Received date: 21/12/2015; Accepted date: 15/02/2016; Published date: 19/02/2016
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Until now, twenty-seven Asteraceae complete chloroplast genomes were uncovered in the Gene bank. The highly conservative nature and slow evolutionary rate of the chloroplast genome demonstrated that it was uniform enough to perform comparative studies across different species but divergent sufficiently to capture evolutionary events, which makes it a suitable and invaluable tool or molecular phylogeny and molecular ecology studies. The researches about the size, genome content, LSC, SSC, IR- LSC/SSC borders, pseudogenes and DNA barcodes of these twenty-seven complete chloroplast genomes of Asteraceae were reviewed here. Based on the above information, the complete chloroplast genome of each species provides a more accurate relationship in Asteraceae and can be used as a more suitable marker for species identification.
Chloroplast Genome, Asteraceae, Pseudogenes, DNA barcodes, Phylogenetic tree.
The family Asteraceae is a complex species belonging to the second largest family of plants in the world and consisting of 2,400 species distributed in 170 genera . With the exception of Antarctica, the Asteraceae are distributed on all continents. The extremely various expressions in secondary chemistry, inflorescence morphology and chromosome number were found in the research of Asteraceae plants . Furthermore, this family includes members of economically important food crops, herbal species, ornamentals for the cut-flower industry, weedy with the economic and ecological impact and some invasive species [3-7].
Chloroplasts (cp), which originate from ancient eubacteria invasions , are multifunctional organelles possessing their own genetic material. As the essential organelle in plant cell, it conducts photosynthesis in the presence of sunlight. The highly conservative nature and slow evolutionary rate of the chloroplast genome demonstrated that it was uniform enough to perform comparative studies across different species but divergent sufficiently to capture evolutionary events, which makes it a suitable and invaluable tool or molecular phylogeny and molecular ecology studies .
Since the publication of the first cp genome, the number of complete cp genomes available (http:// www.ncbi.nlm.nih. gov/genome) has increased rapidly thanks to the development of high-throughput technologies [3,6,9,10]. Today, there are 792 complete cp genome that were deposited in the Genebank organelle Genome Resource, while were 329 in 2014 and about 200 in 2011 [6,7]. In the meantime, from the 2012, the first complete cp genome of Lactuca sativa belonging to the family Asteraceae was published, until now, 26 other Asteraceae plants are reported in the Genebank. Among them, 12 subfamilies were found. Cynara naetica, Cynara cardunculus, Cynara cornigera and Cynara humilis  belonging to Carduoideae; Leontopodium leiolepis belonging to Leontopodium; Parthenium argentatum belonging to Parthenium; Silybum marianum belonging to Silybum subfamily; Artemisia frigida and Artemisia montana belonging to Artemisia; Aster spathulifolius and Jacobaea vulgaris belonging to Aster [2-5,11-13]. Centaurea diffusa is Centaurea species; Chrysanthemum indicum and Chrysanthemum x morifolium are Chysanthemum species; Guizotia abyssinica is Guizotia plant; Heloanthus subfamilies have 8 species were found with the whole cp genome sequences: Helianthus annuus, Helianthus decaetalus, Helianthus divaricatus, Helianthus grosseserratus, Helianthus hirsutus, Helianthus masimiliani, Helianthus strumosus and Helianthus tuberisus [5,14,15]. Praxelis clematidea  and Ageratinn adenophora are Eupatorium subfamily [6,7]. In this article, we describe the size, genome content, LSC, SSC, IR-LSC/SSC borders, Pseudogenes and DNA barcodes of the Asteraceae cp genomes. Based on the above information, the complete chloroplast genome of each species provides a more accurate relationship in Asteraceae and can be used as a more suitable marker for species identification.
