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Phylogenetic analyses of the genes involved in carotenoid biosynthesis in algae
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Shanshan WANG1, Lei ZHANG1, Shan CHI1, Guoliang WANG2, Xumin WANG2, Tao LIU1, *, Xuexi TANG1
Acta Oceanologica Sinica | 2018, 37(4) : 89 - 101
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Acta Oceanologica Sinica | 2018, 37(4): 89-101
• Marine Biology •
Phylogenetic analyses of the genes involved in carotenoid biosynthesis in algae
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Shanshan WANG1, Lei ZHANG1, Shan CHI1, Guoliang WANG2, Xumin WANG2, Tao LIU1, *, Xuexi TANG1
Affiliations
  • 1 College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
  • 2 CAS Key Laboratory of Genome Sciences and Information/Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
Published: 2018-04-25 doi: 10.1007/s13131-018-1178-4
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Carotenoids play a crucial role in absorbing light energy for photosynthesis, as well as in protecting chlorophyll from photodamage. In contrast to the Streptophyta, few studies have examined carotenoid biosynthetic pathways in algae, owing to a shortage of datasets. As part of the 1000 Plants Project, we sequenced and assembled the transcriptomes of 41 marine macroalgal species, including 22 rhodophytes and 19 phaeophytes, and then combined the datasets with publicly available data from GenBank (National Center for Biotechnology Information) and the U.S. Department of Energy Joint Genome Institute. As a result, we identified 68 and 79 full-length homologs in the Rhodophyta and Phaeophyceae, respectively, of seven inferred carotenoid biosynthetic genes, including the genes for phytoene synthase (PSY), phytoene desaturase (PDS), ζ-carotene desaturase (ZDS), ζ-carotene isomerase (Z-ISO), prolycopene isomerase (crtISO), lycopene β-cyclase (LCYB), and lycopene ε-cyclase (LCYE). We found that the evolutionary history of the algal carotenoid biosynthetic pathway was more complex than that of the same pathway in the Streptophyta and, more specifically, that the evolutionary history involved endosymbiotic gene transfer, gene duplication, and gene loss. Almost all of the eukaryotic algae that we examined had inherited the seven carotenoid biosynthesis genes via endosymbiotic gene transfer. Moreover, PSY, crtISO, and the ancestral lycopene cyclase gene (LCY) underwent duplication events that resulted in multiple gene copies, and the duplication and subsequent divergence of LCYB and LCYE specialized and complicated the cyclization of lycopene. Our findings also verify that the loss of LCYE in both the microphytic rhodophytes and phaeophytes explains the differences in their carotenoid patterns, when compared to the macrophytic rhodophytes. These analyses provide a molecular basis for further biochemical and physiological validation in additional algal species and should help elucidate the origin and evolution of carotenoid biosynthetic pathways.

carotenoid biosynthesis  /  algae  /  phylogenetic analysis
Shanshan WANG, Lei ZHANG, Shan CHI, Guoliang WANG, Xumin WANG, Tao LIU, Xuexi TANG. Phylogenetic analyses of the genes involved in carotenoid biosynthesis in algae[J]. Acta Oceanologica Sinica, 2018 , 37 (4) : 89 -101 . DOI: 10.1007/s13131-018-1178-4
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1 Introduction
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Carotenoids are a large family of lipophilic isoprenoid compounds that are synthesized by all photoautotrophs, as well as some nonphotosynthetic organisms (Walter and Strack, 2011; Vílchez et al., 2011). Approximately 750 kinds of natural carotenoids have been reported to date, and these compounds play a variety of roles in light harvesting and photoprotection and as stress hormones and signaling apocarotenoids (Lichtenthaler, 1987; Nisar et al., 2015; Gruszecki and Strzałka, 2005). Despite their great diversity, most of the known carotenoids are tetraterpenoids, which are composed of eight isoprenoid units (Takaichi, 2011), and the initial steps of carotenoids biosynthesis are common among algae and land plants.
