Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence

The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted and grown in a common garden. Morphological measurements from the common garden demonstrated that phenotypic variation among populations is largely explained by underlying genetic variation. An RNA–Seq experiment was conducted with 96 of the individuals grown in the common garden and differentially expressed (DE) transcripts between the two latitudes were identified. A total number of 825 DE transcripts were identified. DE transcripts and non-differentially expressed (NDE) transcripts were then scanned for microsatellites. The abundance of different motif lengths and types in both groups were estimated. Our results indicate that DE transcripts are significantly enriched with mononucleotide repeats and significantly depauperate in trinucleotide repeats. Further, the standardized mononucleotide repeat motif A and dinucleotide repeat motif AG were significantly enriched within DE transcripts while motif types, C, AT, ACC, and AAC in DE transcripts are significantly differentiated in microsatellite tract length between the two latitudes. The tract length differentiation at specific microsatellite motif types across latitudes and their enrichment within DE transcripts indicate a potential functional role for transcribed microsatellites in gene expression divergence in sunflower.

自然种群产生适应性遗传变异的具体机制目前尚未被完全阐明。部分研究提出，微卫星（microsatellites）可作为适应性变异的驱动因素。本研究以普通向日葵（Helianthus annuus L.）的自然种群为研究对象，通过分析微卫星在不同纬度下表现出表达分化的基因中的富集情况，探究转录型微卫星的潜在适应性功能。我们从美国堪萨斯州与俄克拉荷马州两个不同纬度区域的6个种群中采集种子，将其种植于同质种植园（common garden）中进行统一培育。对同质种植园植株的形态学测量结果显示，种群间的表型差异主要由其内在的遗传变异所决定。我们对同质种植园中培育的96株植株开展了RNA测序（RNA–Seq）实验，鉴定出两个纬度种群间的差异表达（differentially expressed, DE）转录本，最终共获得825个差异表达转录本。随后，我们对差异表达转录本与非差异表达（non-differentially expressed, NDE）转录本进行微卫星扫描，并估算了两组转录本中不同基序长度与类型的丰度。研究结果表明，差异表达转录本中显著富集单核苷酸重复序列，而三核苷酸重复序列则显著匮乏。此外，标准化后的单核苷酸重复基序A与二核苷酸重复基序AG在差异表达转录本中显著富集；差异表达转录本中的C、AT、ACC及AAC基序类型，其微卫星序列长度在两个纬度种群间存在显著分化。特定微卫星基序类型的序列长度随纬度产生的分化，及其在差异表达转录本中的富集现象，表明转录型微卫星可能在向日葵的基因表达分化中发挥功能性作用。