Affiliation:
1. College of Agriculture, South China Agricultural University, Guangzhou 510642, China
2. Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China
Abstract
Wild upland rice species, including Oryza granulata, possess unique characteristics that distinguish them from other Oryza species. For instance, O. granulata characteristically has a GG genome and is accordingly classified as a basal lineage of the genus Oryza. Here, we deployed a versatile hybrid approach by integrating Illumina and PacBio sequencing data to generate a high-quality mitochondrial genome (mitogenome) assembly for O. granulata. The mitogenome of O. granulata was 509,311 base pairs (bp) with sixty-seven genes comprising two circular chromosomes, five ribosomal RNA (rRNA) coding genes, twenty-five transfer RNA (tRNA) coding genes, and thirty-seven genes coding for proteins. We identified a total of 378 simple sequence repeats (SSRs). The genome also contained 643 pairs of dispersed repeats comprising 340 palindromic and 303 forward. In the O. granulata mitogenome, the length of 57 homologous fragments in the chloroplast genome occupied 5.96% of the mitogenome length. Collinearity analysis of three Oryza mitogenomes revealed high structural variability and frequent rearrangements. Phylogenetic analysis showed that, compared to other related genera, O. granulata had the closest genetic relationship with mitogenomes reported for all members of Oryza, and occupies a position at the base of the Oryza phylogeny. Comparative analysis of complete mitochondrial genome assemblies for Oryza species revealed high levels of mitogenomic diversity, providing a foundation for future conservation and utilization of wild rice biodiversity.
Subject
Paleontology,Space and Planetary Science,General Biochemistry, Genetics and Molecular Biology,Ecology, Evolution, Behavior and Systematics
Reference97 articles.
1. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza;Stein;Nat. Genet.,2018
2. The rice genome revolution: From an ancient grain to Green Super Rice;Wing;Nat. Rev. Genet.,2018
3. Rapid diversification of five Oryza AA genomes associated with rice adaptation;Zhang;Proc. Natl. Acad. Sci. USA,2014
4. Phylogeny of rice genomes with emphasis on origins of allotetraploid species;Ge;Proc. Natl. Acad. Sci. USA,1999
5. Zou, X.H., Zhang, F.M., Zhang, J.G., Zang, L.L., Tang, L., Wang, J., Sang, T., and Ge, S. (2008). Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol., 9.