To form a 40-carbon backbone, 15-cis-phytoene is the first step in the carotenoid biosynthetic pathway (Cunningham and Gantt, 1998; Sandmann, 2002). This step is finished by phytoene synthase (PSY, EC 2.5.1.32), which catalyzes the head-to-head condensation of two geranylgeranyl diphosphate molecules in a two-step reaction, with pre-phytoene diphosphate as a reaction intermediate (Dogbo et al., 1988). Then, the colorless 15-cis-phytoene is desaturated by plant-type phytoene desaturase phytoene desaturase (PDS, EC 1.3.5.5) and ζ-carotene desaturase (ZDS, EC 1.3.5.6; Sandmann, 2009; Klassen, 2010; Matthews et al., 2003; Breitenbach and Sandmann, 2005) and isomerized by ζ-carotene isomerase (Z-ISO, EC 5.2.1.12) and prolycopene isomerase (crtISO, EC 5.2.1.13; Chen et al., 2010; Chai et al., 2011; Masamoto et al., 2001; Isaacson et al., 2004; Li et al., 2007; Bartnikas et al., 1997; Yu et al., 2011) to form pink or red all-trans-lycopene. Nevertheless, Z-ISO and crtISO may be dispensable since their functions can be partially compensated by photoisomerization (Giuliano et al., 2002; Park et al., 2002; Frigaard et al., 2004). Next, cyclization at the termini of the all-trans-lycopene results in the first branching point of the carotenoid biosynthetic pathway, which either (1) introduces a β-ring to both sides of lycopene, thereby forming β-carotene, or (2) introduces an ε-ring to one side and β-ring to the other side, thereby forming α-carotene. The β- and ε-rings are formed by lycopene β-cyclase (LCYB) and lycopene ε-cyclase (LCYE), respectively (Cunningham et al., 1996; Cui et al., 2011; Krubasik and Sandmann, 2000). Subsequently, different α- and β-carotene derivatives are generated via specialized enzymatic reactions (Ladygin, 2000; Chen et al., 2007; Ruiz-Sola and Rodríguez-Concepción, 2012).
The genetic, biochemical, and molecular mechanisms of this process have been described in great detail for the Streptophyta (land plants) and various microorganisms (Ruiz-Sola and Rodríguez-Concepción, 2012; Sandmann, 1994). Nonetheless, relatively few studies have examined the process of carotenoid biosynthesis in algae, and most of the existing work has focused on microalgae, especially model organisms. Lohr et al. (2005), for example, identified most of the carotenoid biosynthetic genes of Chlamydomonas reinhardtii and conducted phylogenic analysis in order to characterize the carotenoid biosynthetic genes of the Chlorophyta, and Cunningham et al. (2007) identified 11 carotenoid biosynthetic genes in the unicellular rhodophyte Cyanidioschyzon merolae and confirmed the function of lycopene β-cyclase and β-carotene hydroxylase in order to elucidate the evolutionary history of the species’ carotenoid biosynthetic pathway. Meanwhile, Li et al. (2016) reported the carotenoid biosynthetic genes from Rhodomonas sp. Nonetheless, a full-scale phylogenetic analysis of algae has yet to be completed, since the genomes and transcriptomes and some algae, such as the macrophytic rhodophytes and the phaeophytes, have not been sequenced.
In the present study, we sequenced and assembled the transcriptomes of 22 rhodophytes and 19 phaeophytes part of the 1 000 Plants (1KP) Project (http://www.onekp.com). Then, by combining our datasets with public data from GenBank (National Center for Biotechnology Information) and the U.S. Department of Energy Joint Genome Institute (JGI), we identified seven dominant candidate genes that are involved in the early reactions of the carotenoid biosynthesis pathway (up to carotene). Our results provide unequivocal molecular evidence that most of the carotenoid biosynthetic genes are actively transcribed in algae, especially in marine rhodophytes and phaeophytes. Next, we conducted comprehensive phylogenetic analyses using publicly available sequences from cyanobacteria, plants, and other algae. These analyses should help elucidate the origin and evolution of carotenoid biosynthetic pathways.
