Whole Genome Assembly and Annotation of Northern Wild Rice,Zizania palustrisL., Supports a Whole Genome Duplication in theZizaniaGenus

Abstract

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural, and agricultural significance, specifically in the Great Lakes region of the United States. Using long- and short-range sequencing, Hi-C scaffolding, and RNA-seq data from eight tissues, we generated an annotated whole genome de novo assembly of NWR. The assembly is 1.29 Gb, highly repetitive (~76.0%), and contains 46,421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole genome duplication prior to the Zizania-Oryza speciation event have both led to an increase in genome size of NWR in comparison with O. sativa and Z. latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed conservation of large syntenic blocks with Oryza sativa L., which were used to identify putative seed shattering genes. Estimates of divergence times revealed the Zizania genus diverged from Oryza ~26-30 million years ago (MYA), while NWR and Zizania latifolia diverged from one another ~6-8 MYA. Comparative genomics confirmed evidence of a whole genome duplication in the Zizania genus and provided support that the event was prior to the NWR-Z. latifolia speciation event. This high-quality genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.

Interactive transcriptome analyses of Northern Wild Rice (Zizania palustris L.) and Bipolaris oryzae show convoluted communications during the early stages of fungal brown spot development

“…Annotation was done on the longest isoform per gene using Trinotate 3.1.1 (Bryant et al, 2017). For NWR transcript annotations, a set of 16 Gramineae species in the Ensembl Plants database (Aegilops tauschii, Brachypodium distachyon, Eragrostis tef, Hordeum vulgare, Leesia perrieri, Oryza barthii, O. glaberrima, O. nivara, O. rufipogon, O. sativa, Panicum hallii, Saccharum spontaneum, Setaria italica, Sorghum bicolor, Triticum aestivum, and Zea mays), the draft Z. latifolia genome (Yan et al, 2022), and the current annotation of the Z. palustris draft genome (Haas et al, 2021) were used. Annotation of fungal transcripts was done using annotated genomes of 24 fungi in the Pleosporales in the Ensembl Fungi database (Supplementary Table 6) and from previously annotated B. oryzae draft gene sequences (assembly LNFW01000000; Castell-Miller et al, 2016).…”

“…In addition, two other DEGs found in close proximity included a cytochrome P450 76M5 (DN4445_c1_g1, ZPchr0006g40673) and a transcript matching the stemar-13-ene synthase (DN69815_c0_g1, ZPchr0006g45140) potentially involved in oryzalexin synthesis. These seven genes were co-located in ~58,202 bp in chromosome 6 [phytoalexin biosynthetic gene cluster (PBGC)], each separated by an average distance of 5,430 bp (scaffold 48; Haas et al, 2021) (Figure 6). PBGC shows microsynteny and collinearity with the corresponding PBGC of Z. latifolia on chromosome 8 (Yan et al, 2022), and less to that of white rice (Wu et al, 2011).…”

“…The species belongs to the subtribe Zizaniinae (Xu et al, 2010), within the tribe Oryzeae, distinct from the subtribe Oryzinae, containing white rice (Oryza sativa L.) (Guo and Ge, 2005). Despite the subtribes diverging 26-30 million years ago, genomic synteny and collinearity between species of Zizania and Oryza are substantial (Haas et al, 2021;Yan et al, 2022). For example, the genomes of NWR, Z. latifolia, and Oryza spp., including O. sativa, share 14,120 protein-coding orthologous groups (Haas et al, 2021).…”

“…Despite the subtribes diverging 26-30 million years ago, genomic synteny and collinearity between species of Zizania and Oryza are substantial (Haas et al, 2021;Yan et al, 2022). For example, the genomes of NWR, Z. latifolia, and Oryza spp., including O. sativa, share 14,120 protein-coding orthologous groups (Haas et al, 2021). This is a relevant framework to understand the evolutionary history of the NWR genome and guide research for NWR trait development, such as reduced seed-shattering, since microsyntenic gene blocks for shattering between this species and O. sativa have been found (Haas et al, 2021).…”

“…For example, the genomes of NWR, Z. latifolia, and Oryza spp., including O. sativa, share 14,120 protein-coding orthologous groups (Haas et al, 2021). This is a relevant framework to understand the evolutionary history of the NWR genome and guide research for NWR trait development, such as reduced seed-shattering, since microsyntenic gene blocks for shattering between this species and O. sativa have been found (Haas et al, 2021). In addition, microsynteny of genomic areas for genes putatively involved in phytoalexin production is present among NWR, Z. latifolia, and O. sativa (Yan et al, 2022;Wu et al, 2011; this study), which could facilitate future functional gene studies.…”