Organellar Genomes from a ∼5,000-Year-Old Archaeological Maize Sample Are Closely Related to NB Genotype

Abstract

The story of how preColumbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here, we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040–5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected. However, this analysis also indicates that fertile genotype NB is closely related to the archaeological maize sample and evolved before cytoplasmic male sterility genotypes (CMS-S, CMS-T, and CMS-C), thus contradicting previous phylogenetic analysis of mitochondrial genomes from maize. We show that maximum-likelihood infers a tree where CMS genotypes branch at the base of the tree when including sites that have a relative fast rate of evolution thus suggesting long-branch attraction. We also show that Bayesian analysis infer a topology where NB and the archaeological maize sample are at the base of the tree even when including faster sites. We therefore suggest that previous trees suffered from long-branch attraction. We also show that the phylogenetic analysis of the ancient chloroplast is congruent with genotype NB to be more closely related to the archaeological maize sample. As shown here, the inclusion of ancient genomes on phylogenetic trees greatly improves our understanding of the domestication process of maize, one of the most important crops worldwide.

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

“…While recent work has shown encouraging results, studies leveraging the information in the DNA (and/or RNA) fragments present in plant subfossils are still scarce (for review, see Gutaker and Burbano [102]). The number of the species studied spans a large taxonomic range and includes barley [103, 104], wheat [105–109], maize [110–118], sunflower [119], grape [120–122], bottle gourd [123], radish [124], sorghum [125], papyri [126], rice [127], olive [128], orchid [129], Prunus [130], Arabidopsis [131], cotton [132], and trees [133–136]. Similarly, the primary material used for DNA extraction includes a whole variety of tissues, such as fruits, seeds, leaves, and woods, preserved in a wide range of conditions, including charred, waterlogged, desiccated, or mineralized remains.…”

Phylogenomic Analysis of the Plastid Genome of the Peruvian Purple Maize Zea mays subsp. mays cv. ‘INIA 601’

“…Plastid genes and genomes have been widely used in several species to resolve phylogenetic relationships among different taxa [ 12 , 13 , 14 , 15 , 16 , 17 , 18 ]. Some maize plastid genomes are publicly available, including one partial ancient genome (SM10) [ 19 ], four Zea species, the subspecie Zea mays subsp. huehuetenangensis (Iltis & Doebley) Doebley, 1990 [ 20 ], and several domesticated maize lines including ‘B73’ [ 16 , 17 , 18 , 19 , 20 , 21 ], ‘B37’ (C, T, S, N), ‘A188’ [ 22 ], and ‘Zhengdan958’ [ 23 ].…”

“…Some maize plastid genomes are publicly available, including one partial ancient genome (SM10) [ 19 ], four Zea species, the subspecie Zea mays subsp. huehuetenangensis (Iltis & Doebley) Doebley, 1990 [ 20 ], and several domesticated maize lines including ‘B73’ [ 16 , 17 , 18 , 19 , 20 , 21 ], ‘B37’ (C, T, S, N), ‘A188’ [ 22 ], and ‘Zhengdan958’ [ 23 ]. Additionally, the plastid genomes of the close relatives Tripsacum dactyloides (L.) L [ 24 ] and Sorgum bicolor (L.) Moench [ 17 ] are also available.…”

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

“…For instance, high Fe concentrations in surficial sediments could be related to inputs of clastic sediments, and often reflect agricultural activities 77 . We determined 13 plant genera, five belonging to the family Poaceae (58%), including the genus Zea (corn), known to have been cultivated and consumed by early settlers 78 , and Oryza , a fast-growing weed that is indicative of human-mediated habitat disturbance. Twelve microscopic fungal genera were observed, including taxa that are pathogenic on wheat and rice ( Gibberella and Cladochytrium ), plants, keratin, and flies (Supplementary Fig.…”