2 Materials and methods
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2.1 Sample collection and RNA extraction
Marine rhodophyte and phaeophyte samples were collected from the coast of China from October 2010 to March 2012 (Table S1). No specific permission was required for these locations, and the study did not involve any endangered or protected species. Upon collection, the fresh samples were rinsed briefly with sterilized seawater and, then, either stored at -80°C or promptly subjected to RNA extraction.
After the algae samples were immersed in liquid nitrogen and ground into a fine powder using a chilled mortar and pestle, total RNA was extracted using either an improved CTAB method or an improved TRIzol method for the phaeophyte and rhodophyte samples, respectively (Li et al., 2012; Johnson et al., 2012). The quality and quantity of the extracted RNA were assessed using a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
2.2 Transcriptome sequencing and de novo assembly
cDNA library construction and sequencing were performed by the BGI (Shenzhen, China), using Illumina HiSeq instruments (San Diego, CA, USA). Strict read filtering was performed before the assembly. Paired-end reads with primer or adaptor sequences were removed, and reads with more than 10% of bases with quality scores of below Q20 or with more than 5% of unknown bases (Ns) were excluded. De novo assembly was performed using SOAPdenovo-Trans (Li et al., 2008a; Li et al., 2010), and Gapcloser was used fill in gaps in the scaffolds. All the transcriptomes were sequenced within the framework of the 1KP Project.
2.3 Functional annotation and identification of carotenoid biosynthetic genes
To reconstruct the algal carotenoid biosynthetic pathway, all assembled algal sequences were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automatic Annotation Server (KAAS) for functional annotation (Moriya et al., 2007). Briefly, we individually submitted the algal sequences to the server in FASTA format; selected the representative set for eukaryotes, as recommended by KAAS, and all algae and plants as the reference data; and selected the bi-directional best hit (BBH) information method for our analysis.
According to the results of the KEGG pathway analysis, seven dominant carotenoid biosynthetic genes (PSY, PDS, Z-ISO, ZDS, crtISO, LCYB, and LCYE) were analyzed further. Related nucleotide sequences were downloaded from the GenBank and JGI databases and used to search for our target sequences by means of local BLASTn, with an E-value less than 10-5. Matching sequences were manually checked for accuracy using known cDNA sequences and MEGA 5 (Tamura et al., 2011). The resulting output was filtered to exclude exact duplicates, and each sequence was analyzed independently. Afterward, the online BLASTX tool from NCBI was used to examine the homology of cDNA open reading frame sequences from the transcriptome data. All full-length sequences were uploaded to the GenBank database (Table S2).
2.4 Sequence alignments and phylogenetic analyses
Selected full-length sequences were aligned using ClustalX 2.1 (Thompson et al., 1997; Sievers et al., 2011), and Bayesian analysis was performed using MrBayes 3.1.2 (Ronquist and Huelsenbeck, 2003). The analyses were conducted as two independent runs, each of which involved four incrementally heated Metropolis-coupled Monte-Carlo Markov Chains running for 5 000 000 generations, and trees were generated every 100 generations. The first 25% of the trees were discarded during the burn-in phase, and the remaining trees were used to build a 50% majority rule consensus tree, accompanied with posterior probability values. The average standard deviation of split frequencies at the end of the run was below 0.01, indicating stationary conditions. Analysis parameters were as follows: printfreq=1 000, samplefreq=100, nchain=4, and temp=0.2. Tree visualization was implemented in FigTree v. 1.3.1 (http://tree.bio.ed.ac.uk/software/ figtree/).
3 Results
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3.1 Sequencing and unigene annotation
A total of 503 310 608 raw reads (89.2 Gb), with an average length of 180 bp, were generated from the transcriptomes of 22 rhodophytes and 19 phaeophytes, and the reads were assembled into 2 161 986 scaffolds, with an average length of 717 bp and an N50 of 1 751 bp. All the sequences were aligned against the local nr protein database, which was downloaded from NCBI, and when the E-value cutoff was set to 10-5, a total of 585 247 unigenes produced significant BLAST matches.
