Genome-scale mRNA and small RNA transcriptomic insights into initiation of citrus apomixis

Jiang, Long; Zheng, Liduan; Wu, Xiaomeng; Fang, Yan-Ni; Jia, Hui-Hui; Xie, Zongzhou; Deng, Xiuxin; Guo, Wen‐Wu

doi:10.1093/jxb/erw338

Cited by 38 publications

(35 citation statements)

References 70 publications

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“…To identify genes that are differentially expressed between polyembryony and monoembryony, a comparative transcriptome analysis was performed on the ovules from three pairs of monoembryonic and polyembryonic citrus cultivars (pummelo-grapefruit, citron-lemon, clementine-ponkan) at the key stage of nucellar embryo initiation (i.e., 3 d before anthesis) 14,15 . Considering the genetic differences between each pair of citrus cultivars, we performed a pairwise comparison of the three pairs of RNA-seq data.…”

Section: Transcriptome Of Sexual and Nucellar Embryos From Citrusmentioning

confidence: 99%

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Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

et al. 2017

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The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.

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Section: Transcriptome Of Sexual and Nucellar Embryos From Citrusmentioning

confidence: 99%

“…This locus was later mapped to a genomic region that spans approximately 380 kb 12 . Genes differentially expressed during polyembryogenesis have also been identified [13][14][15] .…”

mentioning

confidence: 99%

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

et al. 2017

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“…3B). In our previous study, ARF19 was moderately expressed (RPKM values ranged from 15.69 to 34.50) in the ovules of two mandarin cultivars (the monoembryonic 'Nour' Clementine and the polyembryonic 'Huagan No.2' Ponkan) during nucellar embryo initiation, but was expressed at slightly higher levels in the polyembryonic cultivar [72].…”

Section: Csarf19 Might Be Involved In Citrus Ec Initiationmentioning

confidence: 84%

“…However, ARF19 was not expressed (RPKM = 0) in ovules of the monoembryonic 'Huanong red' pummelo, but accumulated in ovules of the polyembryonic 'Cocktail' grapefruit, with RPKM values of 1.34 and 3.58 prior to and at stage during nucellar embryo initiation [72]. Based on the fact that sweet orange and grapefruit were derived from hybridizations among mandarin and pummelo [43,72,73], we suggest that CsARF19 was originated in mandarin, and has introgression into the hybrids pool. SE initiation is believed to require an induction signal that causes somatic cells to change identity [74].…”

Section: Csarf19 Might Be Involved In Citrus Ec Initiationmentioning

confidence: 96%

Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

Liu

Wu³

et al. 2019

Preprint

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“…The interactions between miRNAs and their predicted targets were verified by the transient assay in Nicotiana benthamiana [60][61][62]. The pg-miR166a-3p precursor was amplified and transferred into the PBI121-GUS vector with an empty vector (EV) as the control.…”

Section: Nicotiana Benthamiana Transient Assaymentioning

confidence: 99%

Small RNA and mRNA Sequencing Reveal the Roles of microRNAs Involved in Pomegranate Female Sterility

Chen

Luo

Yang

et al. 2020

IJMS

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Female sterility is a key factor restricting plant reproduction. Our previous studies have revealed that pomegranate female sterility mainly arose from the abnormality of ovule development. MicroRNAs (miRNAs) play important roles in ovule development. However, little is known about the roles of miRNAs in female sterility. In this study, a combined high-throughput sequencing approach was used to investigate the miRNAs and their targeted transcripts involved in female development. A total of 103 conserved and 58 novel miRNAs were identified. Comparative profiling indicated that the expression of 43 known miRNAs and 14 novel miRNAs were differentially expressed between functional male flowers (FMFs) and bisexual flowers (BFs), 30 known miRNAs and nine novel miRNAs showed significant differences among different stages of BFs, and 20 known miRNAs and 18 novel miRNAs exhibited remarkable expression differences among different stages of FMFs. Gene ontology (GO) analyses of 144 predicted targets of differentially expressed miRNAs indicated that the “reproduction process” and “floral whorl development” processes were significantly enriched. The miRNA–mRNA interaction analyses revealed six pairs of candidate miRNAs and their targets associated with female sterility. Interestingly, pg-miR166a-3p was accumulated, whereas its predicted targets (Gglean012177.1 and Gglean013966.1) were repressed in functional male flowers (FMFs), and the interaction between pg-miR166a-3p and its targets (Gglean012177.1 and Gglean013966.1) were confirmed by transient assay. A. thaliana transformed with 35S-pre-pg-miR166a-3p verified the role of pg-miR166a-3p in ovule development, which indicated pg-miR166a-3p’s potential role in pomegranate female sterility. The results provide new insights into molecular mechanisms underlying the female sterility at the miRNA level.

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Genome-scale mRNA and small RNA transcriptomic insights into initiation of citrus apomixis

Abstract: HighlightIntegrative mRNA and small RNA analysis between poly- and monoembryonic ovules reveals involvement of an oxidative stress response and a novel miRNA-target regulatory module in initiation of citrus apomixis.

Cited by 38 publications

References 70 publications

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

Small RNA and mRNA Sequencing Reveal the Roles of microRNAs Involved in Pomegranate Female Sterility

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