Open Access

Novel exon combinations generated by alternative splicing of gene fragments mobilized by a CACTA transposon in Glycine max

BMC Plant Biology20077:38

DOI: 10.1186/1471-2229-7-38

Received: 26 January 2007

Accepted: 14 July 2007

Published: 14 July 2007



The recent discoveries of transposable elements carrying host gene fragments such as the Pack-MULEs (Mutator-like transposable elements) of maize (Zea mays), rice (Oryza sativa) and Arabidopsis thaliana, the Helitrons of maize and the Tgm-Express of soybeans, revealed a widespread genetic mechanism with the potential to rearrange genomes and create novel chimeric genes affecting genomic and proteomic diversity. Not much is known with regard to the mechanisms of gene fragment capture by those transposon elements or the expression of the captured host gene fragments. There is some evidence that chimeric transcripts can be assembled and exist in EST collections.


We report results obtained from analysis of RT-PCR derived cDNAs of the Glycine max mutant flower color gene, wp, that contains a 5.7-kb transposon (Tgm-Express1) in Intron 2 of the flavanone 3-hydroxylase gene (F3H) and is composed of five unrelated host gene fragments. The collection of cDNAs derived from the wp allele represents a multiplicity of processed RNAs varying in length and sequence that includes some identical to the correctly processed mature F3H transcript with three properly spliced exons. Surprisingly, the five gene fragments carried by the Tgm-Express1 were processed through complex alternative splicing as additional exons of the wp transcript.


The gene fragments carried by the Tgm inverted repeat ends appear to be retained as functional exons/introns within the element. The spliceosomes then select indiscriminately the canonical intron splice sites from a pre-mRNA to assemble diverse chimeric transcripts from the exons contained in the wp allele. The multiplicity and randomness of these events provide some insights into the origin and mechanism of alternatively spliced genes.


A mutation in a soybean flower color gene (Wp) encoding a flavanone 3-hydroxylase (F3H) was characterized as a novel transposon insertion, Tgm-Express1, of the CACTA superfamily, that carried multiple captured host gene fragments [1]. The most visible effect of the wp mutation is production of pink rather than purple flowers and lighter color in the seed coats (Figure 1). It has also been associated with lower oil and higher seed protein content than the purple flowered Wp isoline [2, 3].
Figure 1

Illustration of the effect of wp on flower and seed coat phenotypes. (A) Stable purple flower of plants with Wp genotype (left panel) or stable pink flower of plants with wp genotype (right panel) in lines LN89-5320-6 (i i RtW1Wp) and LN89-5322-2 (i i RtW1wp) both of which have yellow seed coats. In soybean I (CHS), R and T (F3'H) are three independent loci that control pigmentation in seed coats and W1 (F5'3'H) and Wp (F3H) were described as flower color markers, but all five loci seem to be encoding genes of the anthocyanin and proanthocyanidin pathways. Mutant alleles of those loci (i, i i , r, t, w1 and wp) affect flower, seed coat, hypocotyle or pubescence coloration [1, 28, 30, 31]. (B) Imperfect black color of seed coats of plants with iRtW1Wp genotype (left panel) as contrasted with the lighter shaded seed coats of plants with iRtW1wp genotype (right panel). Effect on the seed coat phenotype was revealed by crossing the wp allele into lines having the recessive i allele that allows spatial pigmentation of the entire seed coat [24]. The cracks on both seed coat types result from an epistatic effect of t [31]. (C) Black seed coats of plants with iRTW1Wp genotype where the T allele drives the synthesis of cyanidins (left panel) contrasted with the lighter seed coats of plants with iRTW1wp genotype (right panel). (D) Abbreviated schematic representation of the three branches leading to the synthesis of the three anthocyanin classes and the genes encoding the enzymes relevant to the present study.

The Tgm-Express1 element, like the Pack-MULEs (Mutator-like elements) of maize, rice and Arabidopsis, retroelements in rice and the Helitrons of maize contains several host gene fragments. It carries intronic and exonic regions of five genes: unknown protein (UP), cell division cycle 2 (CDC2), fructose-6-phosphate 2-kinase/fructose-2-6-biphosphatase (FPK), malate dehydrogenase (M) and cysteine synthase (CS) [1]. Little is known about how any of those transposons or retroelements acquired the gene pieces but there is some evidence that they are transcribed creating chimeric cDNAs that exist in EST (expressed sequence tag) collections [47]. Of 475 Pack-MULEs identified on chromosomes 1 and 10 of rice via computer searches, 5% were transcribed based on exact matches to full-length cDNAs [4]. Most of the transcripts (91%) were initiated from promoters at the TIRs (terminal inverted repeats) or within the element while 9% of the transcripts initiated outside the element. Three chimeric transcripts were seen in an RNA blot probed with both a sh2 and a Helitron insertion fragment probes [8]. A single 2,620 bp chimeric transcript spanning the entire Helitron including several gene fragments contained within the element has also been described [6]. The promoter was predicted to reside upstream of the Helitron insertion site.

