied by plant–pathogen interaction [66]. It has been found that hormones are crucial in the process of nodulation [66]. Therefore, WGD shared by legume species could contribute to the hormonal regulation of nodulation. In addition, in Cyamopsis tetragonoloba, WGD retained genes were mainly related to the cell wall and carbohydrate/galactose/mannan/monosaccharide/metabolic process [67]. The cell wall-related genes after WGD were enriched in O. emarginata (Table S25) but not in O. semicastrata. This indicated that the duplicated gene after WGD can be lost or retained for long periods depending on the gene evolution in different species [67].
The TD-related genes in O. emarginata are mainly related to phloem development, the defense response, and various (secondary) biosynthetic/metabolic processes (e.g., alkaloids, anthocyanins, butanoate, flavonoids, glutathione, phenylalanine, terpenoids, tyrosine, and zeatin) (Tables S28 and S29). The TD-related genes in O. semicastrata are mainly related to the defense response, root development, and various (secondary) biosynthetic/metabolic processes (e.g., alkaloids, brassinosteroids, cyanoamino acid, flavonoids, glucosinolate, glutathione, histidine, linoleic acid, pentose, terpenoids, tryptophan, and zeatin) (Tables S30 and S31). When considering PD duplication, enrichment analyses revealed that these genes are mainly related to the defense response and alkaloid/flavonoid/terpenoid biosynthesis/metabolism in O. emarginata and O. semicastrata (Tables S32–S35). Alkaloids are nitrogen-containing secondary metabolites. Unlike terpenoids, which are quite common in higher plants, only a few woody trees, mainly tropical species, contain alkaloids [68,69]. Alkaloids are toxic and, therefore, mainly act as defense compounds in plants [70,71]. Flavonoids are low-molecular-weight polyphenolic secondary metabolites in plants [72,73]. They are found in flowers, leaves, and seeds and participate in a variety of biological activities in plant growth, development, and responses to biotic/abiotic stress [73,74]. Flavonoids are also essential molecules that are partly responsible for the coloration in most flowers, fruits, seeds, and vegetative tissues, thus attracting pollinators and seed-dispersing animals [72,73,74]. Therefore, future studies are needed to explore the association between flavonoids and Ormosia seed coat colors.

4. Conclusions

Legumes are important components in natural and human ecosystems. Ormosia species are valuable for their timber as well as their secondary metabolites for medicine. Their colorful seeds have been used for ornamental purposes and have a rich cultural and historical significance. However, very few Ormosia species have been studied and cultivated. Therefore, our genome assembly and analysis of the genomes of O. emarginata and O. semicastrata provide a crucial resource to understand the biology, ecology, and adaptations of Ormosia and the other legume species. In particular, the assembled genomes revealed that WGD, TD, and PD of genes play a vital role in many biological function processes in Ormosia growth, development, and environmental adaptation. This information will facilitate future genomics-assisted breeding and genetic engineering applications in Ormosia species.
The assembled genomes of two Ormosia species are still fragmented. Further high-quality genome assemblies using Hi-C and other sequencing technologies are needed to generate their chromosome-scale assemblies. Using these assemblies, comparative genome analyses including more model legumes, such as Medicago truncatula and Lotus japonicus, will be conducted. In particular, the genes related to nodulation, which is a characteristic feature of legumes, will be compared in each legume species to investigate their different nodulation mechanisms.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy13071757/s1. Table S1: Protein sequences of species used for gene prediction; Table S2: Species used for comparative genomics; Table S3: Species pairs and their estimated divergence times used for time calibration points to infer time-calibrated phylogeny of two Ormosia species; Table S4: Genome size (bp) estimation using different programs; Table S5: Repeat content of assemblies; Table S6: Summary of gene functional annotations of the Ormosia genome using different databases; Table S7: Summary of gene families; Table S8: GO enrichment results for Ormosia emarginata specific gene families; Table S9: KEGG enrichment results for Ormosia emarginata specific gene families; Table S10: GO enrichment results for Ormosia semicastrata specific gene families; Table S11: KEGG enrichment results for Ormosia semicastrata specific gene families; Table S12: GO enrichment results for Ormosia emarginata significantly expanded gene families; Table S13: KEGG enrichment results for Ormosia emarginata significantly expanded gene families; Table S14: GO enrichment results for Ormosia emarginata siginficantly contracted gene families; Table S15: KEGG enrichment results for Ormosia emarginata significantly contracted gene families; Table S16: GO enrichment results for Ormosia semicastrata significantly expanded gene families; Table S17: KEGG enrichment results for Ormosia semicastrata significantly expanded gene families; Table S18: GO enrichment results for Ormosia semicastrata siginficantly contracted gene families; Table S19: KEGG enrichment results for Ormosia semicastrata significantly contracted gene families; Table S20: GO enrichment results for Ormosia emarginata Fabaceae specific gene families; Table S21: KEGG enrichment results for Ormosia emarginata Fabaceae specific gene families; Table S22: GO enrichment results for Ormosia semicastrata Fabaceae specific gene families; Table S23: KEGG enrichment results for Ormosia semicastrata Fabaceae specific gene families; Table S24: GO enrichment results for Ormosia emarginata WGD genes; Table S25: KEGG enrichment results for Ormosia emarginata WGD genes; Table S26: GO enrichment results for Ormosia semicastrata WGD genes; Table S27: KEGG enrichment results for Ormosia semicastrata WGD genes; Table S28: GO enrichment results for Ormosia emarginata TD genes; Table S29: KEGG enrichment results for Ormosia emarginata TD genes; Table S30: GO enrichment results for Ormosia semicastrata TD genes; Table S31: KEGG enrichment results for Ormosia semicastrata TD genes; Table S32: GO enrichment results for Ormosia emarginata PD genes; Table S33: KEGG enrichment results for Ormosia emarginata PD genes; Table S34: GO enrichment results for Ormosia semicastrata PD genes; Table S35: KEGG enrichment results for Ormosia semicastrata PD genes.

