Comparative chloroplast genomes and phylogenetic relationships of Aglaonema modestum and five variegated cultivars of Aglaonema

Abstract

Aglaonema, commonly called Chinese evergreens, are widely used for ornamental purposes. However, attempts to identify Aglaonema species and cultivars based on leaf morphology have been challenging. In the present study, chloroplast sequences were used to elucidate the phylogenetic relationships of cultivated Aglaonema in South China. The chloroplast genomes of one green species and five variegated cultivars of Aglaonema, Aglaonema modestum, ‘Red Valentine’, ‘Lady Valentine’, ‘Hong Yan’, ‘Hong Jian’, and ‘Red Vein’, were sequenced for comparative and phylogenetic analyses. The six chloroplast genomes of Aglaonema had typical quadripartite structures, comprising a large single copy (LSC) region (91,092–91,769 bp), a small single copy (SSC) region (20,816–26,501 bp), and a pair of inverted repeat (IR) regions (21,703–26,732 bp). The genomes contained 112 different genes, including 79–80 protein coding genes, 28–29 tRNAs and 4 rRNAs. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) were generally conserved among the six sequenced genomes, but the IR-SSC boundary regions were significantly different, and ‘Red Vein’ had a distinct long repeat number and type frequency. For comparative and phylogenetic analyses, Aglaonema costatum was included; it was obtained from the GenBank database. Single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were determined among the seven Aglaonema genomes studied. Nine divergent hotspots were identified: trnH-GUG-CDS1_psbA, trnS-GCU_trnS-CGA-CDS1, rps4-trnT-UGU, trnF-GAA-ndhJ, petD-CDS2-rpoA, ycf1-ndhF, rps15-ycf1-D2, ccsA-ndhD, and trnY-GUA-trnE-UUC. Additionally, positive selection was found for rpl2, rps2, rps3, ycf1 and ycf2 based on the analyses of Ka/Ks ratios among 16 Araceae chloroplast genomes. The phylogenetic tree based on whole chloroplast genomes strongly supported monophyletic Aglaonema and clear relationships among Aroideae, Lasioideae, Lemnoideae, Monsteroideae, Orontioideae, Pothoideae and Zamioculcadoideae in the family Araceae. By contrast, protein coding gene phylogenies were poorly to strongly supported and incongruent with the whole chloroplast genome phylogenetic tree. This study provided valuable genome resources and helped identify Aglaonema species and cultivars.

Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships

“…Interestingly, of these 29 codons, twenty-eight were A/T-ending codons. The result of higher usage frequency of A/T-ending than G/C-ending was also found in Aglaonema modestum [ 29 ], Phaseolus lunatus [ 32 ], and Zingiber montanum [ 33 ].…”

“…Interestingly, the genome of C. viridis had two copies of trnG-GCC , but this tRNA gene showed only one copy in the rest of the 12 genomes (Table 2 , Table S2 ). By contrast, certain events of intron loss, gene duplication and gene loss were reported in Zingiberoideae species [ 28 ], Amorphophallus species [ 38 ] and Aglaonema cultivars [ 29 ].…”

“…IR contraction and expansion have been considered important evolutionary events in chloroplast genomes in some plants, such as genome size variation, gene duplication, and reduction of duplicate genes to one copy [ 23 – 25 , 29 , 39 ]. Our results also indicated that genome lengths and boundaries of IR expansion existed variations among these 13 genomes.…”

Antibacterial Activity of Ethanolic Extracts of Aglaonema commutatum Schott and its Cultivars against Enterococcus faecalis Strains

“…Aglaonema, commonly called Chinese evergreens, belongs to the family Araceae (Henny et al, 2008;Li et al, 2022). The Aglaonema genus comprises 21 species distributed in southeast Asia, northeast India, and southern China southward through Malaysia, New Guinea, and the Philippines (Nicolson, 1969;Govaerts and Frodin, 2002;Chen et al, 2003).…”

“…Plants belonging to this genus readily adapt to low light and low relative humidity levels encountered under interior conditions (Henny et al, 2008;Henny and Chen, 2010). These plants have been widely cultivated by hybridization and tissue-cultured mutation selection for ornamental and medical purposes (Chen et al, 2004;Henny and Chen, 2010;Li et al, 2022).…”