We present here an array of 12 distinct alternatively spliced chimeric transcripts obtained via RT-PCR that were derived from the soybean wp mutant allele in which the second intron of the F3H1 gene is interrupted by the 5.7 kb transposon containing five captured host gene-fragments. The chimeric transcripts analyzed were more abundant in seed coats than in cotyledons and ranged in size from 3,108 bp to a correctly processed one of 1,422 bp that was identical to the transcript derived from the wild type Wp allele. All transcripts isolated initiated at the F3H1 gene (Wp, wp) promoter that is strongly expressed in seed coats.

Alternative splicing is a common regulatory mechanism in higher eukaryotes and the mechanisms governing it have been studied extensively in mammalian systems but sparingly in plants [9, 10]. In general, the splicing pattern of a multiexon pre-mRNA can be altered in many ways. Exons that are always spliced and included in the mature mRNA are known as constitutive exons. However, mechanistic decisions of the splicing components can result in exons that are included at times but excluded at others times from the mature mRNA. These are referred to as cassette exons. There are also occurrences of 5' and 3' alternative splice sites altering the length of some exons. In addition, the failure to remove an intron, referred to as intron retention, is also found. Genes whose pre-mRNAs have multiple locations of alternative splicing produce a family of related proteins with different allosteric regulation, protein localization, or enzymatic activity [9].

We show that the exon/intron regions of gene fragments carried by the Tgm-Express1 of the wp allele are alternatively spliced and assembled with the constitutive exons of the F3H1 gene to generate an array of chimeric transcripts encoding a variety of open reading frames (orfs). Analysis of the derived amino acid sequence from the 12 distinct wp chimeric cDNAs predicted putative chimeric orfs varying in length and frame locations.

The splicing machinery at times eliminates all extraneous (cassette) exons and introns of the Tgm-Express1 element to generate a full length transcript identical to that of the wild type gene and thus likely functional. The number of F3H molecules may be extensive enough to allow the synthesis of sufficient anthocyanin pigment that could account for the pink flower and the lighter seed coat phenotypes in the wp lines (Figure 1). On the other hand, the more complex chimeric transcripts containing cassette exons (UP, CDC2, FPK, M and CS) from the captured gene fragments in the transposon may upon translation generate products that could interfere with function of the wild type host-gene counterparts leading to secondary phenotypes. Whether any of the novel exon combinations derived from alternative splicing of the mobile exons of the Tgm-Express1 element create new phenotypes is unknown. However, there is growing evidence from both plant [11, 7] and animal [12, 13] systems that repeat sequences derived from mobile elements play a significant role in generation and evolution of novel genes and exons. The wp locus in soybean is a unique example of an insertional mutation in the act of de novo generation of fused, multiple chimeric exons through inclusion or exclusion of cassette exons carried by the element into the affected gene.


Complex aberrant expression of the flower color mutant gene wp

We discovered that a pink flower locus (Wp) of soybean encoded a flavanone 3- hydroxylase gene (F3H1) by differential screening of a cDNA soybean microarray using RNAs from mutant pink (wp) and standard purple (Wp) flower isolines [1]. We also showed that the Tgm-Express1 transposon insertion impaired expression of the mutated gene and that the F3H1 gene was strongly expressed in the seed coats but not in cotyledons [1].

Analysis of the wp allele expression by RT-PCR with a pair of F3H1 outermost 5' and 3'-primers revealed a bizarre pattern of amplification resulting in a variety of cDNA sizes from both seed coat and cotyledon RNAs (Figure 2). The broad bright band of PCR product obtained with the seed coat samples (Figure 2A) represents multiple size bands. Shorter exposure photograph of that same gel revealed at least 4 distinct bands (left most lane, Figure 2A). The wp transcriptional activity between the two tissues, cotyledons and seed coats, could be deduced from the difference in the intensity of the PCR products obtained from the two wp RNA sets (Figure 2A and 2B). Even though no hybridization to a F3H probe was apparent by RNA blots with cotyledon RNAs of either genotype (Wp and wp) [1], RT-PCR showed the existence of 1.4 kb transcripts representing the mature F3H1 gene (data not shown) and the aberrant larger transcripts from mutant line RNAs (Figure 2B).
Figure 2

Variant flavanone 3-hydroxylase cDNAs from isolines containing mutant wp alleles. (A) Ethidium bromide-stained gel showing an array of cDNA bands between 5 and 1.4 kb in size that were amplified from RNAs of seed coats of the wp mutant line LN89-5322-2 through RT-PCR reactions. The (+) and (-) at top indicate reactions with and without Superscript RTII. The bright broad bands obtained from mutant RNA samples in the (+) reactions were resolved into a group of discreet bands with shorter photographic exposure of the same gel (far left lane). (B) Ethidium bromide-stained gel showing cDNAs amplified via RT-PCR with RNA from cotyledons of the LN89-5322-2 (wp) mutant line.

