Population Genetics of the Endangered and Wild Edible Plant Ottelia acuminata in Southwestern China Using Novel SSR Markers

De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease

Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.

Mapping the habitat suitability of Ottelia species in Africa

Understanding the influence of environmental covariates on plant distribution is critical, especially for aquatic plant species. Climate change is likely to alter the distribution of aquatic species. However, knowledge of this change on the burden of aquatic macroorganisms is often fraught with difficulty. Ottelia, a model genus for studying the evolution of the aquatic family Hydrocharitaceae, is mainly distributed in slow-flowing creeks, rivers, or lakes throughout pantropical regions in the world. Due to recent rapid climate changes, natural Ottelia populations have declined significantly. By modeling the effects of climate change on the distribution of Ottelia species and assessing the degree of niche similarity, we sought to identify high suitability regions and help formulate conservation strategies. The models use known background points to determine how environmental covariates vary spatially and produce continental maps of the distribution of the Ottelia species in Africa. Additionally, we estimated the possible influences of the optimistic and extreme pessimistic representative concentration pathways scenarios RCP 4.5 and RCP 8.5 for the 2050s. Our results show that the distinct distribution patterns of studied Ottelia species were influenced by topography (elevation) and climate (e.g., mean temperature of driest quarter, annual precipitation, and precipitation of the driest month). While there is a lack of accord in defining the limiting factors for the distribution of Ottelia species, it is clear that water-temperature conditions have promising effects when kept within optimal ranges. We also note that climate change will impact Ottelia by accelerating fragmentation and habitat loss. The assessment of niche overlap revealed that Ottelia cylindrica and O . verdickii had slightly more similar niches than the other Ottelia species. The present findings identify the need to enhance conservation efforts to safeguard natural Ottelia populations and provide a theoretical basis for the distribution of various Ottelia species in Africa.

Deciphering the Taxonomic Delimitation of Ottelia acuminata (Hydrocharitaceae) Using Complete Plastomes as Super-Barcodes

Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved, impeding effective conservation and management practices. Here, we aim to address the long-standing issues concerning species boundary and intraspecific subdivision of O. acuminata using complete plastome sequences as super-barcodes. The taxonomic delimitation of O. acuminata was explored using phylogenetic inference and two independent sequence-based species delimitation schemes: automatic barcode gap discovery (ABGD) and multi-rate Poisson tree processes (mPTP). The reciprocally reinforcing results support the reduction of the closely related congeneric species, O. balansae and O. guanyangensis, as two conspecific varieties of O. acuminata. Within the newly defined O. acuminata, accurate varietal identification can be achieved using plastome super-barcodes. These findings will help inform future decisions regarding conservation, management and restoration of O. acuminata. This case study suggests that the use of plastome super-barcodes can provide a solution for species delimitation and identification in taxonomically difficult plant taxa, thus providing great potential to lessen the challenges of inventorying biodiversity, as well as biologically monitoring and assessing threatened species.

Genetic diversity and population structure of the endangered orchid Pelatantheria scolopendrifolia (Orchidaceae) in Korea

Due to substantial population decline, the Korean orchid P. scolopendrifolia is considered endangered and highly threatened. Like many endangered species, it is vulnerable to biological and anthropogenic threats that can lead to the loss of genetic diversity and, ultimately, extinction. Therefore, the assessment of genetic diversity and population genetic structure is imperative for conservation. In this study, we newly developed 15 polymorphic microsatellite markers. Analyses of genetic diversity and population genetic structure that included 182 samples from 11 populations were conducted using microsatellite markers and four noncoding regions of chloroplast DNA. Our study revealed a relatively low level of genetic diversity (Ho = 0.529, He = 0.356), albeit harboring with private alleles based on microsatellite genotyping data, and high haplotype diversities based on chloroplast DNA sequences data. The results of STRUCTURE and PCoA based on microsatellite genotyping data showed population differentiations. An AMOVA based on chloroplast DNA sequence data further corroborated these conclusions, indicating about 70% of variations found among populations. Low genetic diversity and divergence among the population might have been caused by factors, such as asexual reproduction, demographic events (bottleneck and population expansion), geographic isolation, and low gene flow. The development and implication of conservation strategies and management of P. scolopendrifolia are proposed based on these results.

