Data from: Transcriptome-derived tetranucleotide microsatellites and their associated genes from the giant panda (Ailuropoda melanoleuca)

Recently, an increasing number of microsatellites or Simple Sequence Repeats (SSRs) have been found and characterized from transcriptome. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In the present work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, four CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these four CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes contained these four CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers would pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.

近年来，越来越多的微卫星（Simple Sequence Repeats，SSRs）已从转录组中被发现并完成鉴定。这类SSRs可作为推定的功能标记，用于便捷地标定对应的基因，在生物医学研究与遗传分析中发挥重要作用。然而，目前尚无针对大熊猫（Ailuropoda melanoleuca）的转录组来源SSRs相关资源。本研究从大熊猫血液来源的转录组数据库中，鉴定并表征了20个四核苷酸微卫星位点。此外，我们明确了这些位点的预测转录组定位：16个位点定位于非翻译区（untranslated regions，UTRs），4个位点定位于编码区（coding regions，CDSs）。我们确定了携带对应微卫星的14条转录本的基因注释信息，为研究SSRs在大熊猫基因调控中的潜在作用提供了有效依据。针对16个来自非翻译区的SSRs，其多态信息含量（polymorphic information content，PIC）取值范围为0.293至0.789，平均值为0.603。有趣的是，本研究开发的4个来自编码区的微卫星同样具有多态性，且通过重新分型与测序进一步验证了这4个编码区来源SSRs的不稳定性。携带这4个编码区来源SSRs的基因，嵌入了多种不同类型的重复基序。所有长度发生变化的SSRs之间的相互作用，或许可抵御因微卫星不稳定性引发的编码区移码突变。我们期望这些新开发的基因关联生物标记，能够为未来大熊猫的遗传与生物医学研究铺平道路。综上，这套转录组来源的标记补充了现有的大熊猫遗传资源库。