Sequencing and Analysis of Chrysanthemum carinatum Schousb and Kalimeris indica. The Complete Chloroplast Genomes Reveal Two Inversions and rbcL as Barcoding of the Vegetable.

Qian Yang,Boyang Zhou,Yu Gao,Yuzhuo Lu,Yuan Li,Xia Liu,Hongyuan Yang

doi:10.3390/molecules23061358

Qian Yang, Boyang Zhou + Show 5 more

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https://doi.org/10.3390/molecules23061358

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Abstract

Chrysanthemum carinatum Schousb and Kalimeris indica are widely distributed edible vegetables and the sources of the Chinese medicine Asteraceae. The complete chloroplast (cp) genome of Asteraceae usually occurs in the inversions of two regions. Hence, the cp genome sequences and structures of Asteraceae species are crucial for the cp genome genetic diversity and evolutionary studies. Hence, in this paper, we have sequenced and analyzed for the first time the cp genome size of C. carinatum Schousb and K. indica, which are 149,752 bp and 152,885 bp, with a pair of inverted repeats (IRs) (24,523 bp and 25,003) separated by a large single copy (LSC) region (82,290 bp and 84,610) and a small single copy (SSC) region (18,416 bp and 18,269), respectively. In total, 79 protein-coding genes, 30 distinct transfer RNA (tRNA) genes, four distinct rRNA genes and two pseudogenes were found not only in C. carinatum Schousb but also in the K. indica cp genome. Fifty-two (52) and fifty-nine (59) repeats, and seventy (70) and ninety (90) simple sequence repeats (SSRs) were found in the C. carinatum Schousb and K. indica cp genomes, respectively. Codon usage analysis showed that leucine, isoleucine, and serine are the most frequent amino acids and that the UAA stop codon was the significantly favorite stop codon in both cp genomes. The two inversions, the LSC region ranging from trnC-GCA to trnG-UCC and the whole SSC region were found in both of them. The complete cp genome comparison with other Asteraceae species showed that the coding area is more conservative than the non-coding area. The phylogenetic analysis revealed that the rbcL gene is a good barcoding marker for identifying different vegetables. These results give an insight into the identification, the barcoding, and the understanding of the evolutionary model of the Asteraceae cp genome.

Highlights

IntroductionThe chloroplast (cp) genome encodes many key proteins for photosynthesis and other important metabolic processes of plants’ interactions with their environment, such as drought, salt, light, and so on, which give us insights to understand the plant biology, diversity, evolution and climatic adaptation, DNA barcoding and genetic engineering [1,2,3,4,5,6]
Chloroplasts are crucial for sustaining life on Earth
One region locates the small single copy (SSC) and the other region locates between the trnC-GCA to trnG-UCC in the large single copy (LSC) region, which maybe help shape our understanding of Compositae evolution and the adaptive versus non-adaptive processes for cellular and genomic complexity [13,14,15,16,17,18,19,20,21,22,23,24,25]

Summary

Introduction

The chloroplast (cp) genome encodes many key proteins for photosynthesis and other important metabolic processes of plants’ interactions with their environment, such as drought, salt, light, and so on, which give us insights to understand the plant biology, diversity, evolution and climatic adaptation, DNA barcoding and genetic engineering [1,2,3,4,5,6]. Interestingly, two cp genome regions have a higher inversion frequency in the sunflower family (Asteraceae) compared to most eudicots. For the Asteraceae family, 129 whole cp genomes were sequenced, of which 16 have no inversions in the SSC compared with most other land plants [24,25,26]. If there does turn out to be a relationship between inversion and certain evolutionary factors in certain systems, it would depend on the acquisition of more genome sequence information, and the relationship between the cp genome structure/content and the complexity evolutionary factor [27]

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