Genome-wide identification and expression profiles of phased siRNAs in a male-sterile somatic cybrid of pummelo (Citrus grandis)
Genome-wide identification and expression profiles of phased siRNAs in a male-sterile somatic cybrid of pummelo (Citrus grandis)
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柚子雄性不育体细胞杂种中定相 siRNA 的全基因组鉴定和表达谱
DOI：
10.1007/s11295-020-01437-z
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发表时间：
2020-06-01
影响因子：
2.4
通讯作者：
Guo, Wen-Wu
中科院分区：
文献类型：
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作者：
Fang, Yan-Ni;Yang, Xiao-Ming;Guo, Wen-Wu
阶段性小干扰RNA(PhasiRNAs)是一类21个或24个核苷酸的非编码小RNA，在植物生长发育的各种生物学过程中发挥着重要的调控作用。PhasiRNAs的生物发生通常由miRNAs触发，涉及Dicer处理。在我们之前的研究中，我们利用雄性不育的丝核桃(G1 + HBP)及其可育的原生质体融合亲本平藤柚(Hirado Buntan Pummelo)的发育花构建了高通量的SRNA和降解组测序文库，并鉴定了与柑橘雄性不育相关的miRNA。在这项研究中，在莎草柚及其可育融合亲本的花中发现了280个PHAS座位，产生2235个独特的21个核苷酸的phasiRNAs，其中210个与注释的蛋白质编码基因重叠，以及26个编码植物发育的转录因子家族，包括ARF、MYB、AP2、NAC、GRF、TIR1/AFB和AGL。基于miRNAs、phasiRNA和降解组数据的整合，我们从29个PHASloci中鉴定了9个miRNAs和8个phasiRNAs，并确定了67个具有广泛调控活性的基因是phasiRNAs的靶标。我们进一步鉴定了9个miRNA-PHAs-phasiRNA靶标调控级联，1个phasiRNA-PHAs-phasiRNA靶标级联，以及88个在Cybrid和HBP花中差异表达模式的phasiRNAs。这一分析提供了有关miRNA-Phas-phasiRNA靶标网络的新信息，并提示了phasiRNAs在柑橘雄性不育中的潜在作用，为进一步研究PhsiRNA在柑橘中的功能奠定了基础。
Phased small interfering RNAs (phasiRNAs) are 21- or 24-nucleotide small non-coding RNAs that play important regulatory roles in various biological processes of plant growth and development. Biogenesis of phasiRNAs is typically triggered by miRNAs and involves dicer-processing. In our previous study, we constructed high-throughput sRNA and degradome sequencing libraries out of developing flower of the male sterile cybrid pummelo (G1 + HBP) and its fertile protoplast fusion parent Hirado Buntan pummelo (HBP), and identified the miRNAs involved in citrus male sterility. In this study, 280PHASloci generating 2235 unique 21-nucleotide phasiRNAs were identified in the flowers of the cybrid pummelo and its fertile fusion parent; of them, 210 overlapped with annotated protein coding genes, and 26 encoded transcription factors families involved in plant development, including ARF, MYB, AP2, NAC, GRF, TIR1/AFB, and AGL. Based on integration of miRNAs, phasiRNA and the degradome data, we identified nine miRNAs and eight phasiRNAs that trigger phasiRNAs production out of 29PHASloci, and 67 genes of broad regulatory activities were identified to be targets of phasiRNAs. We further identified nine miRNA-PHAS-phasiRNA-targets regulatory cascades, one phasiRNA-PHAS-phasiRNA-targets cascade, and 88 phasiRNAs with differential expression patterns in flowers between the cybrid and HBP. This analysis provided new information about miRNA-PHAS-phasiRNA-target networks and suggested potential roles of phasiRNAs in male sterility of pummelo and contributed to further study of phasiRNA function in citrus.