Phylogenomics of the aquatic plant genus Ottelia (Hydrocharitaceae): Implications for historical biogeography

Ottelia Pers. is the second largest genus of the family Hydrocharitaceae, including approximately 23 extant species. The genus exhibits a diversity of both bisexual and unisexual flowers, and complex reproductive system comprising cross-pollinated to cleistogamous flowers. Ottelia has been regarded as a pivotal group to study the evolution of Hydrocharitaceae, but the phylogenic relationships and evolutionary history of the genus remain unresolved. Here, we reconstructed a robust phylogenetic framework for Ottelia using 40 newly assembled complete plastomes. Our results resolved Ottelia as a monophyletic genus consisting of two major clades, which correspond to the main two centers of diversity in Asia and Africa. According to the divergence time estimation analysis, the crown group Ottelia began to diversify around 13.09 Ma during the middle Miocene. The biogeographical analysis indicated the existence of the most recent common ancestor somewhere in Africa/Australasia/Asia. Basing on further insights from the morphological evolution of Ottelia, we hypothesized that the ancestral center of origin was in Africa, from where the range expanded by transoceanic dispersal to South America and Australasia, and further from Australasia to Asia. We suggested that the climatic change and global cooling since the mid-Miocene, such as the development of East Asian monsoon climate and tectonic movement of the Yunnan-Guizhou Plateau (YGP), might have played a crucial role in the evolution of Ottelia in China.

The level of genetic diversity and differentiation of tropical lotus, Nelumbo nucifera Gaertn. (Nelumbonaceae) from Australia, India, and Thailand

BACKGROUND

Nelumbo nucifera Gaertn., a perennial aquatic macrophyte species, has been cultivated in several Asian countries for its economic importance, and medicinal uses. Two distinct ecotypes of the species are recognized based on the geographical location where the genotypes are adapted, i.e., tropical lotus and temperate lotus. The genetic diversity levels and differentiation of the tropical lotus from poorly studied geographic regions still remain unclear. Here, the population genetic diversity and structure of 15 tropical lotus populations sampled from the previous understudied natural distribution ranges, including India, Thailand, and Australia, were assessed using nine polymorphic SSR markers.

RESULTS

The SSR markers used to genotype the 216 individuals yielded 65 alleles. The highest and lowest genetic diversity estimates were found in Thailand and Indian populations, respectively. STRUCTURE analysis revealed three distinct genetic clusters, with relatively low admixtures, supported by PCoA cluster analysis. Low levels of gene flow (mean N⁠m = 0.346) among the three genetic clusters signified the Mantel test for isolation by distance, revealing the existence of a positive correlation between the genetic and geographic distances (r = 0.448, P = 0.004). Besides, AMOVA analysis revealed a higher variation among populations (59.98%) of the three groups. Overall, the populations used in this study exposed a high level of genetic differentiation (FST = 0.596).

CONCLUSIONS

The nine polymorphic microsatellite markers used in our study sufficiently differentiated the fifteen tropical N. nucifera populations based on geography. These populations presented different genetic variability, thereby confirming that populations found in each country are unique. The low genetic diversity (HE = 0.245) could be explained by limited gene flow and clonal propagation. Conserving the available diversity using various conservation approaches is essential to enable the continued utilization of this economically important crop species. We, therefore, propose that complementary conservation approaches ought to be introduced to conserve tropical lotus, depending on the genetic variations and threat levels in populations.

Cryptic diversity within the African aquatic plant Ottelia ulvifolia (Hydrocharitaceae) revealed by population genetic and phylogenetic analyses

Revealing cryptic diversity is of great importance for effective conservation and understanding macroevolution and ecology of plants. Ottelia, a typical example of aquatic plants, possesses extremely variable morphology and the presence of cryptic diversity makes its classification problematic. Previous studies have revealed cryptic Ottelia species in Asia, but very little is known about the molecular systematics of this genus in Africa, a center of species diversity of Ottelia. In this study, we sampled Ottelia ulvifolia, an endemic species of tropical Africa, from Zambia and Cameroon. We used six chloroplast DNA regions, nrITS and six polymorphic microsatellite markers to estimate the molecular diversity and population genetic structure in O. ulvifolia. The phylogenetic inference, STACEY and STRUCTURE analyses supported at least three clusters within O. ulvifolia, each representing unique flower types (i.e., bisexual yellow flower, unisexual yellow flower and bisexual white flower types). Although abundant genetic variation (> 50%) was observed within the populations, excessive anthropogenic activities may result in genetic drift and bottlenecks. Here, three cryptic species of O. ulvifolia complex are defined, and insights are provided into the taxonomy of Ottelia using the phylogenetic species concept.

Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.

Ottelia fengshanensis, a new bisexual species of Ottelia (Hydrocharitaceae) from southwestern China

Ottelia fengshanensis, a new species (Hydrocharitaceae) from southwest China is here described and illustrated. Comparing its morphological features to putative close relatives O. guanyangensis, it has 3-4 flowers (vs. 2-5) each spathe, hexagonal-cylindric fruit, white styles (vs. yellow), green leaves (vs. dark green) and fruit tiny winged (vs. winged obviously). Molecular phylogenetic investigation of four DNA sequences (ITS, rbcL, trnK5' intron and trnS-trnG) and the Poisson Tree Processes model for species delimitation (PTP) analysis, further resolves O. fengshanensis as a new species that is close to O. guanyangensis with distinct support.

Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

Dalbergia odorifera T. Chen (Fabaceae) is a semi-deciduous tree species indigenous to Hainan Island in China. Due to its precious heartwood “Hualimu (Chinese)” and Chinese medicinal components “Jiangxiang”, D. odorifera is seriously threatened of long-term overexploitation and has been listed on the IUCN (International Union for Conservation of Nature’s) red list since 1998. Therefore, the elucidation of its genetic diversity is imperative for conservation and breeding purposes. In this study, we evaluated the genetic diversity of 42 wild D. odorifera trees from seven populations covering its whole native distribution. In total, 19 SSR (simple sequence repeat) markers harbored 54 alleles across the 42 samples, and the medium genetic diversity level was inferred by Nei’s gene diversity (0.36), observed (0.28) and expected heterozygosity (0.37). Among the seven wild populations, the expected heterozygosity (He) varied from 0.31 (HNQS) to 0.40 (HNCJ). The analysis of molecular variance (AMOVA) showed that only 3% genetic variation existed among populations. Moderate population differentiations among the investigated populations were indicated by pairwise Fst (0.042–0.115). Structure analysis suggested two clusters for the 42 samples. Moreover, the seven populations were clearly distinguished into two clusters from both the principal coordinate analysis (PCoA) and neighbor-joining (NJ) analysis. Populations from Haikou city (HNHK), Baisha autonomous county (HNBS), Ledong autonomous county (HNLD), and Dongfang city (HNDF) comprised cluster I, while cluster II comprised the populations from Wenchang city and Sansha city (HNQS), Changjiang autonomous county (HNCJ), and Wuzhisan city (HNWZS). The findings of this study provide a preliminary genetic basis for the conservation, management, and restoration of this endemic species.

De Novo Transcriptome Analysis of Dalbergia odorifera and Transferability of SSR Markers Developed from the Transcriptome

Dalbergia odorifera T. Chen (Fabaceae), indigenous to Hainan Island, is a precious rosewood (Hainan hualimu) in China. However, only limited genomic information is available which has resulted in a lack of molecular markers, limiting the development and utilization of the germplasm resources. In this study, we aim to enrich genomic information of D. odorifera, and develop a series of transferable simple sequence repeat (SSR) markers for Dalbergia species. Therefore, we performed transcriptome sequencing for D. odorifera by pooling leaf tissues from three trees. A dataset of 138,516,418 reads was identified and assembled into 115,292 unigenes. Moreover, 35,774 simple sequence repeats (SSRs) were identified as potential SSR markers. A set of 19 SSR markers was successfully transferred across species of Dalbergia odorifera T. Chen, Dalbergia tonkinensis Prain, and Dalbergia cochinchinensis Pierre ex Laness. In total, 112 alleles (3–13 alleles/locus) were presented among 60 Dalbergia trees, and polymorphic information content ranged from 0.38 to 0.75. The mean observed and mean expected heterozygosity was 0.34 and 0.40 in D. odorifera, 0.27 and 0.32 in D. tonkinensis, and 0.29 and 0.33 in D. cochinchinensis, respectively. The cluster analysis classified these 60 trees into three major groups according to the three Dalbergia species based on the genetic similarity coefficients, indicating these newly developed transferable markers can be used to explore the relationships among Dalbergia species and assist genetic research. All these unigenes and SSR markers will be useful for breeding programs in the future.

Genetic diversity and population structure of the endangered basal angiosperm Brasenia schreberi (Cabombaceae) in China

Brasenia schreberi J.F. Gmelin (Cabombaceae), an aquatic herb that occurs in fragmented locations in China, is rare and endangered. Understanding its genetic diversity and structure is crucial for its conservation and management. In this study, 12 microsatellite markers were used to estimate the genetic diversity and variation in 21 populations of B. schreberi in China. A total of 61 alleles were found; assessment of allelic richness (Ar = 1.92) and observed and expected heterozygosity (HO = 0.200, HE = 0.256) suggest lower genetic diversity compared to some endangered species, and higher variation was observed within populations (58.68%) rather than among populations (41.32%). No significant correlation between geographical and genetic distance among populations was detected (Mantel test, r = 0.0694; P = 0.7985), which may have likely resulted from barriers to gene flow (Nm = 0.361) that were produced by habitat fragmentation. However, Bayesian and neighbor-joining cluster analyses suggest a population genetic structure consisting of two clusters (I and II) or four subclusters (I-1, 2 and II-1, 2). The genetic structure and distribution of B. schreberi in China may have involved glacial refugia that underwent range expansions, introgression, and habitat fragmentation. The findings of the present study emphasize the importance for both in situ and ex situ conservation efforts.