Diverse trajectories of plastome degradation in holoparasitic Cistanche and genomic location of the lost plastid genes

Xiaoqing Liu, Weirui Fu, Yiwei Tang, Wenju Zhang, Zhiping Song, Linfeng Li, Ji Yang, Hong Ma, Jianhua Yang, Chan Zhou, Charles C. Davis, Yuguo Wang

Research output: Contribution to journalArticle

Abstract

The plastid genomes (plastomes) of non-photosynthetic plants generally undergo gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequence and assemble the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. mongolica, and C. sinensis) and compare them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences in the entire plastome, long single copy region, and non-coding region, and different patterns of the retention/loss of functional genes. With few exceptions of putatively functional genes, massive plastid fragments, which have been lost and transferred into the mitochondrial or nuclear genomes, are non-functional. In contrast to the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.

Original languageEnglish (US)
Pages (from-to)877-892
Number of pages16
JournalJournal of experimental botany
Volume71
Issue number3
DOIs
StatePublished - Jan 23 2020

All Science Journal Classification (ASJC) codes

  • Physiology
  • Plant Science

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    Liu, X., Fu, W., Tang, Y., Zhang, W., Song, Z., Li, L., Yang, J., Ma, H., Yang, J., Zhou, C., Davis, C. C., & Wang, Y. (2020). Diverse trajectories of plastome degradation in holoparasitic Cistanche and genomic location of the lost plastid genes. Journal of experimental botany, 71(3), 877-892. https://doi.org/10.1093/jxb/erz456