Size and Genome Content
From the information of all sequenced cp genomes, most to them range from 120 to 160 kb in length and have GC contents of 30 to 40% [3,6]. The cp genomes of Asteraceae species are from 149.51 bp (As. spathulifolius) to 153.202 bp (S. marianum) and differ slightly in length (Table 1). These are the larger cp genomes of Asteraceae compared with other plants. Multiple complete Asteraceae cp genomes available provide an opportunity to compare the sequence variation within the family at the genomelevel. The sequence identity of all the twenty-seven Asteraceae cp genome was plotted using VISTA program with the annotation of A. adenophora as reference (Figure 1A-1G), percent identity plot as summarized in (Table S1). The genomes comprise more than eighty protein- coding genes from 83 (Ch. indicum) to 90 (C. diffusa) except one species: P. argentatum, it’s cp genome only contains 55 proteins-coding genes annotation in NCBI, but the number is 85 in Kumar’s paper . The number of rRNA is from seven to nine. Four genes: rrn 23, rrn 16, rrn 5 and rrn 4.5 are double for locating in the two copies of inverted repeats (IRs) can be found in majority species [6,11]. The differences are the disappear of rrn 5 in L. sativa and the join of rps19 in the rRNA in Helianthus subfamily except H. annus. The number of gene is from 106 (P. argentatum) to 138 (H. annuus) [5,12]. For the tRNA, there is also the least 17 in P. argentatum and the maximum 43 in H. annuus (Table 1). The whole aligned sequences indicate that the Asteraceae cp genomes are rather conservative, although some divergent regions are found between these genomes. Similar to other angiosperms, the coding region is more conservative than the non-coding counterpart. Of all genes, ycf1, ycf68 and rps19 gene is the most divergent [3,7]. rpoC1 gene contains two introns same with A. adenophora also shows high sequence divergence . Furthermore, a number of regions are found to show high divergence, including trnk-psbK, aptL-aptF, trnS-trnG, ndhC-trnM, psbL-petG rpl14-rpl16, and accD-psaI  (Table S1).
LSC, SSC and IR-LSC/SSC Borders
The cp genome forms a double stranded, circular molecule, which is highly conserved in size, structure and gene content . The quadripartite organization is shared by almost all cp genomes, consisting of a large-single-copy region (LSC; 80-90 kb) and a small-single-copy region (SSC; 16-27 kb), as well as two copies of inverted repeats (IRs) of ~20 to 28 kb in size [9,10]. The gene content and structure of angiosperm cp genome is highly conserved [11,12]. In 27 Asteraceae species, G. abyssinica cp genome contains one of the largest LSCs. C. diffusa has the smallest LSCs and the largest SSCs. Ar. frigida has the smallest SSC region (Figure 2). Expansion and contraction of the IR as well as gene and intron losses have been documented in a wide range of angiosperms [13,14]. Chloroplast gene order is also highly conserved among land plants, but in most instances when changes do occur, they involve one or few inversions . There are several groups of land plants that have experienced substantial numbers of cpDNA rearrangements, including conifers, the angiosperm families Campanulaceae, Fabaceae, Geraniaceae and Lobeliaceae [17,18]. Two cpDNA inversions of a large about 23kb and a smaller about 3.3 kb are shared by all major clades of Asteraceae, except members of Barnadesioideae, indicating that the two inversions may be a key future of the Asteraceae cp genomes [5,6,12,18]. The possible existence of an inverted SSC in Asteraceae cp genomes is still to be conformed but cannot be exclude given the nature of the flip-flop mechanism of the inverted repeats . In Ar. frigida, a totally inversion SSC were observed compared with other angiosperm species, such as Arabidopsis . However, the specific primers were used to validate the presumed inversion event would amplify the SSC no matter its orientation .
