De novo assembly and characterization of leaf transcriptome for the development of EST-SSR markers of the non-model species Indigofera szechuensis

De Novo Transcriptome Assembly of Anoectochilus roxburghii for Morphological Diversity Assessment and Potential Marker Development

Anoectochilus roxburghii is a rare and precious medicinal and ornamental plant of Orchidaceae. Abundant morphological characteristics have been observed among cultivated accessions. Our understanding of the genetic basis of morphological diversity is limited due to a lack of sequence data and candidate genes. In this study, a high-quality de novo transcriptome assembly of A.roxburghii was generated. A total of 138,385 unigenes were obtained, and a BUSCO (Benchmarking Universal Single-Copy Orthologs) analysis showed an assembly completeness of 98.8%. Multiple databases were used to obtain a comprehensive annotation, and the unigenes were functionally categorized using the GO (Gene Ontology), KOG (Eukaryotic Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes), and Nr databases. After comparing the phenotypic characteristics of five representative cultivars, a set of cultivar-specific, highly expressed unigenes was identified based on a comparative transcriptome analysis. Then, a WGCNA (Weighted Gene Co-expression Network Analysis) was performed to generate gene regulatory modules related to chlorophyll content (red) and sucrose synthase activity (black). In addition, the expression of six and four GO enrichment genes in the red and black modules, respectively, was analyzed using qRT-PCR to determine their putative functional roles in the leaves of the five cultivars. Finally, in silico SSR (Simple Sequence Repeat) mining of the assembled transcriptome identified 44,045 SSRs. Mononucleotide was the most dominant class of SSRs, followed by complex SSRs. In summary, this study reports on the phenomic and genomic resources of A. roxburghii, combining SSR marker development and validation. This report aids in morphological diversity assessments of Anoectochilus roxburghii.

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

Introduction

Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera.

Methods

Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.

Results and discussion

The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection

Hemerocallis spp. commonly known as daylilies and night lilies, are among the most popular ornamental crops worldwide. In Eastern Asia, H. citrina is also widely cultivated as both a vegetable crop and for medicinal use. However, limited genetic and genomic resources are available in Hemerocallis. Knowledge on the genetic diversity and population structure of this species-rich genus is very limited. In this study, we reported transcriptome sequencing of H. citrina cv. 'Datonghuanghua' which is a popular, high-yielding variety in China. We mined the transcriptome data, identified and characterized the microsatellite or simple sequence repeat (SSR) sequences in the expressed genome. From ∼14.15 Gbp clean reads, we assembled 92,107 unigenes, of which 41,796 were annotated for possible functions. From 41,796 unigenes, we identified and characterized 3,430 SSRs with varying motifs. Forty-three SSRs were used to fingerprint 155 Hemerocallis accessions. Clustering and population structure analyses with the genotypic data among the 155 accessions reveal broader genetic variation of daylilies than the night lily accessions which form a subgroup in the phylogenetic tree. The night lily group included accessions from H. citrina, H. lilioasphodelus, and H. minor, the majority of which bloom in the evening/night, whereas the ∼100 daylily accessions bloomed in the early morning suggesting flowering time may be a major force in the selection of night lily. The utility of these SSRs was further exemplified in association analysis of blooming time among these accessions. Twelve SSRs were found to have significant associations with this horticulturally important trait.

SSR marker development in Clerodendrum trichotomum using transcriptome sequencing

Clerodendrum trichotomum, a member of the Lamiaceae (Verbenaceae) family, is an ornamental plant widely distributed in South Asia. Previous studies have focused primarily on its growth characteristics, stress resistance, and pharmacological applications; however, molecular investigations remain limited. Considering germplasm conservation and the extensive applications of this plant, it is necessary to explore transcriptome resources and SSR makers for C. trichotomum. In the present study, RNA sequencing was used to determine the transcriptome of C. trichotomum. Subsequently, unigene annotations and classifications were obtained, and SSRs were mined with MIcroSAtellite. Finally, primer pairs designed with Oligo 6.0 were selected for polymorphism validation. In total, 127,325,666 high-quality reads were obtained, and 58,345 non-redundant unigenes were generated, of which 36,900 (63.24%) were annotated. Among the annotated unigenes, 35,980 (97.51%) had significant similarity to 607 species in Nr databases. In addition, a total of 6,444 SSRs were identified in 5,530 unigenes, and 200 random primer pairs were designed for polymorphism validation. Furthermore, after primary polymorphism identification, 30 polymorphic primer pairs were selected for the further polymorphism screening, and 200 alleles were identified, 197 of which showed polymorphism. In this work, a large number of unigenes were generated, and numerous SSRs were detected. These findings should be beneficial for further investigations into germplasm conservation and various applications of C. trichotomum. These results should also provide a solid foundation for future molecular biology studies in C. trichotomum.

De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing

Rhododendron molle G. Don occupies an important phylogenetic node in the genus rhododendron with unique yellow flower and medicinal functions. However, only limited genetic resources and their genome information are available for the generation of rhododendron flowers. The next generation sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provide a turning point for rhododendron research. Our goal is to use the genetic information to facilitate the relevant research on flowering and flower color formation in R. molle. In total, 66,026 unigenes were identified, among which 31,298 were annotated in the NCBI non-redundant protein database and 22,410 were annotated in the Swiss-Prot database. Of these annotated unigenes, 9490 and 18,680 unigenes were assigned to clusters of orthologous groups and gene ontology categories, respectively. A total of 7177 genes were mapped to 118 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. In addition, 8266 simple sequence repeats (SSRs) were detected, and these SSRs will undoubtedly benefit rhododendron breeding work. Metabolic pathway analysis revealed that 32 unigenes were predicted to be involved in carotenoid biosynthesis. Our transcriptome revealed 32 engines that encode key enzymes in the carotenoid biosynthesis pathway, including PSY, PDS, LCYB, LCYE, etc. The content of β-carotene was much higher than the other carotenoids throughout the flower development. It was consistent with the key genes expression level in the carotenoid biosynthesis pathway by the Illumina expression profile analysis and the qRT-PCR analysis. Our study identified genes associated with carotenoid biosynthesis in R. molle and provides a valuable resource for understanding the flowering and flower color formation mechanisms in R. molle.