Comparative Chloroplast Genome Analysis of Suaeda aralocaspica with Other Amaranthaceae Genomes

Chloroplasts are semi-autonomous organelles needful for the
food manufacturing system of plants. Chloroplast genomes are widely
studied nowadays for comparative analysis which may help elucidate
the differences between species of the same plant family. Suaeda
aralocaspica is a single-cell C4 plant species belonging to the family
Amaranthaceae under subfamily Suaedoideae. However, not all plant
species under Suaedoideae utilize C4 photosynthesis as most of its plant
species utilize C3 photosynthesis. This study therefore aims to evaluate
the chloroplast genome of S. aralocaspica and conduct a comparative
analysis with four other Amaranthaceae species. Chloroplast genome
of S. aralocaspica was obtained by chloroplast isolation and DNA
sequencing as well as by genome assembly and annotation. Genome
comparison was conducted by sequence analysis of genes as well as
the determination of tandem repeats. S. aralocaspica is 151,225 bp
length with a coding size of 77,517 bp. It has a total of 140 genes, 86 of
which are protein-coding. There are 20 duplicated genes in both IRa and
IRb and there are 16 intron-containing genes. Results from 70% cut off
sequence identity showed that S. aralocaspica varied with other species
more apparently in the arrangement of few genes such as matK, atpF,
rpoC2, rpoC1, ycf6, psbM, clpP, petB, rpl16, ndhA, and ycf1. A total
of 66 tandem repeats were found in all of the studied species, most
of which is situated in the intergenic space. Comparative chloroplast
genome analysis showed that S. aralocaspica is much closer to Suaeda
glauca and a little in variance with Suaeda acuminata and the outgroup,
Salsola tragus.