The limits and potential of paleogenomic techniques for reconstructing grapevine domestication

Nathan Wales; Jazmin Ramos Madrigal; Enrico Cappellini; Aldo Carmona Baez; Jose Alfredo Samaniego Castruita; J. Alberto Romero-Navarro; Christian Carøe; Maria del Carmen Avila Arcos; Fernando Peñaloza; José Victor Moreno Mayar; Boris Gasparyan; Diana Zardaryan; Tamara Bagoyan; Alexia Smith; Ron Pinhasi; Giovanna Bosi; Girolamo Fiorentino; Anna Maria Grasso; Alessandra Celant; Guy Bar-Oz; Yotam Tepper; Allan Hall; Simone Scalabrin; Mara Miculan; Michele Morgante; Gabriele Di Gaspero; Tom Gilbert

doi:10.1016/j.jas.2016.05.014

The limits and potential of paleogenomic techniques for reconstructing grapevine domestication

Nathan Wales^*, Jazmin Ramos Madrigal, Enrico Cappellini, Aldo Carmona Baez, Jose Alfredo Samaniego Castruita, J. Alberto Romero-Navarro, Christian Carøe, Maria del Carmen Avila Arcos, Fernando Peñaloza, José Victor Moreno Mayar, Boris Gasparyan, Diana Zardaryan, Tamara Bagoyan, Alexia Smith, Ron Pinhasi, Giovanna Bosi, Girolamo Fiorentino, Anna Maria Grasso, Alessandra Celant, Guy Bar-OzYotam Tepper, Allan Hall, Simone Scalabrin, Mara Miculan, Michele Morgante, Gabriele Di Gaspero, Tom Gilbert

^*Corresponding author for this work

27 Citations (Scopus)

Abstract

In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without genetic recombination, simplifying analyses. While mitochondrial genomes have played a key role in many mammalian aDNA projects, including research focused on prehistoric humans and extinct hominins, it is unclear how useful plant chloroplast genomes (plastomes) may be at elucidating questions related to plant evolution, crop domestication, and the prehistoric movement of botanical products through trade and migration. Such analyses are particularly challenging for plant species whose genomes have highly repetitive sequences and that undergo frequent genomic reorganization, notably species with high retrotransposon activity. To address this question, we explored the research potential of the grape (Vitis vinifera L.) plastome using targeted-enrichment methods and high-throughput DNA sequencing on a collection of archaeological grape pip and vine specimens from sites across Eurasia dating ca. 4000 BCE-1500 CE. We demonstrate that due to unprecedented numbers of sequence insertions into the nuclear and mitochondrial genomes, the grape plastome provides limited intraspecific phylogenetic resolution. Nonetheless, we were able to assign archaeological specimens in the Italian peninsula, Sardinia, UK, and Armenia from pre-Roman to medieval times as belonging to all three major chlorotypes A, C, and D found in modern varieties of Western Europe. Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.

Original language	English
Journal	Journal of Archaeological Science
Volume	72
Pages (from-to)	57-70
Number of pages	14
ISSN	0305-4403
DOIs	https://doi.org/10.1016/j.jas.2016.05.014
Publication status	Published - Aug 2016

Keywords

Ancient DNA
Archaeobotany
Chloroplast DNA
Domestication
Grapevine
High-throughput sequencing
Wine

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10.1016/j.jas.2016.05.014

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Wales, N., Ramos Madrigal, J., Cappellini, E., Baez, A. C., Samaniego Castruita, J. A., Romero-Navarro, J. A., Carøe, C., Avila Arcos, M. D. C., Peñaloza, F., Moreno Mayar, J. V., Gasparyan, B., Zardaryan, D., Bagoyan, T., Smith, A., Pinhasi, R., Bosi, G., Fiorentino, G., Grasso, A. M., Celant, A., ... Gilbert, T. (2016). The limits and potential of paleogenomic techniques for reconstructing grapevine domestication. Journal of Archaeological Science, 72, 57-70. https://doi.org/10.1016/j.jas.2016.05.014

Wales, N, Ramos Madrigal, J , Cappellini, E, Baez, AC, Samaniego Castruita, JA, Romero-Navarro, JA, Carøe, C, Avila Arcos, MDC, Peñaloza, F, Moreno Mayar, JV, Gasparyan, B, Zardaryan, D, Bagoyan, T, Smith, A, Pinhasi, R, Bosi, G, Fiorentino, G, Grasso, AM, Celant, A, Bar-Oz, G, Tepper, Y, Hall, A, Scalabrin, S, Miculan, M, Morgante, M, Di Gaspero, G & Gilbert, T 2016, 'The limits and potential of paleogenomic techniques for reconstructing grapevine domestication', Journal of Archaeological Science, vol. 72, pp. 57-70. https://doi.org/10.1016/j.jas.2016.05.014

