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The complete genome of Ziziphus jujuba cv. dongzao, an economic crop in Yellow River Delta of China.

ABSTRACT: The complete chloroplast genome of Ziziphus jujuba cv. dongzao, known as an important economic cultivar in Yellow River Delta of China was reported. It exhibits a quadripartite structure with 161,493?bp including a large single copy region (89,178?bp), a small single copy region (19,357?bp) and a pair of inverted repeats regions (26,479?bp). It has 36.79% GC content and 114 unique genes. Phylogenetic analysis showed that it was a member of Ziziphus and more closely related to Berchemiella wilsonii. Border analysis revealed that there were some differences in the borders of the four related cultivars.

SUBMITTER: Gao CM

PROVIDER: S-EPMC7800215 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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The complete genome of Ziziphus jujuba cv. dongzao, an economic crop in Yellow River Delta of China.

Gao Chun-Ming CM Gao Ying-Chun YC Liu Xue-Hong XH

Mitochondrial DNA. Part B, Resources 20170929 2

The complete chloroplast genome of Ziziphus jujuba cv. dongzao, known as an important economic cultivar in Yellow River Delta of China was reported. It exhibits a quadripartite structure with 161,493 bp including a large single copy region (89,178 bp), a small single copy region (19,357 bp) and a pair of inverted repeats regions (26,479 bp). It has 36.79% GC content and 114 unique genes. Phylogenetic analysis showed that it was a member of Ziziphus and more closely related to Be ...[more]

PMID: 33473950

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Project description:A previously unreported disease affecting jujube (Ziziphus jujuba Mill.) trees was observed in China (Liaoning province) in 2015 and named jujube yellow mottle disease (JYMD), due to prevalent symptoms on the leaves. Diseased plants produced also malformed and discolored fruits. In an attempt to identify the possible causal agent of JYMD, high-throughput sequencing of small RNA libraries was performed and a novel virus, tentatively named jujube yellow mottle-associated virus (JYMaV), was identified and characterized. Six genomic RNA segments of JYMaV were completely sequenced. Each one contains a single open reading frame in the viral complementary strand and two untranslated regions with complementary 5' and 3' terminal ends, thus showing typical features of other negative-stranded RNA viruses. RNA1 (7.1 kb), RNA2 (2.2 kb) and RNA3 (1.2 kb) encode putative proteins that, based on their conserved motifs, have been identified as the RNA dependent RNA polymerase, the glycoprotein and the nucleocapsid protein, respectively. These proteins share significant sequence identity (52.1-70.4%) with proteins encoded by raspberry leaf blotch virus (RLBV). RNA4 (1.5 kb) and RNA5 (1.2 kb) code for two putative 30 K movement proteins also related to the homologous RLBV protein. The functional role of the protein encoded by JYMaV RNA6 remains unknown. These data together with the phylogenetic relationships of JYMaV with other recognized emaraviruses support the proposal that JYMaV is the representative member of a novel species in the genus Emaravirus. In agreement with this proposal, virus-like particles and double-membrane-bound bodies, similar to those previously reported for other emaraviruses, were observed by transmission electron microscopy in extracts and tissues from symptomatic leaves, respectively. A specific RT-PCR-based detection method has been developed and used in a preliminary field survey that provided results strongly supporting the close association of JYMaV with the novel disease.

Dataset Information

The complete genome of Ziziphus jujuba cv. dongzao, an economic crop in Yellow River Delta of China.

Publications

The complete genome of <i>Ziziphus jujuba</i> cv. dongzao, an economic crop in Yellow River Delta of China.

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