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Genome-Wide Characterization and Expression of Two-Component System Genes in Cytokinin-Regulated Gall Formation in Zizania latifolia.

ABSTRACT: The thickening of Zizania latifolia shoots, referred to as gall formation, depends on infection with the fungal endophyte Ustilago esculenta. The swollen and juicy shoots are a popular vegetable in Asia. A key role for cytokinin action in this process was postulated. Here, trans-zeatin stimulated swelling in fungi-infected Z. latifolia. A two-component system (TCS) linked cytokinin binding to receptors with transcriptional regulation in the nucleus and played important roles in diverse biological processes. We characterized 69 TCS genes encoding for 25 histidine kinase/histidine-kinase-like (HK(L)) (21 HKs and 4 HKLs), 8 histidine phosphotransfer proteins (HP) (5 authentic and 3 pseudo), and 36 response regulators (RR; 14 type A, 14 type B, 2 type C, and 6 pseudo) in the genome of Z. latifolia. These TCS genes have a close phylogenetic relationship with their rice counterparts. Nineteen duplicated TCS gene pairs were found and the ratio of nonsynonymous to synonymous mutations indicated that a strong purifying selection acted on these duplicated genes, leading to few mutations during evolution. Finally, ZlCHK1, ZlRRA5, ZIRRA9, ZlRRA10, ZlPRR1, and ZlPHYA expression was associated with gall formation. Among them, ARR5, ARR9, and ZlPHYA are quickly induced by trans-zeatin, suggesting a role for cytokinin signaling in shoot swelling of Z. latifolia.

SUBMITTER: He L

PROVIDER: S-EPMC7690396 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Zizania latifolia (Griseb.) Turcz. ex Stapf has been cultivated as a popular aquatic vegetable in China due to its important nutritional, medicinal, ecological, and economic values. The complete mitochondrial genome (mitogenome) of Z. latifolia has not been previously studied and reported, which has hindered its molecular systematics and understanding of evolutionary processes. Here, we assembled the complete mitogenome of Z. latifolia and performed a comprehensive analysis including genome organization, repetitive sequences, RNA editing event, intercellular gene transfer, phylogenetic analysis, and comparative mitogenome analysis. The mitogenome of Z. latifolia was estimated to have a circular molecule of 392,219 bp and 58 genes consisting of three rRNA genes, 20 tRNA genes, and 35 protein-coding genes (PCGs). There were 46 and 20 simple sequence repeats (SSRs) with different motifs identified from the mitogenome and chloroplast genome of Z. latifolia, respectively. Furthermore, 49 homologous fragments were observed to transfer from the chloroplast genome to the mitogenome of Z. latifolia, accounting for 47,500 bp, presenting 12.1% of the whole mitogenome. In addition, there were 11 gene-containing homologous regions between the mitogenome and chloroplast genome of Z. latifolia. Also, approximately 85% of fragments from the mitogenome were duplicated in the Z. latifolia nuclear genome. Selection pressure analysis revealed that most of the mitochondrial genes were highly conserved except for ccmFc, ccmFn, matR, rps1, and rps3. A total of 93 RNA editing sites were found in the PCGs of the mitogenome. Z. latifolia and Oryza minuta are the most closely related, as shown by collinear analysis and the phylogenetic analysis. We found that repeat sequences and foreign sequences in the mitogenomes of Oryzoideae plants were associated with genome rearrangements. In general, the availability of the Z. latifolia mitogenome will contribute valuable information to our understanding of the molecular and genomic aspects of Zizania.

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Genome-Wide Characterization and Expression of Two-Component System Genes in Cytokinin-Regulated Gall Formation in Zizania latifolia.

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