Clifton Bryan D, Hariyani Imtiyaz, Kimura Ashlyn, Luo Fangning, Nguyen Alvin, Ranz José M
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
Commun Biol. 2023 Oct 20;6(1):1069. doi: 10.1038/s42003-023-05427-4.
How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple reference-quality genome assemblies. Here we show the existence of a positive correlation between Sdic copy number and total expression, plus vast intrastrain differences in mRNA abundance among paralogs, using RNA-sequencing from testis of four strains with variable paralog composition. Single cell and nucleus RNA-sequencing data expose paralog expression differentiation in meiotic cell types within testis from third instar larva and adults. Additional RNA-sequencing across synthetic strains only differing in their Y chromosomes reveal a tissue-dependent trans-regulatory effect on Sdic: upregulation in testis and downregulation in male accessory gland. By leveraging paralog-specific expression information from tissue- and cell-specific data, our results elucidate the intraspecific functional diversification of a recently expanded tandem gene family.
由于年轻基因拷贝的高序列相似性妨碍了它们的功能表征，因此新起源的基因拷贝如何成为稳定的基因组组成部分仍不确定。串联多基因家族Sdic是黑腹果蝇特有的，并且已在多个参考质量的基因组组装中进行了注释。在这里，我们使用来自四个具有不同旁系同源物组成的品系的睾丸的RNA测序，显示了Sdic拷贝数与总表达之间存在正相关，以及旁系同源物之间mRNA丰度存在巨大的品系内差异。单细胞和细胞核RNA测序数据揭示了三龄幼虫和成虫睾丸中减数分裂细胞类型中的旁系同源物表达差异。仅在Y染色体上不同的合成品系之间进行的额外RNA测序揭示了对Sdic的组织依赖性反式调节作用：在睾丸中上调而在雄性附腺中下调。通过利用来自组织和细胞特异性数据的旁系同源物特异性表达信息，我们的结果阐明了一个最近扩展的串联基因家族的种内功能多样化。
