Genome-wide identification and comparative evolutionary analysis of the Dof transcription factor family in physic nut and castor bean

Abstract

DNA-binding with one finger (Dof) proteins comprise a plant-specific transcription factor family involved in plant growth, development and stress responses. This study presents a genome-wide comparison of Dof family genes in physic nut (Jatropha curcas) and castor bean (Ricinus communis), two Euphorbiaceae plants that have not experienced any recent whole-genome duplication. A total of 25 or 24 Dof genes were identified from physic nut and castor genomes, respectively, where JcDof genes are distributed across nine out of 11 chromosomes. Phylogenetic analysis assigned these genes into nine groups representing four subfamilies, and 24 orthologous groups were also proposed based on comparison of physic nut, castor, Arabidopsis and rice Dofs. Conserved microsynteny was observed between physic nut and castor Dof-coding scaffolds, which allowed anchoring of 23 RcDof genes to nine physic nut chromosomes. In contrast to how no recent duplicate was present in castor, two tandem duplications and one gene loss were found in the Dof gene family of physic nut. Global transcriptome profiling revealed diverse patterns of Jc/RcDof genes over various tissues, and key Dof genes involved in flower development and stress response were also identified in physic nut. These findings provide valuable information for further studies of Dof genes in physic nut and castor.

Genome-wide comparison reveals divergence of cassava and rubber aquaporin family genes after the recent whole-genome duplication

“…At approximately 117 Mya, all core eudicots, including arabidopsis, poplar, physic nut, castor, rubber, and cassava, experienced the γ event [27]. After that, physic nut and castor didn't undergo any additional WGD [3,4,17,[70][71][72], whereas arabidopsis, poplar, rubber, and cassava experienced one or two recent WGDs [1,2,5,6,9,11,12,29,30]. Up to date, genome-wide analysis of the AQP gene family has been reported in most of these species with the exception of cassava.…”

“…According to the tree, 42 MeAQPs were grouped into five subfamilies, i.e. PIP (14), TIP (13), NIP (9), SIP (2), and XIP (4). The PIP subfamily can be further divided into two phylogenetic groups (i.e.…”

“…Cassava (Manihot esculenta Crantz, 2n = 36) is a perennial shrub that belongs to Euphorbiaceae, one of the largest plant families also including rubber (Hevea brasiliensis Muell. Arg., 2n = 36), castor (Ricinus communis L., 2n = 20), and physic nut (Jatropha curcas L., 2n = 22) [1][2][3][4][5][6]. Cassava was domesticated from its wild progenitor, M. esculenta ssp.…”

Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean

“…Jatropha (also known as physic nut, Jatropha curcas L., 2 n = 22) and castor bean ( Ricinus communis L., 2 n = 20) are two economically important non-food oilseed crops of the Euphorbiaceae family (Zou et al, 2015b; Zou et al, 2018; Zou, 2018; Zou & Zhang, 2019). Jatropha is characterized as a small tree native to central America, whereas castor bean is a perennial shrub originated from Africa (Zou et al, 2016a; Zou et al, 2016b; Zou et al, 2018).…”

Peer Review #1 of "Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean (v0.1)"

“…Jatropha (also known as physic nut, Jatropha curcas L., 2n = 22) and castor bean (Ricinus communis L., 2n = 20) are two economically important non-food oilseed crops of the Euphorbiaceae family (Zou et al, 2015b(Zou et al, , 2018Zou, 2018;Zou & Zhang, 2019). Jatropha is characterized as a small tree native to central America,…”