Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response

Abstract

Haberlea rhodopensis is a paleolithic tertiary relict species, best known as a resurrection plant with remarkable tolerance to desiccation. When exposed to severe drought stress, H. rhodopensis shows an ability to maintain the structural integrity of its photosynthetic apparatus, which re-activates easily upon rehydration. We present here the results from the assembly and annotation of the chloroplast (cp) genome of H. rhodopensis, which was further subjected to comparative analysis with the cp genomes of closely related species. H. rhodopensis showed a cp genome size of 153,099 bp, harboring a pair of inverted repeats (IR) of 25,415 bp separated by small and large copy regions (SSC and LSC) of 17,826 and 84,443 bp. The genome structure, gene order, GC content and codon usage are similar to those of the typical angiosperm cp genomes. The genome hosts 137 genes representing 70.66% of the plastome, which includes 86 protein-coding genes, 36 tRNAs, and 4 rRNAs. A comparative plastome analysis with other closely related Lamiales members revealed conserved gene order in the IR and LSC/SSC regions. A phylogenetic analysis based on protein-coding genes from 33 species defines this species as belonging to the Gesneriaceae family. From an evolutionary point of view, a site-specific selection analysis detected positively selected sites in 17 genes, most of which are involved in photosynthesis (e.g., rbcL, ndhF, accD, atpE, etc.). The observed codon substitutions may be interpreted as being a consequence of molecular adaptation to drought stress, which ensures an evolutionary advantage to H. rhodopensis.

The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

“…Among the ten most divergent coding regions in this study, matK has been considered as core universal DNA barcodes in many species (Li et al 2019), and ycf1 has recently been widely applied in plant phylogeny and DNA barcoding studies (Dong et al 2015;Yang et al 2017). Besides, accD, rps19, ccsA and ndhF have also been proved to exhibit large divergence among various plant lineages and can be applied in phylogenetic studies (Ni et al 2016;Ivanova et al 2017). The boundaries of IRs and LSC/SSC differs among various plant species (Nie et al 2012;Ni et al 2016;Yan et al 2019;Li et al 2019), and expansion/extraction of the IR regions often lead to size variation of chloroplast genomes (Wang et al 2008).…”

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

“…We speculate that relaxed neutral selection (Ka/Ks value around 1.0) and potential positive selection (Ka/Ks value greater than 1.0) of rpl23 , rpl36 , and rps7 in various species here reflects the highly diverse environments and adaptions of plants (Table S4). For gene ycf1 , it is one of the largest genes in chloroplast genome and usually has two functional copies [22,25], or one of the two copies was evolved to be a pseudogene in some plants [19,31–33] as well as in 11 mangroves ( Avicennia marina , Xylocarpus moluccensis , Hibiscus tiliaceus , Excoecaria agallocha , Bruguiera sexangula , Kandelia obovata , Rhizophora stylosa , Ceriops tagal , Sonneratia ovata , Pemphis acidula , Laguncularia racemose ). In this study, most species in Malpighiales including one mangrove Excoecaria agallocha , have ycf1 Ka/Ks values around or greater than 1.0, while about 0.4 in Malvales, Myrtales and Sapindales, and about 0.6 in Fabales and Lamiales, showing the diverse evolve rates in different species (Table S4, Figure 4).…”

Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma

“…The RSCU values represented synonymous codon bias with a high proportion of A or T at the third position, similar to the cp genomes of other angiosperms [28][29][30]. The amino acid of high RSCU values infers that the contribution functionally prevents error in the peptide or transcription process [28,30]. Overall, the characterization of three Actaea cp genomes showed that these genomes are highly conserved, similar to the cp genomes of other Actaea species [10,11].…”

“…The value of relative synonymous codon usage (RSCU) was greater than 5 for arginine (Arg), Leu and Ser, as expected ( Figure S2B). The RSCU values represented synonymous codon bias with a high proportion of A or T at the third position, similar to the cp genomes of other angiosperms [28][29][30]. The amino acid of high RSCU values infers that the contribution functionally prevents error in the peptide or transcription process [28,30].…”