Ancient Plant Genomics in Archaeology, Herbaria, and the Environment : Annual Review of Plant Biology

The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research

Pinole, un alimento tradicional mexicano con valor nutrimental

El pinole es un alimento de origen prehispánico que se obtiene principalmente a partir del tostado de los granos enteros de maíz y su posterior molienda. Este polvo de maíz tostado puede ser adicionado con diferentes ingredientes que le confieren distintas características de sabor y aroma, así como propiedades nutricionales, fisicoquímicas, entre otras. El pinole, el cual se consume comúnmente como bebida ya sea en frío o caliente como atole, formó parte importante del desarrollo de diferentes culturas mesoamericana. Hoy en día es conocido como un alimento tradicional mexicano que se ha adaptado a las diferentes necesidades y costumbres de diferentes regiones de México. El consumo de este producto ha ido disminuyendo por su relación con la temporalidad y alto contenido energético, sin embargo, es importante resaltar que estos productos presentan contenidos importantes de fibra dietética y diferentes compuestos bioactivos. Sin considerar, que la adición de nuevos ingredientes altos en proteínas o antioxidantes en la reformulación de este producto, generan alternativas novedosas y atractivas de consumo para la población. El presente reporte tiene como objetivo brindar información del pinole, desde sus orígenes, manera de preparación e ingredientes, características y sus diferentes propiedades, y los efectos del procesamiento para su obtención (tostado del maíz), que son importantes para conocer más sobre este alimento tradicional mexicano. DOI: https://doi.org/10.54167/tecnociencia.v16i1.89

Palaeogenomic insights into the origins of French grapevine diversity

Ramos-Madrigal, Jazmín, Runge, Anne Kathrine Wiborg, Bouby, Laurent, Lacombe, Thierry, Castruita, José Alfredo Samaniego, Adam-Blondon, Anne-Françoise, Figueiral, Isabel, Hallavant, Charlotte, Martínez-Zapater, José M., Schaal, Caroline, Töpfer, Reinhard, Petersen, Bent, Sicheritz-Pontén, Thomas, This, Patrice, Bacilieri, Roberto, Gilbert, M. Thomas P., Wales, Nathan (2019): Palaeogenomic insights into the origins of French grapevine diversity. Nature Plants 5: 595-603, DOI: 10.1038/s41477-019-0437-

Author Correction : The dental proteome of Homo antecessor (Nature, (2020), 580, 7802, (235-238), 10.1038/s41586-020-2153-8)

An amendment to this paper has been published and can be accessed via a link at the top of the paper

The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s–1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37–50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environmen

Near-Random Distribution of Chromosome-Derived Circular DNA in the Condensed Genome of Pigeons and the Larger, More Repeat-Rich Human Genome

Extrachromosomal circular DNA (eccDNA) elements of chromosomal origin are known to be common in a number of eukaryotic species. However, it remains to be addressed whether genomic features such as genome size, the load of repetitive elements within a genome, and/or animal physiology affect the number of eccDNAs. Here, we investigate the distribution and numbers of eccDNAs in a condensed and less repeat-rich genome compared with the human genome, using Columba livia domestica (domestic rock pigeon) as a model organism. By sequencing eccDNA in blood and breast muscle from three pigeon breeds at various ages and with different flight behavior, we characterize 30,000 unique eccDNAs. We identify genomic regions that are likely hotspots for DNA circularization in breast muscle, including genes involved in muscle development. We find that although eccDNA counts do not correlate with the biological age in pigeons, the number of unique eccDNAs in a nonflying breed (king pigeons) is significantly higher (9-fold) than homing pigeons. Furthermore, a comparison between eccDNA from skeletal muscle in pigeons and humans reveals ∼9-10 times more unique eccDNAs per human nucleus. The fraction of eccDNA sequences, derived from repetitive elements, exist in proportions to genome content, that is, human 72.4% (expected 52.5%) and pigeon 8.7% (expected 5.5%). Overall, our results support that eccDNAs are common in pigeons, that the amount of unique eccDNA types per nucleus can differ between species as well as subspecies, and suggest that eccDNAs from repeats are found in proportions relative to the content of repetitive elements in a genome

Near-Random Distribution of Chromosome-Derived Circular DNA in the Condensed Genome of Pigeons and the Larger, More Repeat-Rich Human Genome

Extrachromosomal circular DNA (eccDNA) elements of chromosomal origin are known to be common in a number of eukaryotic species. However, it remains to be addressed whether genomic features such as genome size, the load of repetitive elements within a genome, and/or animal physiology affect the number of eccDNAs. Here, we investigate the distribution and numbers of eccDNAs in a condensed and less repeat-rich genome compared with the human genome, using Columba livia domestica (domestic rock pigeon) as a model organism. By sequencing eccDNA in blood and breast muscle from three pigeon breeds at various ages and with different flight behavior, we characterize 30,000 unique eccDNAs. We identify genomic regions that are likely hotspots for DNA circularization in breast muscle, including genes involved in muscle development. We find that although eccDNA counts do not correlate with the biological age in pigeons, the number of unique eccDNAs in a nonflying breed (king pigeons) is significantly higher (9-fold) than homing pigeons. Furthermore, a comparison between eccDNA from skeletal muscle in pigeons and humans reveals ∼9-10 times more unique eccDNAs per human nucleus. The fraction of eccDNA sequences, derived from repetitive elements, exist in proportions to genome content, that is, human 72.4% (expected 52.5%) and pigeon 8.7% (expected 5.5%). Overall, our results support that eccDNAs are common in pigeons, that the amount of unique eccDNA types per nucleus can differ between species as well as subspecies, and suggest that eccDNAs from repeats are found in proportions relative to the content of repetitive elements in a genome.ISSN:1759-665