Cloning the larger sized RT-PCR cDNAs from plants homozygous for the wp allele resulted in a surprising array of alternatively spliced transcripts. Sequence analysis of the multiple size cDNAs cloned from both seed coat and cotyledons revealed multiple transcripts derived from the wp allele containing the wild type gene (F3H1) exons (1, 2, 3) plus varying portions of exonic and intronic regions of the gene fragments captured by the Tgm-Express1 element that interrupts Intron 2 in the wp allele (Figure 3).
Figure 3

Schematic representation of the wp recessive allele and the novel exon combinations generated in its transcribed RNAs. (A) Represents the genomic sequence of the mutant wp allele obtained from the line LN89-5322-2 (i i RtW1wp). The introns are indicated and their length given in bp. The 5,725 bp Tgm-Express insertion in Intron 2 is drawn at top with the arrow heads representing inverted repeats and the five captured gene fragments color coded. The full length of the mutant gene is 9,251 bp. The three Exons in purple represent the cDNA of the proper spliced wild type gene 1,422 bp in size. The 7F and 1428R primers used in the PCR reactions that generated the chimeric cDNA clones shown in Figure 3B and C map at the 5' end of Exon 1 (7F) and the 3' end of Exon 3 (1428R) respectively. (B) Graphic representation of six chimeric, multi-exon cDNA clones (wp-25s, -22s, -28s, -9s, 12s, -4s) derived from seed coat RNAs of the wp mutant line via RT-PCR. These clones contained besides the F3H three Exons (1, 2, 3) varying numbers of alternatively spliced exons (solid color boxes) and introns (dashed narrower boxes) from 3 or 5 of the Tgm-Express1 captured gene fragments (UP, CDC2, FPK, M and CS). A seventh cDNA clone, wp-15s, also derived from the mutant wp line is composed only of the wild type gene (Wp) Exons 1, 2 and 3. (C) Six chimeric cDNA clones (wp-9c, -8c, -2c, -13c, -12c, -6c) derived from cotyledon RNAs of the wp mutant line via RT-PCR. All clones contained the F3H Exons (1, 2,3) with varying numbers of alternatively spliced exonic and intronic regions from the Tgm-Express1 acquired host-gene fragments separating the Exon 2-Exon 3 junction. Abbreviations: UP, unknown protein; CDC2, cell division cycle 2; FPK, fructose-6-phosphate 2-kinase/fructose-2-6-biphosphatase; M, malate dehydrogenase; CS, cysteine synthase. Two CDC2 intronic regions captured by the transposon element and sandwished between the three exonic regions (C, D and C2, Figure 2A) were spliced out to form the CDC2 exon in the chimeric transcripts (Figure 2B and C). One FPK intronic fragment captured by the transposon between two flanking exons (F and PK, Figure 2A) was also spliced out to form the FPK exon in the chimeric transcripts (Figure 2B and C). A smaller FPK intron flanked by 15 bp exon fragment (narrow orange block not named) at the 5'end (Figure 2A) is not always spliced out (Figure 2B and C).

Figure 3A shows the schematic representation of the genomic sequence of the wp allele with the Tgm-Express1 insertion in Intron 2. The number of gene fragments contained within the element and their exons (solid colored boxes) and introns (striped boxes) were revealed upon sequence analysis of the multiple transcripts derived from wp expression in seed coats (See additional file 1: Seed coat wp RT-PCR cDNA sequence alignment) and cotyledons (See additional file 2: Cotyledons wp RT-PCR cDNA sequence alignment). There were exonic portions of five distinct genes: unknown protein (UP), cell division cycle 2 (CDC2), fructose-6-phosphate 2-kinase/fructose-2-6-biphosphatase (FPK), malate dehydrogenase (M) and cysteine synthase (CS). Some of the intronic regions could be assigned to specific genes (one color stripes) while others (two colors) could not. The solid black line between the solid arrow heads (inverted repeats) could be introns or intergenic DNA regions. Including the latter, all marked intronic regions conform to the canonical 5'GT donor and 3'AG acceptor splice sites.

Figure 3B is a graphic summary of seven distinct RT-PCR cDNA clones derived from seed coat RNAs. The larger clones (wp-25s, wp-22s, wp-28s, wp-9s and wp-12s) contain beside the three exons of the F3H1 gene, all cassette exons of the Tgm-express1 gene fragments and varying intron pieces. The smaller clones (wp-4s and wp-15s) had only the F3H exons (wp-15s) or the F3H exons and three cassette exons (wp-4s). Sequence data from these clones have been deposited with the EMBL/GenBank Data Libraries under accession numbers: EF100865 (wp-25s), EF100866 (wp-22s), EF100867 (wp-28s), EF100868 (w-p9s), EF100869 (wp-12s), EF100870 (wp-4s), EF100871 (wp-15s).

Likewise, Figure 3C shows six cDNA clones obtained via RT-PCR from cotyledon RNAs. As in the case of the seed coat derived cDNA clones, the larger cotyledon cDNA clones (wp-9c, wp-8c, wp-2c and wp-13c) contained some intron fragments besides the three F3H exons and cassette exons from the Tgm-Express1 element. The smaller clones (wp-12c and wp-6c) contained only exons, the three F3H exons and the five cassette exons correctly spliced. The latter two clones diverged only by 61 bp mostly due to two splicing errors in wp-6c deleting 15 bp at the beginning of Exon 2 and 47 bp at the CDC2/FPK exons junction (See additional file 2: Cotyledons wp RT-PCR cDNA sequence alignment). Of the six cotyledon cDNAs cloned, only one (wp-8c) was identical to one (wp-22s) of the seed coat cDNA clones. Sequence data from these clones have been deposited with the EMBL/GenBank Data Libraries under accession numbers: EF100872 (wp-9c), EF100873 (wp-8c), EF100874 (wp-2c), EF100875 (wp-13c), EF100876 (wp-12c), and EF100877 (wp-6c).

Overall, we isolated 12 different transcripts synthesized from the wp allele. These are a good representation of the chimeric transcripts generated by the spliceosome machinery in the tissues examined. We conclude that the most abundant transcripts shown by the discrete bands in figure 2A (left lane) have been cloned based on their size. The four most abundant bands are between 2 and 3 kb in size as are 11 of the 12 different cloned cDNAs. Our results also demonstrated that alternative splicing at the wp allele occurs in two tissues, one (the seed coats) in which the F3H promoter is highly expressed and another (cotyledons) in which it is not.

Open reading frames of chimeric, multi-exon wp transcripts

The amino acid sequences derived from the cDNA sequences of seed coat and cotyledon wp-cDNA clones shown in Figure 3B and 3C, varied significantly from clone to clone and consequently the putative open reading frames (orfs) of these chimeric transcripts. A search for orfs consisting of more than 100 amino acids (aa) found that many were chimeric (Figure 4 and additional file 3: Seed coat wp RT-PCR cDNA derived amino acid sequences and open reading frames, and additional file 4: Cotyledon wp RT-PCR cDNA derived amino acid sequences and open reading frames). Of interest were two putative chimeric orfs present in several of the wp-cDNAs. One was composed of approximately 210 bp (70 aa) of the UP exon fragment and 192 bp (64 aa) of the CDC2 exon fragment. It was present in seed coat transcripts wp-25s, -22s, -28s, -9s, -12s, -4s, and cotyledon transcripts wp-9c, -8c, -2c, -13c, -12c, -6c, always in a (+) frame. In half the clones this orf appears as just described (seed coat wp-25s, -22s, -12s and cotyledon wp-9c, -8c, -2c) (Figure 4-D). In the other half the orf is part of a larger chimeric orf containing also the F3H1 Exon 1 and Exon 2 sequences (Figure 4-A and 4C) (seed coat wp-28s, -9s, -4s and cotyledon wp-13c, -6c, -12c). A second chimeric orf predicted for five of the wp-cDNAs (seed coat wp-25s, -22s, -9s and cotyledon wp-9c, -8c) consisted of approximately 103 bp (35 aa) of FPK/M intronic fragment and 212 bp (70 aa) of FPK exonic region, always in one of the three (-) frames (Figure 4-E). A related chimeric orf containing FPK exonic sequence of approximately 231/199 bp (77/66 aa) appears in seed coat wp-12s clone and cotyledon wp-13c and wp-6c, all three in a (+) frame (Figure 4-F).
Figure 4

Schematic of relevant chimeric and non-chimeric orfs generated by the wp allele. In order of decreasing aa length the chimeric orfs from several of the chimeric mRNAs isolated were: A (418 aa) containing F3H Exons 1 and 2, the UP and CDC2 Exons; C (293 aa) with F3H Exon 1, 3'end 16 aa, and Exon 2 plus UP and CDC2 Exons; D (143 aa) had 9 aa of the UP intron plus the UP and CDC2 Exons. E (105 aa) with 34 aa of the FPK/MDH Intron plus 71 aa of the FPK Exon; F (105 aa) had 19 aa of FPK Intron, 77 aa of FPK Exon and 9 aa of MDH Exon. The non chimeric orf B (394 aa) had the three F3H Exons identical to the ones translated from the Wp allele the only cDNA clone with this orf was wp-15s. The chimeric orfs were generated from several of the cDNAs sequenced and they are listed underneath each orf class and also the frame in each one of the clones. * The orf from the wp-6c clone was 5 aa shorter. ** The orf from the wp-6c was 2 aa longer.

The products of these chimeric orfs may not serve enzymatic functions per se but if translated, they could potentially affect the function of wild type proteins synthesized from the intact host genes (UP, CDC2 or FPK). In addition to the chimeric orfs, we also found a cDNA that reconstituted the F3H1. The seed coat wp-15s cDNA clone in the (+3) frame contained an orf of 394 amino acids identical to the orf derived from the functional allele F3H1 of the purple flower isoline (Wp) (Figure 4-B). The product of this F3H1orf has the full potential to be translated into a functional F3H enzyme.

Expression of host genes with homology to the Tgm-Express1captured gene fragments

To analyze the expression of the host genes related to the exons captured by the Tgm-Express1 element, we amplified the cassette exons from the seed coat derived wp-12 cDNA clone (Figure 3B) to generate a chimeric radiolabeled probe that would hybridized to all RNAs with homology to the probe's exon fragments. These include those transcripts derived from the related host genes as well as the chimeric transcripts expressed from the wp mutant allele. This probe contained sequence fragments with similarity to an unknown protein (UP), cell division cycle 2 (CDC2), fructose-6-phosphate 2-kinase/fructose-2-6-biphosphatase (FPK), malate dehydrogenase (M) and cysteine synthase (CS) genes.

