Adaptation of Arabidopsis thaliana to the Yangtze River basin

Abstract

BackgroundOrganisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different.ResultsWe sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping.Conclusions A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1378-9) contains supplementary material, which is available to authorized users.

Archaic lineages broaden our view on the history of Arabidopsis thaliana

“…Particularly surprising was the finding that all African populations, including South Africans and Tanzanians, are native and that all sampled African individuals represent relicts when compared to the major Eurasian clade (Durvasula et al ., ). Other notable findings are that the island of Madeira harbors the most extremely diverged individuals sampled to date (Fulgione et al ., ) and that diverged samples from Central Asia (Tibet, Zeng et al ., ; Yunnan, Zou et al ., ; Western Himalayas, Tyagi et al ., ; the Altai Mountains, Yin et al ., ) suggest additional refugia.…”

“…These two factors limited the scope of the conclusions that could be drawn. However, several recent studies examined complete genome sequences of accessions from outside Eurasia, including Africa (Durvasula et al ., ), Madeira (Fulgione et al ., ) and Central Asia (Zeng et al ., ; Zou et al ., ) and compared them to results from across Eurasia (1001 Genomes Consortium, ). These studies reveal several surprises and helped to reconcile previous inconsistencies, as outlined below.…”

“…Contrary to the idea that the center of A. thaliana diversity lies within Eurasia, the joint analysis of variation across continents revealed evidence for deep divergence among several relict lineages (1001 Genomes Consortium, ; Durvasula et al ., ; Fulgione et al ., ; Zeng et al ., ; Zou et al ., ). Particularly surprising was the finding that all African populations, including South Africans and Tanzanians, are native and that all sampled African individuals represent relicts when compared to the major Eurasian clade (Durvasula et al ., ).…”

“…Relicts in Western Europe may represent a separate migration from Africa (possibly through Gibraltar (Fulgione et al ., )) from that which populated Central Asia (likely through the Levant). More recent splits between South Africa and Tanzania and between the currently widespread European and Asian clades are inferred at around 45 ka based on joint analyses of Eurasian, African and East Asian data sets (Durvasula et al ., ; Zou et al ., ). This suggests that non‐relicts spread through Eurasia well before the current interglacial, but a third post‐glacial expansion, as hypothesized in Lee et al .…”

On the postglacial spread of human commensal Arabidopsis thaliana: journey to the East

“…Zou et al . () have studied A. thaliana accessions from China and shown that the population in the Yangtze River Basin arrived relatively recently. They also showed that genes associated with the immune response as well as flowering time were significantly enriched in the list of selected genes in the Yangtze population.…”