3.2 Carotenoid biosynthetic pathway analysis
All 41 algal transcriptome datasets were subject to KEGG pathway analysis. The numbers of partial key putative genes in the carotenoid biosynthetic pathways of marine rhodophytes and phaeophytes are listed in Table 1.
According to the results of the KEGG pathway analysis, seven dominant carotenoid biosynthetic genes (PSY, PDS, Z-ISO, ZDS, crtISO, LCYB, and LCYE) were selected, and their sequences were BLASTed against the algal transcriptomes. As a result of BLAST analysis, we identified 68 and 79 full-length homologs in the 22 rhodophyte and 19 phaeophyte transcriptomes, respectively, and we found that PSY, PDS, ZDS, crtISO, and LCYB were expressed in all 41 rhodophyte and phaeophyte species, which suggests that they are indispensable in the production of carotenes.
Notably, Z-ISO was absent in the rhodophyte transcriptomes, whereas LCYE was absent in the phaeophyte transcriptomes, and we confirmed this trend by examining published rhodophyte and ochrophyte genomes, respectively (Table S3). Therefore, it is possible that the Z-ISO gene was lost during the evolutionary history of the Rhodophyta. However, the absence of Z-ISO did not lead to the interruption of carotenoid synthesis, which indicated that the relevant isomerization may be compensated by other mechanisms, such as those involving light, as in cyanobacteria and plants (Chen et al., 2010; Masamoto et al., 2001). On the other hand, the phaeophytes were deficient in α-carotenoids, owing to the absence of LCYE, which explains why both α-carotenoids and β-carotenoids are found in macrophytic rhodophytes but only β-carotenoids are found in phaeophytes.
3.3 Duplication of the phytoene synthase gene (PSY) in algae
Homology analysis identified 13 and 11 putative PSY sequences in the rhodophyte and phaeophyte 1KP transcriptome data, respectively, and the full-length PSY cDNAs of the rhodophytes and phaeophytes ranged from 1 197 to 1 515 bp and shared 40.68%–52.23% identity.
When combined with the PSY sequences of cyanobacteria, other algae, and plants, the translated PSY amino acid sequences were used to construct a Bayesian phylogenetic tree (Fig. 1). The PSY sequences from the cyanobacteria and Glaucophyta were the first to diverge at the base of the tree, followed by two large and strongly supported (PP=1) clades that included other eukaryotic algal PSYs. This topology suggests that algae inherited PSY from cyanobacteria via endosymbiotic gene transfer (EGT).
Furthermore, the tree contained two separate gene duplication events. In aglae (expected Glaucophyta), an ancient gene duplication gave rise to two distinct PSY classes, followed by a gene loss, and both PSY classes were only retained by the Prasinophyceae. In contrast, the other chlorophytes retained only Class I PSY, and both the rhodophytes and secondary symbiotic algae (Ochrophyta, Haptophyta, and Cryptophyta) retained only Class II PSY. Then, a subsequent gene duplication event generated multiple paralogs in various chlorophytes. Although different organisms possess different PSY classes, all PSY versions share a similar substrate-Mg2+-binding site and catalytic residues, and the major differences in the genes occur in regions that are unessential for the enzymatic function (Fig. 2).
3.4 Phylogeny of common-origin algal desaturase genes: PDS and ZDS
Twenty-eight putative PDS genes and 28 putative ZDS genes were identified in the 22 rhodophyte and 19 phaeophyte transcriptomes. The shared identity (28.70%–36.56%) and similar N- and C-terminal regions of the putative PDS and ZDS genes suggests that the two phylogenetically related (Fig. 3). The Bayesian phylogenetic tree of the PDS and ZDS sequences (Fig. S1) includes two separate clusters, which prompted us to construct the Bayesian phylogenetic trees of PDS and ZDS separately.
