4.5 Article

Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana

Journal

DNA RESEARCH
Volume 29, Issue 5, Pages -

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/dnares/dsac030

Keywords

Pueraria lobata var; montana; chromosomal-level genome; graphic genome; comparative genomics; structural variants

Funding

  1. National Natural Science Foundation of China [31960420]
  2. Guangxi Natural Science Foundation Project [2021GXNSFBA220026]
  3. Science and Technology Development Fund of Guangxi Academy of Agricultural Sciences [Guinongke 2021JM11]
  4. Special project for basic scientific research of Guangxi Academy of Agricultural Sciences [Guinongke 2021YT057]

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This study reports the chromosome-level and graphic genomes of Pueraria montana, revealing the genetic differences and metabolic characteristics between P. montana and its sister species P. thomsonii. These findings are of great significance for the breeding and evolution studies of Pueraria.
Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.

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