Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion

Susan A Smith; Xyrus X Maurer-Alcalá; Ying Yan; Laura A Katz; Luciana F Santoferrara; George B McManus

doi:10.1093/gbe/evaa185

Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion

Genome Biol Evol. 2020 Sep 1;12(9):1616-1622. doi: 10.1093/gbe/evaa185.

Authors

Susan A Smith¹, Xyrus X Maurer-Alcalá², Ying Yan³, Laura A Katz³, Luciana F Santoferrara^{1

4}, George B McManus¹

Affiliations

¹ Department of Marine Sciences, University of Connecticut, Groton.
² Institute of Cell Biology, University of Bern, Switzerland.
³ Department of Biological Sciences, Smith College, Northampton, Massachusetts.
⁴ Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs.

Abstract

Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new nonmodel genome resource for the study of ciliate ecology and genomic biology and provides a detailed functional counterpart to ecological research on S. arcuata.

Keywords: Ciliophora; genome architecture; macronucleus; micronucleus; single-cell ‘omics; tintinnid.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Ciliophora / genetics*
Ciliophora / metabolism
Genome, Protozoan*
Genomic Structural Variation
Transcriptome*