In the Bayesian phylogenetic tree of PDS (Fig. 4), the sequences were grouped into four main clades: (1) cyanobacteria; (2) Glaucophyta; (3) Rhodophyta; and (4) Ochrophyta, Haptophyta, Cryptophyta, Chlorophyta, and Streptophyta. The topological structure indicated that the primary endosymbiotic algae (Glaucophyta, Rhodophyta, and Chlorophyta) inherited PDS from cyanobacteria during primary endosymbiosis via EGT. Nevertheless, the PDS sequences from the Ochrophyta, Haptophyta, and Cryptophyta are clearly distinct from the sequences from Rhodophyta and are strongly supported (PP=1) as a sister taxon of Chlorophyta. These data suggest that secondary symbiotic algae may have shared a common PDS origin (from Chlorophyta) before their divergence.
In the Bayesian phylogenetic tree of ZDS (Fig. 5), cyanobacterial sequences clustered at the base, whereas the photosynthetic eukaryotic sequences clustered into two large and well-separated clades. Accordingly, the topology supports the hypothesis that algal ZDS has a cyanobacterial origin. In contrast to PDS (Fig. 4), the ZDS from the secondary symbiotic algae is more closely related to the rhodophyte gene than to the chlorophyte gene, which suggests that ZDS from the secondary symbiotic algae was acquired from a rhodophyte endosymbiont during the secondary endosymbiosis via EGT.
3.5 Phylogeny of different-origin algal isomerase genes: Z-ISO and crtISO
No rhodophyte Z-ISO genes were detected in the 1KP transcriptomic data or published databases. Nonetheless, 11 full-length putative rhodophyte Z-ISOs were obtained from the 1KP Project, and each sequence had an unabridged C-terminal region, which is responsible for the ζ-carotene isomerase activity. The number of crtISO copies among the marine rhodophytes and phaeophytes was different, with only a single copy of crtISO obtained from the rhodophytes and three obtained from the phaeophytes (Table S2).
Unlike the algal PDS and ZDS genes, Z-ISO is not a paralog of crtISO; and Z-ISO shares 21.46%–25.11% identity with the nitrite and nitric oxide reductase U gene (NnrU) from denitrifying bacteria, whereas crtISO only shares 16.73%–23.71% identity with the bacterial phytoene desaturase gene (crtI). Furthermore, Z-ISO mediates isomerization via electron transfer activity, which may be inherent in NnrU (Chen et al., 2010). On the other hand, the isomerization executed by crtISO is a reversible desaturation reaction that is followed by reoxidation, thereby yielding a trans-configuration of the newly formed double bond (Giuliano et al., 2002). Together, this suggests that Z-ISO has a NnrU progenitor and that crtISO is an evolutionary descendant of crtI.
The topology of the Z-ISO phylogenetic tree was relatively simple, when compared to the topologies of the other trees (Fig. 6), and indicated that Z-ISO originated from cyanobacteria. Although the grouping of sequences from the Ochrophyta, Cryptophyta, Haptophyta, and Chlorophyta was strongly supported (PP=1), the loss of the rhodophyte Z-ISO makes the origin of the secondary symbiotic algae uncertain.
The phylogenetic tree of crtISO also validated the cyanobacterial provenance of the gene in algae and plants (Fig. 7). Nonetheless, the analysis of crtISO is a little complicated, owing to its duplication in the Rhodophyta and Ochrophyta and its loss in the Rhodophyta. The Glaucophyta, Rhodophyta, and Chlorophyta obtained this gene from cyanobacteria. A prior gene duplication produced two types of crtISO genes in the Rhodophyta, followed by a gene loss in the macrophytic rhodophytes. The Ochrophyta, Cryptophyta, and Haptophyta inherited one type of crtISO from the Rhodophyta, and subsequent duplication of the gene occurred at least three times in the Ochrophyta.
3.6 Independent duplications of the lycopene cyclase gene (LCY) in algae
We found only 11 putative rhodophyte LCYBs in the 1KP transcriptomic data. Nevertheless, 14 putative LCYBs and eight putative LCYEs were identified in the rhodophyte species. It is exciting that this is the first detailed report of LCYE in the Rhodophyta. Two lycopene cyclase genes from the marine rhodophytes were highly conserved, with shared identities of 39.47%–44.04%, and all the putative rhodophyte LCYB and LCYE sequences contained three conserved motifs that were similar to those found in the LCY from Chlorophyta, Streptophyta, and cyanobacteria.
