Genome architecture used to supplement species delineation in two cryptic marine ciliates
Genome architecture used to supplement species delineation in two cryptic marine ciliates
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DOI：
10.1111/1755-0998.13664
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发表时间：
2022-06-26
影响因子：
7.7
通讯作者：
McManus，George B.
中科院分区：
文献类型：
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作者：
Smith，Susan A.;Santoferrara，Luciana F.;McManus，George B.
本研究的目的是确定哪种分类方法可以阐明两种隐秘纤毛虫物种之间清晰且可量化的差异，并测试基因组结构作为新的诊断特征在区分其他难以区分的类群中的实用性。通过传统的分类学特征，包括 lorica 形态测量、核糖体 RNA (rRNA) 基因条形码和生态生理学特征，对两种隐秘的丁丁纤毛虫——弓形Schmidingerella 和 Schmidingerella meunieri 进行了比较。此外，单细胞组学分析（单细胞转录组学和基因组学）用于阐明和比较同系物之间的微核基因组结构模式。结果包括高度相似的 lorica，其尺寸更大。 meunieri，rRNA 基因条形码存在 0%–0.5% 的差异，11 种猎物处理中存在两种不同和 9 种无法区分的生长反应，以及在两种纤毛虫中检测到的基因微核基因组结构的不同模式。总之，这些结果表明，虽然 S 之间存在微小差异。 arcuata 和 S.尽管 meunieri 与分类学鉴定的共同指标（即 lorica 形态、DNA 条形码序列和生态生理学）不同，但它们的基因组结构存在差异，这表明潜在的遗传不相容性。两种分离株共享的基因中微核结构的不同模式也使得物种特异性引物的设计成为可能，这些引物在本研究中用作独特的“结构条形码”，以证明从西北大西洋河口收集的样本中两种纤毛虫的共现。这些结果支持基因组结构作为物种描述工具的实用性，特别是对于那些神秘的或难以使用传统识别方法区分的纤毛虫。
The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates,Schmidingerella arcuataandSchmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single‐cell ‘omics analyses (single‐cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger inS. meunieri, a 0%–0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist betweenS. arcuataandS. meunieriin common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species‐specific primers, which are used in this study as unique “architectural barcodes” to demonstrate the co‐occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification.