Integrative genomics analysis of the ever-shrinking pectin methylesterase (PME) gene family in foxtail millet (

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.

Identification, molecular evolution, codon bias, and expansion analysis of NLP transcription factor family in foxtail millet (Setaria italica L.) and closely related crops

“…With regard to Si6G248300.1 , its three-dimensional structure was the most unique among the seven NLP proteins, and unlike the other six members, it have almost no β-folding. The unique structure hints at its distinctive function ( Ge et al, 2022 ). Also, only Si6G248300.1 was involved in biometabolic processes and had the most complex and robust protein interaction network.…”

“…We were surprised to find an evolutionary trend of gradual expansion of the NLP gene family as a whole, with more duplications than losses throughout the expansion journey. This is because all other gene families that we know about have more losses than duplications ( Song et al, 2018 ; Chen and Ge, 2022 ; Ge et al, 2022 ; Yu et al, 2022 ; Zuo et al, 2022 ). This reflects the evolutionary particularity of NLP genes, reflects the plant’s demand for NLP genes, and also reflects the functional importance of NLP genes.…”

Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages

“…Based on previous studies [ 37 , 58 ], rice, maize, sorghum, foxtail millet, green foxtail, Brachypodium , and barley can be considered representative species for Poaceae lineages. Therefore, we obtained genomic and annotation data for these seven Gramineae species from public databases.…”

“…Moreover, since the evolutionary trajectory of the grass TLP gene family is not yet known, we aimed to fill this gap and provide unique insights into the evolution of the Gramineae TLP gene family. We also performed evolutionary analysis of TLP gene families in the seven examined grass species using our previously established gene family analysis pipeline [ 36 , 37 ]. The purpose of this study was to determine whether TRD facilitated the evolution of the TLP gene family and to explore the evolutionary footprint of the TLP gene family in grass species.…”

Integrated Characterization of Cassava (Manihot esculenta) Pectin Methylesterase (MePME) Genes to Filter Candidate Gene Responses to Multiple Abiotic Stresses

“…In seed plants, PMEs belong to a super-family that is present at different numbers in different species. According to existing reports, the number of PME family members in different plant species ranges from 41 in foxtail millet [14] to 121 in tobacco [15]. In addition, the number of PME genes reported in dicotyledonous plants is generally higher than that reported in monocotyledonous plants.…”