The main difference among these sequences is the three amino acid residues inserted into the putative rhodophyte LCYB (Fig. 8). The nucleotide sequences of the rhodophyte LCYE sequences were used for further searches in the genomes of Cyanidioschyzon merolae and Galdieria sulphuraria, but nothing was found. Therefore, we assumed that only macrophytic rhodophytes possess both LCYB and LCYE, whereas microphytic rhodophytes possess only LCYB. This may explain why both α- and β-carotenoids are present in macrophytic rhodophytes, whereas only β-carotenoids are present in microphytic rhodophytes.
As expected, the topological structure of the lycopene cyclase phylogenetic tree (Fig. 9) indicated that LCYs of primary endosymbiotic algae also have a cyanobacterial origin and that the secondary endosymbiotic algae acquired LCYB from a rhodophyte-like secondary endosymbiont via EGT. In addition, independent gene duplications and subsequent divergence generated LCYB and LCYE after the differentiation of each algal lineage. Moreover, the gene loss of LCYE did occur in the microphytic rhodophytes or in the Ochrophyta, according to the results of multiple alignments and phylogenetic analyses.
4 Discussion
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4.1 Cyanobacterial origin of carotenoid biosynthetic genes in diverse algae
During primary endosymbiosis, cyanobacteria were engulfed by a eukaryotic host and slowly evolved into plastids (McFadden, 2001a), and subsequently, during the secondary endosymbiosis event, eukaryotic hosts engulfed and retained a red or green alga, which ultimately resulted in the modern diversity of algae (Cavalier-Smith, 1999; Douzery et al., 2004; Bhattacharya and Medlin, 1998). Accordingly, cyanobacteria are regarded as the progenitor of the chloroplast, and since then, EGT has been a ubiquitous and continuous process in modern algae and plants, providing opportunities for gene transfer to algal genomes and the replacement of pre-existing and functionally equivalent host genes. This phenomenon seems to be a prominent mechanism governing the evolution of nucleus-encoded plastid-targeted proteins, such as carotenoid biosynthetic enzymes (Timmis et al., 2004; Martin et al., 2002; Ni et al., 2012; Keeling and Palmer, 2008; Martin and Herrmann, 1998).
The present study is in agreement with other studies and demonstrates that all seven dominant genes involved in the early reactions of carotenoid biosynthesis have cyanobacterial origins (Sandmann, 2002; Cui et al., 2011; Bhattacharya and Medlin, 1998; Martin et al., 2002). The Glaucophyta, Rhodophyta, and Chlorophyta obtained carotenoid biosynthesis genes from cyanobacteria via primary endosymbiosis-mediated EGT, whereas the phylogenetic trees of PSY, ZDS, crtISO, and LCY, indicate that the Ochrophyta, Haptophyta, and Cryptophyta acquired their genes from a rhodophyte-like organism via secondary endosymbiosis-mediated EGT. This transfer breaks down the interspecies barrier between algal lineages and has allowed algae to survive. In the present study, we found that EGT has occurred frequently among algal carotenoid biosynthetic genes and that the mechanism seems to have played an important role in the evolution of eukaryotic algae.
4.2 Duplication of carotenoid biosynthetic genes
In line with previous studies, we found that gene duplication has played an important role in the evolution of the carotenoid biosynthetic pathway (Klassen, 2010; Cui et al., 2011; Hittinger and Carroll, 2007; Tran et al., 2009). In fact, duplication events have occurred constantly among different algal lineages (Figs 1, 7 and 8), and as reported by Tran et al. (2009), the duplication of the phytoene synthase gene is a typical example. An ancient gene duplication also created the two PSY classes, and more recent gene duplication events have mainly occurred in the Chlorophyta, thereby generating various paralogs. Another similar example is the duplication of the crtISO gene. A prior gene duplication produced two kinds of crtISO in the Rhodophyta, whereas a subsequent duplication event produced additional paralogs in the Ochrophyta.
