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，目前尚未得到充分阐释。部分研究提出，微卫星（microsatellites）可作为适应性变异的驱动因子。本研究以普通向日葵（Helianthus annuus L.）的自然种群为研究对象，通过评估微卫星在不同纬度下呈现表达分化的基因中的富集情况，验证转录型微卫星是否具备潜在的适应性功能。我们从美国堪萨斯州与俄克拉荷马州两个不同纬度的6个种群中采集种子，将其播种于同质园进行统一栽培。同质园的形态学测定结果显示，种群间的表型变异主要由其内在的遗传变异所决定。我们对同质园栽培的96株个体开展了RNA测序（RNA–Seq）实验，鉴定出两个纬度种群间的差异表达转录本（differentially expressed transcripts，DE），最终共得到825个DE转录本。随后，我们对DE转录本与无差异表达转录本（non-differentially expressed，NDE）进行了微卫星扫描，并对两组转录本中不同基序长度与类型的丰度进行了估算。研究结果显示，DE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DE转录本中显著富集；而DE转录本中的C、AT、ACC及AAC等基序类型，其微卫星延伸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延伸长度在纬度间的分化，及其在DE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。