Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species.

Zhiqiang Wu,Cuihua Gu,Dong Zhang,Song Ge,Luke R Tembrock,Zhong-Jian Liu

doi:10.1371/journal.pone.0177553

Abstract

Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B). A total of 110 unique genes are annotated, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. The genome structure, gene order, GC content, and other features are similar to those of other angiosperm cp genomes. When comparing the cp genomes between Oryzinae and Zizaniinae subtribes, the main differences were found between the junction regions and distribution of simple sequence repeats (SSRs). In comparing the two Chikusichloa species, the genomes were only 40 bp different in length and 108 polymorphic sites, including 83 single nucleotide substitutions (SNPs) and 25 insertion-deletions (Indels), were found between the whole cp genomes. The complete cp genome of C. mutica will be an important genetic tool for future breeding programs and understanding the evolution of wild rice relatives.

Highlights

The grass family (Poaceae) is one of the most diverse angiosperm families and contains numerous economically important crop species [1]Grass Phylogeny Work
The chloroplast genome of C. mutica is a typical quadripartite structure consisting of a pair of inverted repeats (IRs) with a length of 20,839 bp separated by a small single-copy region (SSC) of 12,598 bp and a large single-copy region (LSC) of 82,327 bp, respectively
Using traditional high-quality Sanger sequencing technology, we presented the complete chloroplast genome of Chikusichloa mutica, performed comparative analyses in related species of the rice tribe, and deposited the genome into GenBank with accession number KU696970

Summary

Methods

Complete chloroplast genome of Chikusichloa mutica Fresh leaves of the Chikusichloa mutica were collected from a plant Amplification and Sanger sequencing methods were employed to complete the whole chloroplast genome of C. mutica. Conditions for PCR amplification were 4 min of initial denaturation at 94 ̊C, 35 cycles of 45 s at 94 ̊C, 45 s annealing at 52 ̊C, and 90 s extension at 72 ̊C, followed by a final 10-min incubation at 72 ̊C. The PCR products were purified as described in Tang et al [34] and directly sequenced on an ABI 3730 (Applied Biosystems, Foster City, CA, USA). The final Sanger sequences were trimmed and assembled with the ContigExpress program from the Vector NTI Suite 6.0 (Informax Inc., North Bethesda, MD)

Results

Discussion

Conclusion