GaTE Lab, Depto, de Botânica, Inst, de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil.
BMC Genomics. 2012 Apr 16;13:137. doi: 10.1186/1471-2164-13-137.
Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out.
Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements.
Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.
甘蔗是全球重要的糖料作物，也是可再生能源的重要来源。现代品种具有多倍体、大型复杂基因组，其祖先基因组的贡献极不均衡。长末端重复反转录转座子（LTR-RTs）是大多数植物基因组中最大的单一组成部分，它们可以在许多方面对基因组产生重大影响。因此，了解它们对基因组和转录组的贡献至关重要，但以前尚未对甘蔗中的 LTR-RTs 进行详细研究。
鉴定了 60 个完整的 LTR-RT 元件，它们分为 35 个家族，隶属于 4 个 Copia 和 3 个 Gypsy 谱系。结构上，谱系内元件相似，谱系间元件大小差异较大。FISH 分析显示 Gypsy/异染色质、Copia/常染色质的预期模式，但在两个谱系中，一些染色体上存在局部聚类。相关 EST 和 RT-PCR 分析表明组织和家族之间存在转录变化。在 sRNA 图谱分析中观察到四种不同的模式，其中最不寻常的是 Ale1，其在编码区有大量的 24nt sRNAs。研究结果表明，在甘蔗中，不同的小 RNA 调控途径针对 LTR-RT 元件的谱系。
单个 LTR-RT 甘蔗家族具有独特的结构、转录和调控特征。我们的研究结果表明，在甘蔗中，不同的 LTR-RT 家族具有不同的行为，并可能以不同的方式影响基因组。例如，这些转座元件可能通过产生一系列不同的小 RNA，触发基因沉默机制，从而影响附近的基因。还有一些证据表明，在现代甘蔗品种基因组中，来自特定 LTR-RT 谱系的祖先基因组对元件数量的贡献有显著差异。
