A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences

Abstract

The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies—Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae—which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated (de novo) the plastid genomes of 24 taxa together with seven published species representing all the seven subfamilies of Iridaceae and performed comparative genomics using the Illumina MiSeq platform. The plastomes of the autotrophic Iridaceae represent 79 protein-coding, 30 tRNA, and four rRNA genes, with lengths ranging from 150,062 to 164,622 bp. The phylogenetic analysis of the plastome sequences based on maximum parsimony, maximum likelihood, and Bayesian inference analyses suggested that Watsonia and Gladiolus were closely related, supported by strong support values, which differed considerably from recent phylogenetic studies. In addition, we identified genomic events, such as sequence inversions, deletions, mutations, and pseudogenization, in some species. Furthermore, the largest nucleotide variability was found in the seven plastome regions, which can be used in future phylogenetic studies. Notably, three subfamilies—Crocoideae, Nivenioideae, and Aristeoideae—shared a common ycf2 gene locus deletion. Our study is a preliminary report of a comparative study of the complete plastid genomes of 7/7 subfamilies and 9/10 tribes, elucidating the structural characteristics and shedding light on plastome evolution and phylogenetic relationships within Iridaceae. Additionally, further research is required to update the relative position of Watsonia within the tribal classification of the subfamily Crocoideae.

The complete chloroplast genome of Eremurus zoae Vved. (Asphodelaceae), an endemic species of Kyrgyz Republic

“… 2019 ), Aloe vera (NC035506), Aloe maculata (NC035505), Aloidendron pillansii (NC044761), Dianella nigra (MN239902), Xanthorrhoea preissii (NC035996), Theropogon pallidus (NC070131), Asparagus officinalis (NC034777), Scilla siberica (NC061320), Milla biflora (NC036000), Aphyllanthes monspeliensis (NC035968), Amaryllis belladonna (MZ433380), Xeronema callistemon (NC072587, Kamra et al. 2023 ), Moraea spathulata (NC072577, Kamra et al. 2023 ), and Iris petrana (NC063920, Volis et al.…”

“… 2023 ), Moraea spathulata (NC072577, Kamra et al. 2023 ), and Iris petrana (NC063920, Volis et al. 2022 ).…”

Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes

“…In accordance with recent genomic advances, several studies have been conducted on the plastid genomes of Iris. However, the Iris plastomes exhibited relatively conservative sizes and structures [31,32]. Given the significance of plastid markers with maternally inherited characteristics, identifying plastid markers with varying levels of polymorphism is of great importance to understanding the complexity of the phylogenetic relationships among Iris taxa.…”