hyRAD RNA probes preparation and capture v2

hyRAD RNA probes preparation and capture v1

10.17504/protocols.io.rzqd75w ◽

2018 ◽

Author(s):

Tomasz Suchan ◽

Ludovic Orlando

Keyword(s):

Ancient Dna ◽

Molecular Ecology ◽

Rna Probes ◽

Dna Capture

Supplemental Information for: Suchan, T., Kusliy, M.A., Khan, N., Chauvey, L., Tonasso-Calvière, L., Schiavinato, S., Southon, J., Keller, M., Kitagawa, K., Krause, J., Bessudnov, A.N., Bessudnov, A.A., Graphodatsky, A.S., Lamas, S.V., Wilczyński, J., Pospuła, S., Tunia, K., Nowak, M., Moskal-delHoyo, M., Tishkin, A.A., Pryor, A.J.E., Outram, A.K., Orlando, L. (2021) Performance and automation of ancient DNA capture with RNA hyRAD probes. Molecular Ecology Resources, accepted.

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Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA

Scientific Reports ◽

10.1038/s41598-020-72146-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Joanna Pawłowska ◽

Jutta E. Wollenburg ◽

Marek Zajączkowski ◽

Jan Pawlowski

Keyword(s):

Ancient Dna ◽

Sequence Data ◽

Planktonic Foraminifera ◽

Molecular Ecology ◽

The Arctic ◽

Marine Biodiversity ◽

Neogloboquadrina Pachyderma ◽

Rna Genes ◽

The Last Glacial Maximum ◽

The Last Glacial

Abstract Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.

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