Development of Chloroplast Genomic Resources for Oryza Species Discrimination

Abstract

Rice is the most important crop in the world as the staple food for over half of the population. The wild species of Oryza represent an enormous gene pool for genetic improvement of rice cultivars. Accurate and rapid identification of these species is critical for effective utilization of the wild rice germplasm. In this study, we developed valuable chloroplast molecular markers by comparing the chloroplast genomes for species identification. Four chloroplast genomes of Oryza were newly sequenced on the Illumina HiSeq platform and other 14 Oryza species chloroplast genomes from Genbank were simultaneously taken into consideration for comparative analyses. Among 18 Oryza chloroplast genomes, five variable regions (rps16-trnQ, trnTEYD, psbE-petL, rpoC2 and rbcL-accD) were detected for DNA barcodes, in addition to differences in simple sequence repeats (SSR) and repeat sequences. The highest species resolution (72.22%) was provided by rpoC2 and rbcL-accD with distance-based methods. Three-marker combinations (rps16-trnQ + trnTEYD + rbcL-accD, rps16-trnQ + trnTEYD + rpoC2 and rpoC2 + trnTEYD + psbE-petL) showed the best species resolution (100%). Phylogenetic analysis based on the chloroplast genome provided the best resolution of Oryza. In the comparison of chloroplast genomes in this study, identification of the most variable regions and assessment of the focal regions of divergence were efficient in developing species-specific DNA barcodes. Based on evaluation of the chloroplast genomic resources, we conclude that chloroplast genome sequences are a reliable and valuable molecular marker for exploring the wild rice genetic resource in rice improvement.

Development of high‐resolution DNA barcodes for Dioscorea species discrimination and phylogenetic analysis

“…DNA barcodes show a relatively variable species discrimination efficiency in different plants (Gogoi & Bhau, 2018;Hollingsworth et al, 2011;Liu et al, 2017;Sun et al, 2015Sun et al, , 2012, and more DNA barcodes for specieslevel resolution have been developed and tested (Dong et al, 2015;Song et al, 2017). At present, the devel opment of universal primers for highly variable regions relies on the availability of sequences for different species.…”

“…Plastid markers, such as rbcL, matK, and trnHpsbA, have been widely used with high amplification success in these regions (Hollingsworth et al, 2011). The internal transcribed spacers from nuclear ribosomal DNA, complete plastid genomes, and single copy nuclear genes have also been used in species discrimination (Cheng et al, 2016;Duarte et al, 2010;Song et al, 2017). In this study, we selected primers covering highly variable regions in the Dioscorea chloroplast genome.…”

“…Dong et al () were analyzed available plastid genomes and designed suitable primers for the most variable regions, and finally found that ycf1 b generally performed better than any of the mat K, rbc L, and trn H‐ psb A barcodes. Among 18 Oryza chloroplast genomes, five variable regions ( rps16 ‐ trnQ , trnTEYD , psbE ‐ petL , rpoC2 , and rbcL ‐ accD ) were analyzed for species discrimination (Song et al, ). However, systematic comparisons for plastid genome sequences have not been conducted between Dioscorea species and would provide useful information for identifying better‐performing DNA barcodes for Dioscorea species.…”

Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

“…The chloroplast genome is conserved similar to the majority of plants; no rearrangement events were detected in all species. The mVISTA results and nucleotide diversity tests indicate high similarities between the chloroplast genomes implying that the divergence of the Atractylodes chloroplast genome is lower than that of other species [6,37,38].…”

Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis

“…Chloroplast genome encodes many key proteins that are involved in photosynthesis and other important metabolic processes for plant interactions with their environment, such as drought, salt and light [ 1 , 2 , 3 , 4 ]. The availability of over 2400 sequenced chloroplast genomes ( ) gave us insights to understand the plant biology diversity, evolution, climatic adaptation, DNA barcoding and expression high-value agricultural or biomedical products by genetic engineering [ 1 , 2 , 5 , 6 , 7 , 8 , 9 ].…”