Figure 5 shows the hybridization of the chimeric radiolabelled probe to an RNA blot containing flower bud, seed coat and cotyledon RNAs from the wp, Wp and wp m isolines. It appears that the hybridization signal in the seed coats from the wp line that contains the Tgm-Express1 insertion is greater than the signal in the Wp line that lacks the insertion, suggesting that the chimeric fragments within the wp allele are detected in the RNA blots along with hybridization to the host genes. In cotyledons on the other hand, hybridization levels to RNAs from both isolines Wp and wp were similar. Since we have previously shown that the F3H1 promoter is strongly expressed in seed coats but with practically undetectable expression in the cotyledons by RNA blot analysis [1], we deduced that the hybridization seen with cotyledon RNAs is likely to represent expression from one or more of the host genes. We have RNA blot data showing transcripts hybridizing to a soybean FPK cDNA clone (Gm-c1023-5325) of a size similar to those of the chimeric transcripts and that were more highly expressed in cotyledons of all three isolines than in seed coats (data not shown). This would explain the hybridization results observed for the cotyledons of the Wp where no chimeric transcripts should be synthesized.
Figure 5

Expression of the Tgm-Express1 captured gene fragments and related host genes in the Wp -flower color isolines. (A) RNA gel blot with total RNA samples purified from flower buds, seed coats of three developmental stages and cotyledons of two developmental stages of the flower color isolines: LN89-5320-8-53 (wp m wp m ), LN89-5320-6 (WpWp) and LN89-5322-2 (wpwp). Seed fresh weight of each seed coat and cotyledon sample in mg is shown at bottom. The chimeric DNA probe containing UP, CDC2, FPK, M and CS sequences was an amplification product from the seed coat RT-PCR derived wp-12 cDNA clone (Figure 3). (B) Ethidium bromide-stained gel prior to membrane transfer. The 25 S rRNA is shown to compare RNA sample loading.

In addition, the hybridizing RNAs shown in Figure 5 are large transcripts of size similar to those recovered by RT-PCR suggesting that most likely there are no internal transcription initiation sites within the Tgm-Express1 element to generate truncated smaller transcripts.


Plant transposable elements have long been known to cause changes in gene expression as a result of insertion or deletion in coding regions and gene promoters and their effect on RNA processing [14]. However, more than 20 years of research on tracking the movements of individual transposable elements at the molecular level has revealed only a few examples that these elements were capable of transposing non-element associated coding regions from the host genome. A part of a host gene was carried by a Mutator (Mu) related element [15] and another by the Bs1 retroviral element [16]. More recently, with the availability of entire genome sequences for rice and Arabidopsis, many Mu-like elements associated with fragments of host cellular genes have been found in those two plant species [17, 18, 4]. Bioinformatics analysis of the rice genome uncovered 898 intact retrogenes of which 380 were predicted to have chimeral protein coding sequences and several of these were confirmed by expression data [7]. A novel family of maize transposons, the Helitrons, has been found recently to be embedded with portions of cellular gene fragments [8, 19, 5, 6]. The Tgm-Express1, a member of the CACTA family, was shown to carry four genic fragments [1]. An additional exonic region, UP, was identified upon analysis of the RT-PCR cDNA sequences obtained in the present study. More significantly, we show also that the wp allele carrying the Tgm-Express1 spawns an array of chimeric transcripts resulting from alternative splicing events at this locus, some of which lead to novel open reading frames.

If one were to envision an evolutionary advantageous mechanism for the novo generation of mutations, it likely would be one that would alter the splicing of a gene's constitutive exons to produce novel proteins without the complete loss of the wild-type protein. The wp pink flower mutation of soybean that we describe offers an example of how a transposon insertion in the intron of the wild-type gene (F3H1) could generate an array of alternatively spliced transcripts with potential to be translated into novel proteins without totally losing the ability to synthesize the wild-type transcript and encoded protein. The transposon insertion, Tgm-Express1, responsible for this mutation carries five host gene fragments, UP, CDC2, FPK, M and CS, which we show are exons that are alternatively spliced with F3H1 exons. Sequence analysis of multiple RT-PCR derived cDNAs from two different tissues, the seed coat and the cotyledon, revealed the processing of at least 12 distinct putative transcripts, 11 of which contained besides the F3H exons (1, 2 and 3) varying numbers of cassette exons with or without small host gene-fragment intronic portions. In addition, transcripts with only the constitutive F3H exons were also synthesized from the wp mutant allele. Although observations of element removal from maize exons [20, 21] and introns [22] has previously been observed, the splicing of the very large wp intron of 6.44 kb (consisting of the 718 bp F3H intron 2 and the 5722 bp Tgm-Express1 transpon within it) is an unusual event. Plant introns are generally short and splicing of extremely large introns is rare [10].

In alternative splicing processes in other eukaryotic systems, splicing of the pre-messenger RNA required five ribonucleoproteins and numerous accessory proteins to form four complexes (E, A, B and C) to join two adjacent exons with the release of an intervening sequence [9]. It is remarkable to see the variety of processed transcripts that were created from the wp mutant allele leading to the precise splicing of the F3H and the cassette exons from within the Tgm-Express1 element (Figure 3B and 3C, seed coat wp-4s, wp-15s and cotyledon wp-12c and wp-6c, for example). Of greater interest also is the proper processing of the three CDC2 and two FPK exons in some of the transcripts that results in fusion of unrelated exons.

