A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research. / Canales, Nataly Allasi; Pérez-Escobar, Oscar A.; Powell, Robyn F.; Töpel, Mats; Kidner, Catherine; Nesbitt, Mark; Maldonado, Carla; Barnes, Christopher J.; Rønsted, Nina; Przelomska, Natalia A. S.; Leitch, Ilia J.; Antonelli, Alexandre.

In: GigaByte, Vol. 2022, 71, 2022.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Canales, NA, Pérez-Escobar, OA, Powell, RF, Töpel, M, Kidner, C, Nesbitt, M, Maldonado, C, Barnes, CJ, Rønsted, N, Przelomska, NAS, Leitch, IJ & Antonelli, A 2022, 'A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research', GigaByte, vol. 2022, 71. https://doi.org/10.46471/gigabyte.71

APA

Canales, N. A., Pérez-Escobar, O. A., Powell, R. F., Töpel, M., Kidner, C., Nesbitt, M., Maldonado, C., Barnes, C. J., Rønsted, N., Przelomska, N. A. S., Leitch, I. J., & Antonelli, A. (2022). A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research. GigaByte, 2022, [71]. https://doi.org/10.46471/gigabyte.71

Vancouver

Canales NA, Pérez-Escobar OA, Powell RF, Töpel M, Kidner C, Nesbitt M et al. A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research. GigaByte. 2022;2022. 71. https://doi.org/10.46471/gigabyte.71

Author

Canales, Nataly Allasi ; Pérez-Escobar, Oscar A. ; Powell, Robyn F. ; Töpel, Mats ; Kidner, Catherine ; Nesbitt, Mark ; Maldonado, Carla ; Barnes, Christopher J. ; Rønsted, Nina ; Przelomska, Natalia A. S. ; Leitch, Ilia J. ; Antonelli, Alexandre. / A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research. In: GigaByte. 2022 ; Vol. 2022.

Bibtex

@article{7bd50c5db02b4bd9968c565eabb2a80d,
title = "A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research",
abstract = "The Andean fever tree ( Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82 % of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree. ",
author = "Canales, {Nataly Allasi} and P{\'e}rez-Escobar, {Oscar A.} and Powell, {Robyn F.} and Mats T{\"o}pel and Catherine Kidner and Mark Nesbitt and Carla Maldonado and Barnes, {Christopher J.} and Nina R{\o}nsted and Przelomska, {Natalia A. S.} and Leitch, {Ilia J.} and Alexandre Antonelli",
note = "{\textcopyright} The Author(s) 2022.",
year = "2022",
doi = "10.46471/gigabyte.71",
language = "English",
volume = "2022",
journal = "GigaByte",
issn = "2709-4715",
publisher = "GigaScience Press",

}

RIS

TY - JOUR

T1 - A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

AU - Canales, Nataly Allasi

AU - Pérez-Escobar, Oscar A.

AU - Powell, Robyn F.

AU - Töpel, Mats

AU - Kidner, Catherine

AU - Nesbitt, Mark

AU - Maldonado, Carla

AU - Barnes, Christopher J.

AU - Rønsted, Nina

AU - Przelomska, Natalia A. S.

AU - Leitch, Ilia J.

AU - Antonelli, Alexandre

N1 - © The Author(s) 2022.

PY - 2022

Y1 - 2022

N2 - The Andean fever tree ( Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82 % of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree.

AB - The Andean fever tree ( Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82 % of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree.

U2 - 10.46471/gigabyte.71

DO - 10.46471/gigabyte.71

M3 - Journal article

C2 - 36950143

VL - 2022

JO - GigaByte

JF - GigaByte

SN - 2709-4715

M1 - 71

ER -

ID: 390731826