Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR

OrangeExpDB: an integrative gene expression database for Citrus spp

BACKGROUND

Citrus is a major fruit crop, and RNA-sequencing (RNA-seq) data can be utilized to investigate its gene functions, heredity, evolution, development, and the detection of genes linked to essential traits or resistance to pathogens. However, it is challenging to use the public RNA-seq datasets for researchers without bioinformatics training, and expertise.

RESULTS

OrangeExpDB is a web-based database that integrates transcriptome data of various Citrus spp., including C. limon (L.) Burm., C. maxima (Burm.) Merr., C. reticulata Blanco, C. sinensis (L.) Osbeck, and Poncirus trifoliata (L.) Raf., downloaded from the NCBI SRA database. It features a blast tool for browsing and searching, enabling quick download of expression matrices for different transcriptome samples. Expression of genes of interest can be easily generated by searching gene IDs or sequence similarity. Expression data in text format can be downloaded and presented as a heatmap, with additional sample information provided at the bottom of the webpage.

CONCLUSIONS

Researchers can utilize OrangeExpDB to facilitate functional genomic analysis and identify key candidate genes, leveraging publicly available citrus RNA-seq datasets. OrangeExpDB can be accessed at http://www.orangeexpdb.com/ .

High-Throughput Genotyping Technologies in Plant Taxonomy

Molecular markers provide researchers with a powerful tool for variation analysis between plant genomes. They are heritable and widely distributed across the genome and for this reason have many applications in plant taxonomy and genotyping. Over the last decade, molecular marker technology has developed rapidly and is now a crucial component for genetic linkage analysis, trait mapping, diversity analysis, and association studies. This chapter focuses on molecular marker discovery, its application, and future perspectives for plant genotyping through pangenome assemblies. Included are descriptions of automated methods for genome and sequence distance estimation, genome contaminant analysis in sequence reads, genome structural variation, and SNP discovery methods.

Phylogenetic relationship of Paramignya trimera and its relatives: an evidence for the wide sexual compatibility

The genus Paramignya (Rutaceae) comprises about 30 species typically distributing in tropical Asia. Like other genera of the family Rutaceae, the significant variation in the morphology of Paramignya species makes the taxonomic study and accurate identification become difficult. In Vietnam, Paramignya species have been mostly found in Khanh Hoa and Lam Dong provinces and used as traditional medicines. Recently, Paramignya trimera, a species of the genus Paramignya with local name “Xao tam phan” has been drawn attention and intensively exploited to treat liver diseases and cancers. However, the significant variations in the morphology and different local names of P. trimera have caused confusion and difficulty in the accurate identification and application of this plant for medicine. In this study, the combination of both morphological and DNA sequence data has effectively supported the taxonomic identification of P. trimera and some relatives collected in Khanh Hoa and Lam Dong provinces. The comparison of the morphology and analysis of the phylogenetic trees suggested that there was a significant variation of P. trimera. In addition, some accessions of P. trimera with morphological characteristics similar and Atalantia buxifolia were likely the intergeneric hybrids between the two species. Analysis of genetic variation, interspecific and intraspecific distances using ITS, matK and rbcL sequences shown that P. trimera was closely related to A. buxifolia, Severinia monophylla and Luvunga scandens. In addition, matK sequences represented as the effective candidate DNA barcode to identify and distinguish Paramignya species from others of the family Rutaceae.

Citrus species and hybrids depicted by near- and mid-infrared spectroscopy

BACKGROUND

Citrus trees are among the most cultivated plants in the world, with a high economic impact. The wide sexual compatibility among relatives gave rise to a large number of hybrids that are difficult to discriminate. This work sought to explore the ability of infrared spectroscopy to discriminate among Citrus species and/or hybrids and to contribute to the elucidation of its relatedness.

RESULTS

Adult leaves of 18 distinct Citrus plants were included in this work. Near- and mid-infrared (NIR and FTIR) spectra were acquired from leaves after harvesting and a drying period of 1 month. Spectra were modelled by principal component analysis and partial least squares discriminant analysis. Both techniques revealed a high discrimination potential (78.5-95.9%), being the best results achieved with NIR spectroscopy and air-dried leaves (95.9%).

CONCLUSION

Infrared spectroscopy was able to successfully discriminate several Citrus species and/or hybrids. Our results contributed also to enhance insights regarding the studied Citrus species and/or hybrids. Despite the benefit of including additional samples, the results herein obtained clearly pointed infrared spectroscopy as a reliable technique for Citrus species and/or hybrid discrimination. © 2018 Society of Chemical Industry.