Analysis of the derived amino acid sequence from the 12 distinct wp chimeric cDNA sequences predicted putative chimeric open reading frames (orfs) varying in location and length within the cDNAs (Figure 4). Alternative splicing of the cassette exons within Tgm-Express1 creates premature termination codons in many of the transcripts which could lead to their being targets for nonsense-mediated mRNA decay, the surveillance mechanism that degrades selectively nonsense mRNAs [23]. However the larger 5'-end chimeric orfs (seed coats wp-28s, -9s, and cotyledons wp-13c and wp-6c) may have a higher chance to be translated (Figure 4-A). This orf is 418 aa, 24 aa longer than the one like the F3H wild type orf of 394 aa (Figure 4-B).

The correctly processed transcript, represented by the isolated wp-15s clone (Figure 4-B), would allow the synthesis of functional F3H protein which could explain the existence of residual anthocyanin pigment in the pink flowers and the lighter colored seed coats in plants with wpwp genotype (Figure 1). F3H function is a required step in the synthesis of all three branches of anthocyanin and proanthocyanidins (Figure 1D). The results presented here demonstrate that wp is not a null mutation and that correctly spliced F3H1 transcripts are synthesized in sufficient amounts to allow the synthesis of anthocyanin pigment coloring the pink flowers (Figure 1A) and seed coats of plants with the i, t, wp (Figure 1B) and i, T, wp, (Figure 1C) genotypes. The fact that wp is not a null mutation suggests that the residual anthocyanins being synthesized in the wp flowers are most likely the same as in the Wp purple flowered isolines. The only difference between the colors of the two phenotypes may be the amount of pigment being synthesized.

We cloned two similar F3H genomic sequences (F3H1 and F3H2) and found that the F3H2 gene is not expressed in the tissues discussed here [1]. Therefore, the residual flower and seed coat color- phenotypes displayed by wp allele (Figure 1 right panels) are not the result of the expression of other F3H family member genes elsewhere in the genome.

Except for the wild-type like orf in the wp-15 cDNA clone with the three correctly spliced Exons (1, 2 and 3), that reconstitute F3H, most other orfs of more than 100 amino acids were chimeric. The more extensive ones were composed of the two first exons of F3H and varying portions of UP and CDC2 (418 aa and 293 aa; Figure 4-A and 4C). In addition, two other chimeric orfs encoding 143 and 105 amino acids respectively were created in several of the cDNA clones analyzed. The first contains portions of UP and CDC2 sequences in (+) frames while the second has FPK and FPK/M intron-derived sequences in (-) frames (Figure 4-D and 4E). Since both the host genes and the wp chimeric transcripts appear to be weakly expressed in the tissues examined (Figure 5 and data not shown), any polypeptide fragments translated from the putative orfs, might interfere with the assembly and function of their active host protein counterparts. Thus, the CDC2 and FPK polypeptide pieces translated from the wp mutant allele may have potential to interfere with the functional enzymes translated from intact CDC2 or FPK host genes. Intriguingly, the second phenotype manifested in the wp mutant plants is seeds with lower oil and higher protein content than the Wp plants [2, 3]. Inhibition of key metabolic enzymes such as FPK could potentially influence the direction of metabolic flux resulting in decreased fatty acid metabolism and linked increases in protein synthesis.


The multiplicity of transcript isoforms described here add an additional layer of complexity reinforcing the tremendous potential these gene-fragment-loaded-transposon elements such as Tgm-Express, Pack-MULEs, Helitrons, and retroelements can have not only in disrupting or modifying gene function but in the creation of new or modified genes leading to an increase in plant genome and possibly proteome diversity. Analysis of human and other vertebrate genomes [12, 13] revealed that recently evolved exons are more likely to be alternatively spliced cassette exons originating from highly repeated DNA elements including transposons, SINEs, LINEs, and Alu repeats, emphasizing the importance of mobile elements in creating diversity during evolution of both animal and plant species.


Plant material and genotypes

The Glycine max cultivars and isolines used for this study were: LN89-5320-6 (Wp, purple-flowered plants), LN89-5322-2 (wp, a stable line with pink flowered plants), and LN89-5320-8-53 (wp m , a mutable line with chimeric flower colors or sectors of pink and purple flowers). Each is homozygous for the indicated alleles of the Wp locus. The origin, genetics, and isolation of the wp allele have been described previously [2, 3, 25, 1]. Plants were grown in the greenhouse. Seed coats dissected from seeds at varying stages of development, cotyledons of various stages of seed development, flower buds, stems, mature leaves and roots from two week old plants, and shoot tips (meristems surrounded by primordial leaves) were frozen in liquid nitrogen, freeze dried (Multi-dry lyophilazer; FTS systems), and stored at -20°C. For seed coat's (cotyledon's) developmental stages, seeds were divided into the following groups according to the fresh weight of the entire seed: 10–25 mg, 25–50 mg, 50–75 mg.

