Integrative genomics analysis of the ever-shrinking pectin methylesterase (PME) gene family in foxtail millet (Setaria italica)
Weina Ge
A # , Huilong Chen A B # , Yingchao Zhang A # , Shuyan Feng A , Shuailei Wang A , Qian Shang A , Meng Wu A , Ziqi Li A , Lan Zhang A , He Guo A , Yongchao Jin C and Xiyin Wang A *
+ Author Affiliations
- Author Affiliations
A School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China.
B School of Information Science and Technology, Yanching Institute of Technology, Langfang 065000, Hebei, China.
C College of Science, North China University of Science and Technology, Tangshan 063210, China.
* Correspondence to: wangxiyin@vip.sina.com
# These authors contributed equally to this paper
Handling Editor: Peter Bozhkov
Functional Plant Biology 49(10) 874-886 https://doi.org/10.1071/FP21319
Submitted: 5 December 2021 Accepted: 10 June 2022 Published: 4 July 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Pectin methylesterase (PME) plays a vital role in the growth and development of plants. Their genes can be classified into two types, with Type-1 having an extra domain, PMEI. PME genes in foxtail millet (Setaria italica L.) have not been identified, and their sequence features and evolution have not been explored. Here, we identified 41 foxtail millet PME genes. Decoding the pro-region, containing the PMEI domain, revealed its more active nature than the DNA encoding PME domain, easier to be lost to produce Type-2 PME genes. We inferred that the active nature of the pro-region could be related to its harbouring more repetitive DNA sequences. Further, we revealed that though whole-genome duplication and tandem duplication contributed to producing new copies of PME genes, phylogenetic analysis provided clear evidence of ever-shrinking gene family size in foxtail millet and the other grasses in the past 100 million years. Phylogenetic analysis also supports the existence of two gene groups, Group I and Group II, with genes in Group II being more conservative. Our research contributes to understanding how DNA sequence structure affects the functional innovation and evolution of PME genes.
Keywords: algorithm, CFVisual, CyDotian, evolution, foxtail millet, genome, grass, intragenic repeat, pectin methylesterase.
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