At the two SSC boundaries in cp genomes, the general structure was revealed in dicots (i.e., tobacco, Panax and Arabidopsis), and includes ycf1 spans and a ycf1 peseudogene adjacent to JSB in IRb . The locations of the genes: rps19, ycf1, ndhF, ycf1* and rps19* except trnH are un-conservative in Asteraceae cp genomes (Figure 2). The ycf1 gene is distributed in the SSC region or IRb/SSC region, but only locates in the IRb region in C. indicum. In Ar. Montana the rps19* gene is in the IRa region, but others in the LSC region except being disappear in As. spathulifolius, C. diffusa, Ch. indicum, Ch. x morilolium, J. vulgaris and L. sativa. The ndhF varied in distance from the IRa/SSC border, and was entirely located in the SSC region in all Asteraceae species except H. decapetalus in IRa region and S. marianim in SSC/IRa border. In both L. sativa and Ar. frigida, ndhF located only 1 bp and 75 bp near the IRb/SSC border, and both the two species are invasive plants . Compared with other monocot and dicot species, the position of the trnH gene in the cp genome is quite conserved. In general, the trnH gene is located in the IR region in the monocots, compared with its location in the LSC region in the dicots [21,22]. Same with all the dicots, in all Asteraceae species, the trnH gene is located in the LSC region .
Pseudogenes are functionless relatives of genes that have lost their gene expression in the cell or their ability to code protein . Pseudogenes often result from the accumulation of multiple mutations within a gene, whose product is not required for the survival of the organism. Although not protein-coding, the DNA of pseudogenes may be functional, similar to other kinds of non-coding DNA which can have a regulatory role . Twenty-two cp genomes were found pseudogenes among the twenty-seven Asteraceae plants (Table 1) and the different pseudogenes can be found in each cp genomes. In C. cardunculus three pseudogenes were identified: ycf68, in the IR, contains a premature stop codon in its coding sequence; the remaining two pseudogenes, ycf1 and rps19, are located in the boundary regions between IRb/SSC and Ira/SSC, respectively. The lack of their protein-coding ability is due to partial gene duplication . The same three pseudogenes can also be found in A. adenophora, Ar. Frigida and Praxelis clematiea [6,7,13]. The difference is ycf68 in the IR become pseudogene due to several premature stop codons present in its coding sequence in Ar. frigida . The atpB gene in relation to coding genes in As. spathulifolius , contained a start codon and formed a pseudogene due to deletion. The atpB gene is related to ATP synthase, and much more closely related to the rbcL gene with respect to its genetic structure. The atpB gene has often been used in evaluations of the upper family level And it also considered to be beneficial to phylogenetic research of the genus Aster and closely related groups . But in As. spathulifolius it is not registered in the Genebank. In a major invasive species, P. argentatum, twelve pseudogenes were found: atpF, ycf3, ycf4, rps12, clpP, rpl16, rps3, rpl2, rps12, ycf1, ndhA, ndhB . However, in Helianthus species, no more than two pseudogenes were found as ycf1 and rps19 in H. annuus and ycf1 in H. decapetalus. The gene ycf1 encodes a protein of unknown function that is essential, which appears to be a multi-pass trans-membrane protein, with no clear association to known functional domains [5,26].
|Species||Accession number||Size (Kb)||Protein||rRNA||tRNA||Gene||Pseudogene|
|Chrysanthemum x morifolium||NC_020092.1||151.033||85||8||35||128||-|
Table 1. Size and genes of 27 Asteraceae cp genomes.
Several studies have analyzed the phylogenetic relationships in Asteraceae family based on cp sequences. One of the most comprehensive analyses included 108 taxa . But until now, there were still no some special gene or combined genes can be the suitable DNA barcodes to discriminate all Asteraceae plants at the species level and below. For Asteraceae, the ycf1 and ndhF genes existed at the bottomed at first and ended up in a loss after gradually falling apart [12,13]. This region were known to be helpful to analysis of inter- genus evolution. The ycf1 gene is also be found the most divergent of all the genes in A.adenophora and P.argentatum . So ycf1 gene may be the best suited gene for the phylogenetic analysis even though it was no effect to some species of Asteraceae. The matK gene was used to analyze eight Asteraceae species, and it had no use to difference Parthenium with Lactuca subfamilies . Even it can provide the sufficient information to differentiate three Parthenium species, the matKbarcode did not differentiate P. argrntatum or P. argentatum or P. agentatum lines from each other . Using the combined barcodes, such as matK and psbA-trnH, the additional differentiation at the some species level and below . The genes ndhF and trnL-F were also chosen for the phylogenetic analysis of the 90 species in the Asteraceae family . Other DNA barcodes were found in the Asteraceae phylogenetic research such as trnSUGA-trnfMCAU and trnSGCU-trnCGCA, rps32-trnL and psbA-trnH and other more genes were shown in Table 2 [2,3,7,13,28,29]. In Figure 3, the combination of ndhC, ndhA and ndhG were used to analysis 27 Asteraceae species, seven species in Helianthus, two in Chrysanthemum and four in Cynara subfamily can be clustered in one group and be differentiated at species level. However, it also separated two Eupatorium species in to two groups. In Curci’s research, whole cp sequence provided a higher phylogenetic resolution than using a subset of variable characters in Cynara . With the more and more cp genomes registered in Genebank, The efficacy of the whole cp genome may be a super-barcode alongside with the reduction of sequencing costs of the Asteraceae family.