RNA extraction, purification and cDNA synthesis

Total RNA was isolated from seed coats and other soybean tissues using a phenol-chloroform and lithium chloride precipitation method [25, 26]. RNA was stored at -70°C until used.

cDNA copies of the F3H1 gene from the three isolines (LN89-5320-6, LN89-5322-2 and LN89-5320-8-53) were amplified from a first-strand cDNA pool synthesized using 1 μg of seed coat or cotyledon total RNA and the Superscript first strand synthesis system for reverse transcriptase (RT)-PCR with oligo (dT)12–18 primers (Invitrogen, San Diego). The total RNAs used for these RT-PCR reactions were treated with DNAaseI using Ambion's DNA-free kit and concentrated in Microcon YM-30 columns (Millipore, Bedford, MA). For each RNA sample, parallel reactions were allowed in the absence of Superscript (- controls) to assess the extent of DNA contamination. The sequences of the two primers used were: 5'-GCATTGCATTCTGCTATTTAATTCC-3' (7F) and 5'-AAAGACAGTGCCACTTATTTTCATT-3' (1428R). These primers map at the 5' and 3' ends of the F3H1 gene respectively. The numbering correspond to the base pair of the F3H1 gene cDNA sequence (Figure 3A)

Primer synthesis, PCR reaction conditions, cDNA cloning and DNA sequencing

Oligonucleotide primers were synthesized on an Applied Biosystems (Foster City, CA) model 394A DNA synthesizer at the Keck Center, a unit of the University of Illinois Biotechnology Center. PCR reactions were performed by an initial denaturation step at 94°C for 2 min followed by 30 cycles of denaturing at 94°C for 30 sec, annealing at 56°C for 1 min, extension at 68°C for 9 min, to end with a 10 min extension at 72°C. High-fidelity and -efficiency ExTaq (Takara Bio Inc. Otsu, Japan) polymerase was used at 0.75 units per 50 μl reaction. Amplified cDNAs were separated from oligonucleotides with a QIAquick PCR Purification kit (QIAGEN), cloned into pGem-T easy and sequenced in an ABI 3730 × l (Applied Biosystems, Inc. Foster City, CA) at the Keck Center.

RNA gel-blot analysis and cDNA probe synthesis

RNA (10 μg/sample) was electrophoresed in a 1.2% agarose-3% formaldehyde gel [27]. Size-fractionated RNAs were transferred to Optitran-supported nitrocellulose membrane (Midwest Scientific, Valley Park, MO) by capillary action as described in Sambrook et al. (1989) [27] and cross-linked with UV light (Stratagene, La Jolla, CA). Nitrocellulose RNA blots were prehybridized, hybridized, washed, and exposed to Hyperfilm (Amersham, Arlington Heights, IL) as described by Todd and Vodkin (1996) [28]. All the RNA blot results presented are from autoradiographs exposed for 7 days.

Cloned DNAs used as probes were PCR amplified, electrophoresed, and purified from the agarose using the QIAquick gel extraction kit (QIAGEN, Valencia, CA). DNA concentration of the final eluate was determined with a NanoDrop (NanoDrop Technologies, Inc. Rockland, DE). Purified DNA fragments (25–250 ng) were labeled with [a-32P]dATP by random primer reaction [29].



We thank Laura Guest and Virginia Lukas who directed the DNA sequencing and synthesis of the oligonucleotide primers. Special thanks to Kay Wallheimer for her assistance with the graphic display of figures 2 and 3, and to Katie Carberry who helped with the display of the wp-cDNAs open reading frames in the Additional Material files 3 and 4. We gratefully acknowledge support from grants of the Illinois Soybean Association, USDA, and United Soybean Board.

