Data from: Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents

Background: When populations evolve under disparate environmental conditions, they experience different selective pressures that shape patterns of sequence evolution and gene expression. These may be manifested in genetic and phenotypic differences such as a diverse immunogenetic repertoire in species from tropical latitudes that have greater and/or different parasite burdens than more temperate species. To test this idea, we compared the transcriptomes of one tropical species (Heteromys desmarestianus) and two species from temperate latitudes (Dipodomys spectabilis and Chaetodipus baileyi) from the Heteromyidae. We did so in a search for positive selection on sequences and/or differential expression, while controlling for phylogenetic history in our choice of species. Results: We identified 127,812 contigs and annotated 34,878 of these, identifying immune genes associated with interleukins, cytokines, and the production of mast cells. We identified 632 genes that were upregulated in H. desmarestianus (8.7% of genes tested) and 492 (6.7%) that were downregulated. Gene ontology terms including “immune response” were associated with 31 (4.9%) of the 632 upregulated genes. We found preliminary evidence for positive selection on three genes (Palmitoyltransferase ZDHHC5 Ubiquitin-conjugating enzyme E2 N, Krueppel-like factor 10, and Spindle and kinetochore-associated protein 1) along the H. desmarestianus lineage. Conclusions: Overall our findings pinpoint genes in species from disparate environments that are on different evolutionary trajectories in terms of expression levels and/or nucleotide sequence. Our data indicate there are significant differences in the expression of genes among the spleen transcriptomes of these species and that a number of these differentially expressed genes do not show the same pattern of differential expression in another tissue type. This points to the possibility of expression differences between these species specific to the spleen transcriptome.

背景：当种群在迥异的环境条件下演化时，会受到不同的选择压力，进而塑造序列演化与基因表达模式。这类差异可体现为遗传与表型特征的不同，例如相较于温带物种，热带纬度地区的物种因寄生虫负荷更高且/或种类更具多样性，其免疫遗传组库更为丰富。为验证该假说，我们选取异鼠科（Heteromyidae）的1个热带物种——长吻鼩形鼠（Heteromys desmarestianus），以及2个温带纬度物种——壮冠囊鼠（Dipodomys spectabilis）、贝氏异鼠（Chaetodipus baileyi）的转录组开展比较分析，旨在检测序列水平的正选择与/或差异表达，同时在物种选取中校正系统发育历史因素。
结果：本研究共获得127,812条重叠群（contig），并对其中34,878条进行了基因注释，鉴定出与白细胞介素、细胞因子及肥大细胞生成相关的免疫基因。我们鉴定出长吻鼩形鼠中上调基因632个（占检测基因总数的8.7%），下调基因492个（占6.7%）。在这632个上调基因中，有31个（占比4.9%）关联到包含“免疫应答”在内的基因本体（Gene Ontology, GO）术语。我们在长吻鼩形鼠的演化支中，发现了3个基因存在正选择的初步证据：棕榈酰转移酶ZDHHC5、泛素结合酶E2 N、Krüppel样因子10以及纺锤体与动粒相关蛋白1。
结论：总体而言，本研究的发现明确了来自不同环境的物种中，在基因表达水平和/或核苷酸序列上处于差异化演化轨迹的基因。本研究数据显示，这些物种的脾脏转录组中基因表达存在显著差异，且其中多个差异表达基因在另一组织类型中未呈现相同的差异表达模式。这提示这些物种间存在脾脏转录组特异性基因表达差异的可能性。