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Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes.

Wang BB, O'Toole M, Brendel V, Young ND - BMC Plant Biol. (2008)

Bottom Line: Intron retention is the most common form of AS in all four plant species (~50%), with slightly lower frequency in legumes compared to Arabidopsis and rice.The results also indicate that the frequency of AS in plants is comparable to that observed in mammals.Finally, our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Pathology, University of Minnesota, St, Paul, MN 55108, USA. wangx741@umn.edu

ABSTRACT

Background: Although originally thought to be less frequent in plants than in animals, alternative splicing (AS) is now known to be widespread in plants. Here we report the characteristics of AS in legumes, one of the largest and most important plant families, based on EST alignments to the genome sequences of Medicago truncatula (Mt) and Lotus japonicus (Lj).

Results: Based on cognate EST alignments alone, the observed frequency of alternatively spliced genes is lower in Mt (approximately 10%, 1,107 genes) and Lj (approximately 3%, 92 genes) than in Arabidopsis and rice (both around 20%). However, AS frequencies are comparable in all four species if EST levels are normalized. Intron retention is the most common form of AS in all four plant species (~50%), with slightly lower frequency in legumes compared to Arabidopsis and rice. This differs notably from vertebrates, where exon skipping is most common. To uncover additional AS events, we aligned ESTs from other legume species against the Mt genome sequence. In this way, 248 additional Mt genes were predicted to be alternatively spliced. We also identified 22 AS events completely conserved in two or more plant species.

Conclusion: This study extends the range of plant taxa shown to have high levels of AS, confirms the importance of intron retention in plants, and demonstrates the utility of using ESTs from related species in order to identify novel and conserved AS events. The results also indicate that the frequency of AS in plants is comparable to that observed in mammals. Finally, our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing.

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Ratio of different AS types in a reliable subset of AS events. The reliable data set consisted of AS events with multiple supporting ESTs for each isoform. IntronR is still the most abundant AS type in the subset. The error bar represents the ratio for each AS type in full data set described in Table 2.
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Figure 3: Ratio of different AS types in a reliable subset of AS events. The reliable data set consisted of AS events with multiple supporting ESTs for each isoform. IntronR is still the most abundant AS type in the subset. The error bar represents the ratio for each AS type in full data set described in Table 2.

Mentions: To minimizes false AS events caused by sequencing errors or contaminations in the EST collection, we repeated the above analysis for the subset of AS events that are supported by at least two transcript sequences [40]. As shown in Figure 3, the ratio of IntronR decreased ~5% in all plants in this subset. Mt has the lowest ratio of IntronR (45%), 6–7% lower than in At and Os. The ratio of ExonS remains unchanged compared with the full data set. In Mt and Os, 10–11% AS events are ExonS compared to 7% in At. The AltD ratio in Mt increased significantly to 21% in the subset, nearly double the ratio in At and Os. In At, the AltA ratio is ~30% compared to 23% in Mt and Os. Similar tendencies were observed for subset data with even more transcripts supporting each isoform. Both the full and subset data indicate that Mt has a lower ratio of IntronR and a higher ratio of AltD, and that At has a lower ratio of ExonS but a higher ratio of AltA.


Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes.

Wang BB, O'Toole M, Brendel V, Young ND - BMC Plant Biol. (2008)

Ratio of different AS types in a reliable subset of AS events. The reliable data set consisted of AS events with multiple supporting ESTs for each isoform. IntronR is still the most abundant AS type in the subset. The error bar represents the ratio for each AS type in full data set described in Table 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2277414&req=5

Figure 3: Ratio of different AS types in a reliable subset of AS events. The reliable data set consisted of AS events with multiple supporting ESTs for each isoform. IntronR is still the most abundant AS type in the subset. The error bar represents the ratio for each AS type in full data set described in Table 2.
Mentions: To minimizes false AS events caused by sequencing errors or contaminations in the EST collection, we repeated the above analysis for the subset of AS events that are supported by at least two transcript sequences [40]. As shown in Figure 3, the ratio of IntronR decreased ~5% in all plants in this subset. Mt has the lowest ratio of IntronR (45%), 6–7% lower than in At and Os. The ratio of ExonS remains unchanged compared with the full data set. In Mt and Os, 10–11% AS events are ExonS compared to 7% in At. The AltD ratio in Mt increased significantly to 21% in the subset, nearly double the ratio in At and Os. In At, the AltA ratio is ~30% compared to 23% in Mt and Os. Similar tendencies were observed for subset data with even more transcripts supporting each isoform. Both the full and subset data indicate that Mt has a lower ratio of IntronR and a higher ratio of AltD, and that At has a lower ratio of ExonS but a higher ratio of AltA.

Bottom Line: Intron retention is the most common form of AS in all four plant species (~50%), with slightly lower frequency in legumes compared to Arabidopsis and rice.The results also indicate that the frequency of AS in plants is comparable to that observed in mammals.Finally, our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Pathology, University of Minnesota, St, Paul, MN 55108, USA. wangx741@umn.edu

ABSTRACT

Background: Although originally thought to be less frequent in plants than in animals, alternative splicing (AS) is now known to be widespread in plants. Here we report the characteristics of AS in legumes, one of the largest and most important plant families, based on EST alignments to the genome sequences of Medicago truncatula (Mt) and Lotus japonicus (Lj).

Results: Based on cognate EST alignments alone, the observed frequency of alternatively spliced genes is lower in Mt (approximately 10%, 1,107 genes) and Lj (approximately 3%, 92 genes) than in Arabidopsis and rice (both around 20%). However, AS frequencies are comparable in all four species if EST levels are normalized. Intron retention is the most common form of AS in all four plant species (~50%), with slightly lower frequency in legumes compared to Arabidopsis and rice. This differs notably from vertebrates, where exon skipping is most common. To uncover additional AS events, we aligned ESTs from other legume species against the Mt genome sequence. In this way, 248 additional Mt genes were predicted to be alternatively spliced. We also identified 22 AS events completely conserved in two or more plant species.

Conclusion: This study extends the range of plant taxa shown to have high levels of AS, confirms the importance of intron retention in plants, and demonstrates the utility of using ESTs from related species in order to identify novel and conserved AS events. The results also indicate that the frequency of AS in plants is comparable to that observed in mammals. Finally, our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing.

Show MeSH