Authors’ Affiliations

Department of Crop Sciences, University of Illinois


  1. Zabala G, Vodkin LO: The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily. Plant Cell. 2005, 17: 2619-2632. 10.1105/tpc.105.033506.PubMedPubMed CentralView ArticleGoogle Scholar
  2. Stephens PA, Nickell CD: Inheritance of pink flower color in soybean. Crop Sci. 1992, 32: 1131-1132.View ArticleGoogle Scholar
  3. Stephens PA, Nickell CD, Vodkin LO: Pink flower color associated with increased protein and seed size in soybean. Crop Sci. 1993, 33: 1135-1137.View ArticleGoogle Scholar
  4. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR: Pack-MULE transposable elements mediate gene evolution in plants. Nature. 2004, 431: 569-573. 10.1038/nature02953.PubMedView ArticleGoogle Scholar
  5. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A: Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nature Genetics. 2005, 37: 997-627. 10.1038/ng1615.PubMedView ArticleGoogle Scholar
  6. Brunner S, Pea G, Rafalski A: Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize. Plant J. 2005, 43: 799-810. 10.1111/j.1365-313X.2005.02497.x.PubMedView ArticleGoogle Scholar
  7. Wang W, Zheng H, Fan C, Li J, Shi J, Cai Z, Liu D, Zhang J, Vang S, Lu Z, Wong GK-S, Long M, Wang J: High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell. 2006, 18: 1791-1802. 10.1105/tpc.106.041905.PubMedPubMed CentralView ArticleGoogle Scholar
  8. Lal SK, Giroux MJ, Brendel V, Vallejos E, Hannah LC: The maize genome contains a Helitron Insertion. Plant Cell. 2003, 15: 381-391. 10.1105/tpc.008375.PubMedPubMed CentralView ArticleGoogle Scholar
  9. Black DL: Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem. 2003, 72: 291-336. 10.1146/annurev.biochem.72.121801.161720.PubMedView ArticleGoogle Scholar
  10. Wang B-B, Brendel V: Genomewide comparative analysis of alternative splicing in plants. PNAS. 2006, 103: 7175-7180. 10.1073/pnas.0602039103.PubMedPubMed CentralView ArticleGoogle Scholar
  11. Bennetzen JL: Transposable elements, gene creation and genome rearrangement in flowering plants. Current Opinion in Genet & Dev. 2005, 15: 621-627. 10.1016/j.gde.2005.09.010.View ArticleGoogle Scholar
  12. Zhang XH-F, Chasin LA: Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. PNAS. 2006, 103: 13427-13432. 10.1073/pnas.0603042103.PubMedPubMed CentralView ArticleGoogle Scholar
  13. Xing J, Wang H, Belancio VP, Cordaux R, Deininger PL, Batzer MA: Emergence of primate genes by retrotransposon-mediated sequence transduction. PNAS. 2006, 103: 17608-17613. 10.1073/pnas.0603224103.PubMedPubMed CentralView ArticleGoogle Scholar
  14. Weil CF, Wessler SR: The effects of plant transposable element insertion on transcription initiation and RNA processing. Annu Rev Plant Physiol Plant Mol Biol. 1990, 41: 527-552. 10.1146/annurev.pp.41.060190.002523.View ArticleGoogle Scholar
  15. Talbert LE, Chandler VL: Characterization of a highly conserved sequence related to mutator transposable elements in maize. Mol Biol Evol. 1988, 5: 519-529.PubMedGoogle Scholar
  16. Jin Y-K, Bennetzen JL: Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bs1 retroelement of maize. Plant Cell. 1994, 6: 1177-1186. 10.1105/tpc.6.8.1177.PubMedPubMed CentralView ArticleGoogle Scholar
  17. Yu Z, Wright SI, Bureau TE: Mutator-like elements in Arabidopsis thaliana: structure, diversity, and evolution. Genetics. 2000, 156: 2019-2031.PubMedPubMed CentralGoogle Scholar
  18. Turcotte K, Srinvasan S, Bureau T: Survey of transposable elements from rice genomic sequences. Plant J. 2001, 25: 169-179. 10.1046/j.1365-313x.2001.00945.x.PubMedView ArticleGoogle Scholar
  19. Gupta S, Gallavotti A, Stryker GA, Schmidt RJ, Lal SK: A novel class of Helitron- related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol Biol. 2005, 57: 115-127. 10.1007/s11103-004-6636-z.PubMedView ArticleGoogle Scholar
  20. Wessler SR, Baran G, Varagona M: The maize transposable element Ds is spliced from RNA. Science. 1987, 237: 916-918. 10.1126/science.3039661.PubMedView ArticleGoogle Scholar
  21. Giroux MJ, Clancy M, Baier J, Ingham L, McCarty D, Hannah LC: De novo synthesis of an intron by the maize transposable element, Dissociation. PNAS. 1994, 91: 12150-12154. 10.1073/pnas.91.25.12150.PubMedPubMed CentralView ArticleGoogle Scholar
  22. Marillonnet S, Wessler SR: Retrotransposon insertion into the maize waxy gene results in tissue-specific RNA processing. Plant Cell. 1997, 9: 967-978. 10.1105/tpc.9.6.967.PubMedPubMed CentralView ArticleGoogle Scholar
  23. Lewis BP, Green RE, Brenner SE: Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. PNAS. 2003, 100: 189-192. 10.1073/pnas.0136770100.PubMedPubMed CentralView ArticleGoogle Scholar
  24. Johnson EOC, Stephens PA, Fasoula DA, Nickell CD, Vodkin LO: Instability of a novel multicolored flower trait in inbred and outcrossed soybean lines. J Hered. 1998, 89: 508-515. 10.1093/jhered/89.6.508.View ArticleGoogle Scholar
  25. McCarty D: A simple method for extraction of RNA from maize tissue. Maize Genet Coop Newsl. 1986, 60: 61.Google Scholar
  26. Wang C, Todd J, Vodkin LO: Chalcone synthase mRNA and activity are reduced in yellow soybean seed coats with dominant I alleles. Plant Physiol. 1994, 105: 739-748. 10.1104/pp.105.2.739.PubMedPubMed CentralView ArticleGoogle Scholar
  27. Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: A laboratory manual. 1989, Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2Google Scholar
  28. Todd JJ, Vodkin LO: Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell. 1996, 8: 687-699. 10.1105/tpc.8.4.687.PubMedPubMed CentralView ArticleGoogle Scholar
  29. Feinberg AP, Vogelstein B: A technique for radiolabeling DNA restriction fragments to high specific activity. Anal Biochem. 1983, 132: 6-13. 10.1016/0003-2697(83)90418-9.PubMedView ArticleGoogle Scholar
  30. Zabala G, Vodkin LO: A rearrangement resulting in small tandem repeats in the F3'5'H gene of white flower genotypes is associated with the soybean W1locus. The Plant Genome. 2007, Google Scholar
  31. Zabala G, Vodkin LO: Cloning of the pleiotropic T locus in soybean and two recessive alleles that differentially affect structure and expression of the encoded flavonoid 3' hydroxylase. Genetics. 163: 295-309.


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