Author Contributions

Conceptualization, H.-L.C. and Z.-F.W.; methodology, H.-L.C. and Z.-F.W.; validation, H.-L.C. and Z.-F.W.; formal analysis, P.-P.L., E.-P.Y., Z.-J.T., H.-M.S., W.-G.Z., Z.-F.W. and H.-L.C.; investigation, P.-P.L., E.-P.Y., Z.-J.T., H.-M.S., W.-G.Z., Z.-F.W. and H.-L.C.; resources, P.-P.L., E.-P.Y., Z.-J.T., H.-M.S., W.-G.Z., Z.-F.W. and H.-L.C.; data curation, H.-L.C. and Z.-F.W.; writing—original draft preparation, P.-P.L., E.-P.Y., Z.-J.T., H.-M.S., W.-G.Z., Z.-F.W. and H.-L.C.; writing—review and editing, P.-P.L., E.-P.Y., Z.-J.T., H.-M.S., W.-G.Z., Z.-F.W. and H.-L.C.; project administration, H.-L.C.; funding acquisition, H.-L.C. All authors have read and agreed to the published version of the manuscript.

Funding

The study is supported by the Project from Financial Funds of Zhongshan City—Preliminary study on conservation ecology of Ormosia species in Wuguishan, “Conservation of endemic Ormosia species of Guangdong Province and Ormosia species center creation” from Forest Bureau of Guangdong Province—Plan on provincial plant ex-situ conservation system, propagation and expansion of national key protected plant in ex-situ conservation areas, and the “One Center and Three Bases” Project for Flora and Fauna Conservation of Guangdong Province.

Data Availability Statement

We deposited the sequenced reads to NCBI Sequence Read Archive under the accession number SRR22805615 for the Nanopore reads, SRR21047276 for the BGISEQ reads, and SRR21705960 for the RNA-seq reads in Ormosia emarginata; SRR22805496 for the Nanopore reads, SRR21047305 for the BGISEQ reads, and SRR21705959 for the RNA-seq reads in Ormosia semicastrata. The assembled O. emarginata and O. semicastrata genome assemblies were submitted to GenBank under the accession number JAQQTP000000000 and JAQQTO000000000. Genome assembly and gene annotation data are available at https://doi.org/10.6084/m9.figshare.21225467.v3 (accessed on 3 April 2023).

Conflicts of Interest

The authors declare no conflict of interest.

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Agronomy 13 01757 g001 550
Figure 1. A phylogenetic tree and contracted (−) and expanded (+) gene family of two Ormosia species with the other Fabaceae species and outgroup.
Figure 1. A phylogenetic tree and contracted (−) and expanded (+) gene family of two Ormosia species with the other Fabaceae species and outgroup.
Agronomy 13 01757 g001
Agronomy 13 01757 g002 550
Figure 2. Whole genome duplication analysis comparing the synonymous substitutions per synonymous site (Ks) value distribution for two Ormosia species.
Figure 2. Whole genome duplication analysis comparing the synonymous substitutions per synonymous site (Ks) value distribution for two Ormosia species.
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Table
Table 1. Statistics of genome assembly.
Table 1. Statistics of genome assembly.
Ormosia emarginataOrmosia semicastrata
The Length of Sequence (bp)The Order of Sequence LengthThe Length of Sequence (bp)The Order of Sequence Length
N10 = 81,285,628L10 = 2N10 = 89,031,100L10 = 2
N20 = 63,464,384L20 = 4N20 = 79,796,434L20 = 3
N30 = 43,593,171L30 = 7N30 = 73,253,298L30 = 5
N40 = 37,463,220L40 = 10N40 = 56,807,054L40 = 8
N50 = 28,195,512L50 = 15N50 = 48,976,089L50 = 11
N60 = 25,800,464L60 = 20N60 = 45,239,136L60 = 14
N70 = 20,527,781L70 = 26N70 = 31,722,207L70 = 18
N80 = 13,438,452L80 = 35N80 = 22,051,163L80 = 23
N90 = 7,895,810L90 = 49N90 = 12,933,450L90 = 31
N100 = 173,104L100 = 90N100 = 128,272L100 = 63
Total length1,420,917,605 bp1,511,766,959 bp
Average length15,787,973.39 bp23,996,300.94 bp
Largest length84,853,091 bp144,833,628 bp
Minimum length173,104 bp128,272 bp
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Liu, P.-P.; Yu, E.-P.; Tan, Z.-J.; Sun, H.-M.; Zhu, W.-G.; Wang, Z.-F.; Cao, H.-L. Genome Assemblies of Two Ormosia Species: Gene Duplication Related to Their Evolutionary Adaptation. Agronomy 2023, 13, 1757. https://doi.org/10.3390/agronomy13071757

AMA Style

Liu P-P, Yu E-P, Tan Z-J, Sun H-M, Zhu W-G, Wang Z-F, Cao H-L. Genome Assemblies of Two Ormosia Species: Gene Duplication Related to Their Evolutionary Adaptation. Agronomy. 2023; 13(7):1757. https://doi.org/10.3390/agronomy13071757

Chicago/Turabian Style

Liu, Pan-Pan, En-Ping Yu, Zong-Jian Tan, Hong-Mei Sun, Wei-Guang Zhu, Zheng-Feng Wang, and Hong-Lin Cao. 2023. "Genome Assemblies of Two Ormosia Species: Gene Duplication Related to Their Evolutionary Adaptation" Agronomy 13, no. 7: 1757. https://doi.org/10.3390/agronomy13071757

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