Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae) : Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

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Abdullah , Henriquez , C L , Mehmood , F , Carlsen , M M , Islam , M , Waheed , M T , Poczai , P , Croat , T B & Ahmed , I 2020 , ' Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae) : Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution ' , Journal of Molecular Evolution , vol. 88 , no. 7 , pp. 562-574 . https://doi.org/10.1007/s00239-020-09958-w

Title: Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae) : Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution
Author: Abdullah,; Henriquez, Claudia L.; Mehmood, Furrukh; Carlsen, Monica M.; Islam, Madiha; Waheed, Mohammad Tahir; Poczai, Peter; Croat, Thomas B.; Ahmed, Ibrar
Contributor: University of Helsinki, Botany
Date: 2020-09
Language: eng
Number of pages: 13
Belongs to series: Journal of Molecular Evolution
ISSN: 0022-2844
URI: http://hdl.handle.net/10138/320258
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) andPothos scandens(size: 164,719 bp). The chloroplast genome ofP. scandensshowed 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 inP. scandenswhen compared withA. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 inP. scandensand 2.12 inA. 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.
Subject: Araceae
Pothoideae
Pothos
Anthurium
Inverted repeat contraction and expansion
Gene rearrangement
Gene evolution
SEQUENCE
INSIGHTS
TREE
IDENTIFICATION
ORGANIZATION
PHYLOGENY
SELECTION
DYNAMICS
MAIZE
TOOLS
1181 Ecology, evolutionary biology
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