In contrast, the duplication of LCY seems more significant. An independent duplication event followed by functional divergence generated LCYB and LCYE in both cyanobacteria and algae. As a result, algae can synthesize lycopene with both β- and ε-rings, rather than with only a single ring type (Cunningham et al., 1996; Krubasik and Sandmann, 2000; Cunningham et al., 1994; Stickforth et al., 2003). Because gene duplication is necessary for genetic novelty and for environmental adaptation (Hittinger and Carroll, 2007; Tran et al., 2009), the multiple copies of carotenoid biosynthetic genes make the carotenoid biosynthetic pathway specialized and complicated, as well as flexible and adaptable. This state of affairs can also result in differential regulation in response to developmental or environmental cues (Sandmann, 2009; Krubasik and Sandmann, 2000; Li et al., 2008b).
4.3 Loss of carotenoid biosynthetic genes
There is no doubt that algae gained more cyanobacterial carotenoid biosynthetic genes via EGT and gene duplication (Ni et al., 2012; Tran et al., 2009). Nevertheless, the loss of specific genes is also an important mechanism in the evolution of the carotenoid biosynthetic pathway. The role of gene loss in the evolution of PSY is relatively complicated, in that the Chlorophyta (except the Prasinophyceae) and Streptophyta only retained Class I PSY, whereas the Rhodophyta and secondary endosymbiotic algae only retained Class II PSY. In contrast, the loss of the rhodophyte Z-ISO is extraordinarily complete, and the continued synthesis of ζ-carotene suggests that rhodophytes might use light to compensate for the isomerization, as in cyanobacteria and plants (Takaichi, 2011; Breitenbach and Sandmann, 2005; Chen et al., 2010; Masamoto et al., 2001; Takaichi et al., 2016). Meanwhile, both α-carotene and its derivatives are absent in the Cyanidiophyceae, Ochrophyta, Haptophyta, and Cryptophyta, which suggests that the loss of LCYE prevents the formation of ε-rings. Taken together, these data indicate that differential gene loss has caused an unbalanced distribution of genes among the algal lineages. It is also interesting that every duplication event was associated with subsequent gene loss. This phenomenon may result from evolutionary adaptation to various environments (Bhattacharya and Medlin, 1998; Lund et al., 2008; McFadden, 2001b; Millen et al., 2001). In summary, the present study provides a comprehensive analysis of carotenoid biosynthetic genes in algae and reveals that EGT, gene duplication, and gene loss have all contributed to the successful evolution of the carotenoid biosynthetic pathway. These findings provide a molecular basis for further biochemical and physiological validation in additional algal species and should help elucidate the origin and evolution of the carotenoid biosynthetic pathway. In addition, the present study analyzes the phylogenetics of algal Z-ISO and crtISO genes. The study also raises some new questions, such as the function of multiple gene copies and the mechanism of gene loss. As additional algal omics data are published, more algal carotenoid biosynthetic genes will be explored and will help researchers answer interesting questions in this field.
Acknowledgements
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The authors are grateful to Michael Melkonian from Universität zu Köln for providing transcriptomic data for Glaucophyta, Cryptophyta, and Haptophyta.
Funding
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  • The Leading Talents Program in Taishan Industry of Shandong Province under contract No. LJNY2015010; the China Agriculture Research System under contract No. CARS-50; the Regional Demonstration Project of Marine Economic Innovation and Development under contract No. 12PYY001SF08-ZGHYDX-2; the China-ASEAN Maritime Cooperation Fund.
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doi: 10.1007/s13131-018-1178-4
  • Receive Date：2017-01-17
  • Online Date：2026-04-13
  • Published：2018-04-25
Article Data
Affiliations
History
  • Received：2017-01-17
  • Accepted：2017-06-02
Funding
The Leading Talents Program in Taishan Industry of Shandong Province under contract No. LJNY2015010; the China Agriculture Research System under contract No. CARS-50; the Regional Demonstration Project of Marine Economic Innovation and Development under contract No. 12PYY001SF08-ZGHYDX-2; the China-ASEAN Maritime Cooperation Fund.
Affiliations
    1 College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
    2 CAS Key Laboratory of Genome Sciences and Information/Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China

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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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