Rice Genomics and Genetics 2024, Vol.15, No.4, 178-189 http://cropscipublisher.com/index.php/rgg 179 migration and domestication of Oryza species, tracing the roots of one of the world’s most important crops. 2 Origins and Early Evolution of OryzaSpecies 2.1 Phylogenetic overview The genus Oryza, which includes both domesticated and wild rice species, has a complex phylogenetic history. Molecular phylogenetic studies using DNA sequences from chloroplast, mitochondrial, and nuclear genomes have shown that the rice tribe (Oryzeae) is monophyletic and can be divided into two main clades corresponding to traditionally recognized subtribes. The divergence of Oryza and Leersia from other genera in the Oryzeae tribe is estimated to have occurred around 20 million years ago (mya), with Oryza and Leersia themselves diverging approximately 14 mya (Guo and Ge, 2005). This long evolutionary history has been marked by significant genetic conservation, turnover, and innovation across the genus, as evidenced by the study of 13 reference genomes spanning the Oryza species tree (Figure 1) (Stein et al., 2018). Figure 1 Geographic distribution and phylogenetic reconstruction of wild species of Oryza and Leersia (Adopted from Stein et al., 2018) Image caption: a, Geographic ranges of wild Oryza species and the outgroup species L. perrieri sequenced in this study. Dashed red lines show the limits of rice cultivation. Mapped ranges are adapted from IRRI’s Knowledge Bank (see URLs). b: Most frequently estimated species phylogeny in supermatrix and MP-EST analyses of each chromosome (inferred in 10 of 12 chromosomes and 11 of 12 chromosomes, respectively). Bootstrap proportions were obtained from 400 supermatrix bootstrap replicates, and MP-EST support values were obtained as described in the Methods. All clades were supported by both methods at 100%, except as indicated. Divergence times within the Oryza genus were estimated by PATHd8, assuming an age of 15 million years for the Oryza crown group. Bars on nodes represent the range of PATHd8 age estimates across all 12 chromosomes. Mya, million years ago (Adopted from Stein et al., 2018)
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