Abstract
The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae: Anthurium huixtlense (size: 163,116 bp) and Pothos scandens (size: 164,719 bp). The chloroplast genome of P. scandens showed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small single-copy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats in P. scandens when compared with A. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 in P. scandens and 2.12 in A. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.
Highlights
IntroductionAraceae is a large and ancient monocot family that dates back to the Early Cretaceous period (Nauheimer et al 2012)
The plant family Araceae belongs to the order Alismatales
Previous studies of subfamilies Lemnoideae and Aroideae revealed unique and uneven contraction and expansion of inverted repeats (IRs) regions, which led to a variable number of genes and gene rearrangements in the chloroplast genomes of several of their respective taxa (Wang and Messing 2011; Choi et al 2017; Tian et al 2018; Kim et al 2019; Henriquez et al 2020b)
Summary
Araceae is a large and ancient monocot family that dates back to the Early Cretaceous period (Nauheimer et al 2012). This family consists of 144 genera and 3645 species (Boyce and Croat 2018). Pothoideae is the second largest subfamily, with approximately 1010 described species and approximately 2072 estimated species (Boyce and Croat 2018). The largest genera are Pothos and Anthurium, with approximately 57 and 950 described, and approximately 70 and 2000 estimated species, respectively (Boyce and Croat 2018). Pothos is distributed in south and Southeast Asia, Australia, the Malagasy region, and the Malay Archipelago, while Anthurium is a strictly Neotropical genus that ranges from southern Mexico to southern Brazil, extending into the West Indies (Mayo et al 1997; Carlsen and Croat 2013)
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