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Open AccessArticle

Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae

1
Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
2
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
3
Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA
4
Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
5
Alpha Genomics Private Limited, Islamabad 45710, Pakistan
*
Authors to whom correspondence should be addressed.
Plants 2020, 9(6), 737; https://doi.org/10.3390/plants9060737
Received: 9 April 2020 / Revised: 6 June 2020 / Accepted: 8 June 2020 / Published: 11 June 2020
The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae. View Full-Text
Keywords: Araceae; chloroplast genome; substitutions; gene evolution; inverted repeats; contraction and expansion; phylogenetics Araceae; chloroplast genome; substitutions; gene evolution; inverted repeats; contraction and expansion; phylogenetics
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Abdullah; Henriquez, C.L.; Mehmood, F.; Shahzadi, I.; Ali, Z.; Waheed, M.T.; Croat, T.B.; Poczai, P.; Ahmed, I. Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae. Plants 2020, 9, 737.

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