Limited Polymorphisms between Two Whole Plastid Genomes in the Genus Zizania (Zizaniinae)

Abstract

Plastids, originated from cyanobacteria through endosymbiosis, contain their own DNA genome (plastome), and are uniparentally inherited in most of plant species. In this study, we reported the complete plastome sequence of Manchurian wild rice (Zizania latifolia) obtained by traditional Sanger sequencing and compared it with the previously published plastome of North America wild rice (Z. aquatica) from the same genus. The plastome of Z. latifolia has a total sequence length of 136,461 bp exhibiting a typical circular structure including a pair of 20,878 bp inverted repeats (IRa, b) separated by a large single-copy region (LSC) of 82,115 bp and a small single-copy region (SSC) of 12,590 bp, and it is only 97 bp longer than North America wild rice. The gene content, order, and orientation are similar to all other grass species. Four junctions in two plastome structures are exactly the same between the Zizania species. From complete genome comparisons, 744 (568, 46 and 130 for LSC, IR and SSC) substitutions are found between the two Zizania plastomes including 267 from coding regions and 477 from non-coding regions. Insertions/deletions (Indels) are mainly found in non-coding regions (136) except the only one repeat indel from coding regions in rpoC2 gene. The most informative biomarkers (rps16-trnQ, ndhF and matK) are also the most divergent between the two Zizania species. The completed plastome and comparative analyses from these two Zizania species would be as important resource for further systematic or population genetic studies in the Zizaniinae subtribe, marker assisted breeding, and plastomic transformation.

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

“…The chloroplast genome of C . mutica is extremely conserved in structure compared with other published grass chloroplasts, with the gene content and number the same as other published chloroplast genomes [14, 15, 16, 51]. In comparison with the other species in Chikusichloa , C .…”

“…The dynamic variation in IR regions can cause the size changes of chloroplast genome. For example, previous studies have shown that the variation of the junctions in Oryza exceeds the junction variability in Zizania [ 15 ]. Between C .…”

“…latifolia and Z . aquatica [ 15 ]. Several reasons might explain the differences found between the two genera.…”

“…mutica . Based on the conserved features of chloroplast genome in land plants [ 21 , 24 ] and our previous result [ 14 , 15 ], by using the chloroplast primers from Wu et al [ 35 ], we successfully amplified the entire chloroplast in overlapping fragments. 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.…”

“…In addition to these species, many wild relatives in the Oryzeae tribe possess enormously useful genetic resources for improving rice breeding through increasing yields [ 9 ] and providing tolerance from environmental stress [ 10 ]. While the species in the Oryzinae tribe have been studied in depth with regard to their genetic importance [ 2 , 11 , 12 , 13 ], the species in Zizaniinae have not been as thoroughly examined, except for the organelle genomes [ 14 , 15 , 16 ]. Chikusichloa is one such example of a genus from Zizaniinae for which we have only limited knowledge regarding the chloroplast genome.…”