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title = "The limits and potential of paleogenomic techniques for reconstructing grapevine domestication",

abstract = "In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without genetic recombination, simplifying analyses. While mitochondrial genomes have played a key role in many mammalian aDNA projects, including research focused on prehistoric humans and extinct hominins, it is unclear how useful plant chloroplast genomes (plastomes) may be at elucidating questions related to plant evolution, crop domestication, and the prehistoric movement of botanical products through trade and migration. Such analyses are particularly challenging for plant species whose genomes have highly repetitive sequences and that undergo frequent genomic reorganization, notably species with high retrotransposon activity. To address this question, we explored the research potential of the grape (Vitis vinifera L.) plastome using targeted-enrichment methods and high-throughput DNA sequencing on a collection of archaeological grape pip and vine specimens from sites across Eurasia dating ca. 4000 BCE-1500 CE. We demonstrate that due to unprecedented numbers of sequence insertions into the nuclear and mitochondrial genomes, the grape plastome provides limited intraspecific phylogenetic resolution. Nonetheless, we were able to assign archaeological specimens in the Italian peninsula, Sardinia, UK, and Armenia from pre-Roman to medieval times as belonging to all three major chlorotypes A, C, and D found in modern varieties of Western Europe. Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.",

keywords = "Ancient DNA, Archaeobotany, Chloroplast DNA, Domestication, Grapevine, High-throughput sequencing, Wine",

author = "Nathan Wales and {Ramos Madrigal}, Jazmin and Enrico Cappellini and Baez, {Aldo Carmona} and {Samaniego Castruita}, {Jose Alfredo} and Romero-Navarro, {J. Alberto} and Christian Car{\o}e and {Avila Arcos}, {Maria del Carmen} and Fernando Pe{\~n}aloza and {Moreno Mayar}, {Jos{\'e} Victor} and Boris Gasparyan and Diana Zardaryan and Tamara Bagoyan and Alexia Smith and Ron Pinhasi and Giovanna Bosi and Girolamo Fiorentino and Grasso, {Anna Maria} and Alessandra Celant and Guy Bar-Oz and Yotam Tepper and Allan Hall and Simone Scalabrin and Mara Miculan and Michele Morgante and {Di Gaspero}, Gabriele and Tom Gilbert",

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AU - Wales, Nathan

AU - Ramos Madrigal, Jazmin

AU - Cappellini, Enrico

AU - Baez, Aldo Carmona

AU - Samaniego Castruita, Jose Alfredo

AU - Romero-Navarro, J. Alberto

AU - Carøe, Christian

AU - Avila Arcos, Maria del Carmen

AU - Peñaloza, Fernando

AU - Moreno Mayar, José Victor

AU - Gasparyan, Boris

AU - Zardaryan, Diana

AU - Bagoyan, Tamara

AU - Smith, Alexia

AU - Pinhasi, Ron

AU - Bosi, Giovanna

AU - Fiorentino, Girolamo

AU - Grasso, Anna Maria

AU - Celant, Alessandra

AU - Bar-Oz, Guy

AU - Tepper, Yotam

AU - Hall, Allan

AU - Scalabrin, Simone

AU - Miculan, Mara

AU - Morgante, Michele

AU - Di Gaspero, Gabriele

AU - Gilbert, Tom

PY - 2016/8

Y1 - 2016/8

N2 - In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without genetic recombination, simplifying analyses. While mitochondrial genomes have played a key role in many mammalian aDNA projects, including research focused on prehistoric humans and extinct hominins, it is unclear how useful plant chloroplast genomes (plastomes) may be at elucidating questions related to plant evolution, crop domestication, and the prehistoric movement of botanical products through trade and migration. Such analyses are particularly challenging for plant species whose genomes have highly repetitive sequences and that undergo frequent genomic reorganization, notably species with high retrotransposon activity. To address this question, we explored the research potential of the grape (Vitis vinifera L.) plastome using targeted-enrichment methods and high-throughput DNA sequencing on a collection of archaeological grape pip and vine specimens from sites across Eurasia dating ca. 4000 BCE-1500 CE. We demonstrate that due to unprecedented numbers of sequence insertions into the nuclear and mitochondrial genomes, the grape plastome provides limited intraspecific phylogenetic resolution. Nonetheless, we were able to assign archaeological specimens in the Italian peninsula, Sardinia, UK, and Armenia from pre-Roman to medieval times as belonging to all three major chlorotypes A, C, and D found in modern varieties of Western Europe. Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.

AB - In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without genetic recombination, simplifying analyses. While mitochondrial genomes have played a key role in many mammalian aDNA projects, including research focused on prehistoric humans and extinct hominins, it is unclear how useful plant chloroplast genomes (plastomes) may be at elucidating questions related to plant evolution, crop domestication, and the prehistoric movement of botanical products through trade and migration. Such analyses are particularly challenging for plant species whose genomes have highly repetitive sequences and that undergo frequent genomic reorganization, notably species with high retrotransposon activity. To address this question, we explored the research potential of the grape (Vitis vinifera L.) plastome using targeted-enrichment methods and high-throughput DNA sequencing on a collection of archaeological grape pip and vine specimens from sites across Eurasia dating ca. 4000 BCE-1500 CE. We demonstrate that due to unprecedented numbers of sequence insertions into the nuclear and mitochondrial genomes, the grape plastome provides limited intraspecific phylogenetic resolution. Nonetheless, we were able to assign archaeological specimens in the Italian peninsula, Sardinia, UK, and Armenia from pre-Roman to medieval times as belonging to all three major chlorotypes A, C, and D found in modern varieties of Western Europe. Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.

KW - Ancient DNA

KW - Archaeobotany

KW - Chloroplast DNA

KW - Domestication

KW - Grapevine

KW - High-throughput sequencing

KW - Wine

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VL - 72

SP - 57

EP - 70

JO - Journal of Archaeological Science

JF - Journal of Archaeological Science

ER -

The limits and potential of paleogenomic techniques for reconstructing grapevine domestication

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Keywords

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