|Paper||DNA barcodes for phylogenetic tree|
|Kumar et al. ||matK, psbA-trnH, conbined matK and psbA-trnH|
|Garcia et al. ||trnSUGA-trnfMCAU, trnSGCU-trnCGCA|
|Doorduin et al. ||ndhC-trnV, ndhC-atpE, rps18-rp120,clpP, psbM-trnD, petN-psbM, rps8-rps14, ycf1, ycf3-trnS, ndhA, petD,petB, ndhl, rps8-rps3, rps15, rpoC1, psbB, rpoC2, nshG, rpoB, cemA, psaC, combined regions|
|Nie et al. ||atpA, atpB, matK, petA, petB, petD, petG, petN, psaA, psaB, psbA, psbB, psbC, psbD, psbE,psbF, psbH, psbI, psbJ, psbK, psbN, psbT, rpoB, rpoC1, rpoC2,rps8, rps11, rps14, ycf3, ndhA, ndhD, dhH, ndhF, rpoA|
|Riggins et al. ||rps32-trnL,psbA-trnH|
|Liu et al. ||ndhF，trnL-F|
|Zhang et al. ||ccsA-trnL, trnG-trnfM, rpl33-rps18, lhbA-trnG,rpoC2-rps2,cemA-petA,ndhG-ndhE,psbK-psb1,rpl16-rps3,clpP,matK,ycf3,rps15,psbH,psbI,rbcL,ycf4,ndhK,atpF,rpl20,ndhI,rps8,rpoA,infA,cemA,rps14,ndhG,ndhH, combined regions|
|Choi et al. ||accD, atpB, atpE, cemA, clpP, infA,matK, ndhC, ndhJ, ndhK, petA, petB, petD, petG, petL, psaA, psaB, psaI, psaJ,psbA, psbB, psbC, psbD, psbF, psbH, psbI, psbK, psbL, psbN, psbT, psbZ, rbcL,rpl14, rpl16, rpl20, pl22, rpl23, rpl33, rpl36, rpoA, rps3, rps4, rps8, rps11,rps14, rps16, rps18, rps19 and ycf2|
|Curci et al. ||matK,ndhD,ndhF,ndhl,rncL,rpoB and the first exon of rpoC1|
Table 2. DNA barcodes were used for phylogenetic tree in Asteraceae species.
With the uncovered information of twenty-seven Asteraceae whole cp genomes in Genebank, we can get the following conclusion: From the size of cp genome, these are the larger cp genomes of Asteraceae compared with other plants. The Asteraceae cp genomes form a double stranded, circular molecule, which is highly conserved in size, structure and gene contents same with other plants. Pseudogenes can be found in most Asteraceae species and the genes are inconvenient. For the DNA barcodes, there were still no some special gene or combined genes can be the suitable DNA barcodes to discriminate all Asteraceae plants at the species level and below. But, with the more and more cp genomes registered in Gene bank, the efficacy of the whole cp genome may be a super-barcode alongside with the reduction of sequencing costs of the Asteraceae family.
This work was supported national Science Foundation of China (No. 31360173).