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. 2021 Oct;104(4):368504211059973.
doi: 10.1177/00368504211059973.

The first complete chloroplast genome sequences in Resedaceae: Genome structure and comparative analysis

Dhafer Alzahrani  1 , Enas Albokhari  1   2 , Abidina Abba  1   3 , Samaila Yaradua  1   4
Affiliations

The first complete chloroplast genome sequences in Resedaceae: Genome structure and comparative analysis

Dhafer Alzahrani et al. Sci Prog. 2021 Oct.

Abstract

Caylusea hexagyna and Ochradenus baccatus are two species in the Resedaceae family. In this study, we analysed the complete plastid genomes of these two species using high-throughput sequencing technology and compared their genomic data. The length of the plastid genome of C. hexagyna was 154,390 bp while that of O. baccatus was 153,380 bp. The lengths of the inverted repeats (IR) regions were 26,526 bp and 26,558 bp, those of the large single copy (LSC) regions were 83,870 bp and 83,023 bp; and those of the small single copy (SSC) regions were 17,468 bp and 17,241 bp in C. hexagyna and O. baccatus, respectively. Both genomes consisted of 113 genes: 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Repeat analysis showed that the plastid genome included all types of repeats, with more frequent occurrences of palindromic sequences. Comparative studies of SSR markers showed that there were 256 markers in C. hexagyna and 255 in O. baccatus; the majority of the SSRs in these plastid genomes were mononucleotide repeats (A/T). All the clusters in the phylogenetic tree had high support. This study reported the first complete plastid genomes of the genera Caylusea and Ochradenus and the first for the Resedaceae family.

Keywords: Caylusea hexagyna; Ochradenus baccatus; Resedaceae; chloroplast genome (cp); genetics; phylogenetic relationships.

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Conflict of interest statement

The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Figures

Figure 1.
Figure 1.
Gene map of the C. hexagyna and O. baccatus chloroplast genomes. Genes shown outside the circles are transcribed in the counter-clockwise direction, and those inside the circles are transcribed in the clockwise direction. The coloured bars indicate functional genes. In the inner circle, the dark grey area indicates the GC content, while the light grey colour indicates the AT contents. LSC indicates the large single copy region; SSC, indicates the small single copy region, and IR indicates inverted repeats.
Figure 2.
Figure 2.
Amino acid frequencies in the protein-coding sequences of C. hexagyna and O. baccatus chloroplast genomes protein-coding sequences.
Figure 3.
Figure 3.
Number of different repeats in the chloroplast genomes of C. hexagyna and O. baccatus. P = palindromic, F = forward, R = reverse and C = complement.
Figure 4.
Figure 4.
Frequency of different SSR motifs in different repeat types in the C. hexagyna and O. baccatus chloroplast genomes.
Figure 5.
Figure 5.
Number of SSR types in the complete genomes, protein-coding regions and noncoding genes in C. hexagyna and O. baccatus.
Figure 6.
Figure 6.
Comparison of the borders of the IR, SSC and LSC regions between the two chloroplast genomes of Resedaceae.
Figure 7.
Figure 7.
The synonymous (dS) subsituation and dN/dS ratio values of 79 protein-coding genes from two Resedaceae plastid genomes.
Figure 8.
Figure 8.
Phylogenetic tree reconstruction based on the complete chloroplast genome of sixteen taxa inferred from Bayesian inference (BI) methods showing relationships within resedaceae and other families in brassicales. Numbers in the clade represent posterior probability (PP) values.
See this image and copyright information in PMC

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