Comparative analysis of the variable 3′ UTR and gene expression of the KIN and KIN-homologous LEA genes in Capsella bursa-pastoris

Peng, Tao; Peng, Lifang; Huang, Xiaojun; Wang, Jianbo

doi:10.1007/s00299-012-1290-4

Cited by 8 publications

(2 citation statements)

References 35 publications

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“…This approach of using the 3′ end of a transcript to estimate expression levels was also used in previous array technologies for estimating transcript abundance (http://www.affymetrix.com/estore/browse/level_three_category_and_children.jsp?category35871). Untranslated region (UTR) sequences have been shown to vary between gene family members (Lee et al ., ; Tao et al ., ), and as such may provide more accurate estimates of transcript abundance between family members. We observed a larger deviation and higher variation of observed/expected values in the middle of transcripts when requiring unique alignments.…”

Section: Discussionmentioning

confidence: 99%

Genomic limitations to RNA sequencing expression profiling

2015

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SUMMARYThe field of genomics has grown rapidly with the advent of massively parallel sequencing technologies, allowing for novel biological insights with regards to genomic, transcriptomic, and epigenomic variation. One widely utilized application of high-throughput sequencing is transcriptional profiling using RNA sequencing (RNAseq). Understanding the limitations of a technology is critical for accurate biological interpretations, and clear interpretation of RNAseq data can be difficult in species with complex genomes. To understand the limitations of accurate profiling of expression levels we simulated RNAseq reads from annotated gene models in several plant species including Arabidopsis, brachypodium, maize, potato, rice, soybean, and tomato. The simulated reads were aligned using various parameters such as unique versus multiple read alignments. This allowed the identification of genes recalcitrant to RNAseq analyses by having over-and/or under-estimated expression levels. In maize, over 25% of genes deviated by more than 20% from the expected count values, suggesting the need for cautious interpretation of RNAseq data for certain genes. The reasons identified for deviation from expected expression varied between species due to differences in genome structure including, but not limited to, genes encoding short transcripts, overlapping gene models, and gene family size. Utilizing existing empirical datasets we demonstrate the potential for biological misinterpretation resulting from inclusion of 'flagged genes' in analyses. While RNAseq is a powerful tool for understanding biology, there are limitations to this technology that need to be understood in order to improve our biological interpretations.

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Section: Discussionmentioning

confidence: 99%

Genomic limitations to RNA sequencing expression profiling

2015

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“…As most landlocked populations represent independent freshwater invasions, this distribution presumably reflects nonrandom survival of β‐thymosin genotypes in freshwater conditions. SNPs in 3′UTRs can alter transcriptional and/or translational regulation (Hobert, ; Ryan et al, ) and confer differential responses to abiotic stresses (Tao et al, ). We report that β‐thymosin expression in landlocked populations is higher and more responsive to salinity changes than in anadromous populations, suggesting that the gene contributes to the spectacular success of alewife in freshwater environments.…”

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Beta‐thymosin gene polymorphism associated with freshwater invasiveness of alewife (Alosa pseudoharengus)

et al. 2014

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Predicting the success of a species' colonization into a novel environment is routinely considered to be predicated on niche-space similarity and vacancy, as well as propagule pressure. The role genomic variation plays in colonization success (and the interaction with environment) may be suggested, but has not rigorously been documented. To test an hypothesis that previously observed ecotype-specific polymorphisms between anadromous and landlocked alewife (Alosa pseudoharengus) populations are an adaptive response to osmoregulatory challenges rather than a result of allele sampling at founding, we examined multiple anadromous and landlocked (colonized) populations for their allelic profiles at a conserved region (3'-UTR end) of a β-thymosin gene whose protein product plays a central role in the organization of cytoskeleton. The putatively ancestral β-thymosin allele was prevalent in anadromous populations, whereas a newly derived allele was overrepresented in landlocked populations; a third allele was exclusive to the anadromous populations. We also conducted a complementary set of salinity exposure experiments to test osmoregulatory performance of the alewife ecotypes in contrasting saline environments. The pattern of variation and results from these challenges indicate a strong association of β-thymosin with colonization success and a transition from species with an anadromous life history to one with only a freshwater component.

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Comparative analysis of alternative splicing, alternative polyadenylation and the expression of the two KIN genes from cytoplasmic male sterility cabbage (Brassica oleracea L. var. capitata L.)

Peng

Huang

et al. 2014

Mol Genet Genomics

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The KIN genes are crucial members of the cold-regulated gene family. They play exclusive roles during the developmental processes of many organs and respond to various abiotic stresses in plants. However, little is known about the regulation of KIN gene expression in cytoplasmic male sterility (CMS) cabbages (Brassica oleracea L. var. capitata L.). We carried out a genome-wide analysis to identify the KIN genes in the CMS cabbage. Two non-redundant KIN genes, named BoKIN1 (Bol021262) and BoKIN2 (Bol030498), were identified. Reverse transcriptase PCR detected alternative splicing (AS) products of BoKIN1 (four AS products) and BoKIN2 (three AS products). In addition, alternative polyadenylation (APA) was observed for BoKIN1 and BoKIN2 in the CMS cabbage, resulting in variable 3'UTRs in their transcripts. Furthermore, the transcription levels of BoKIN1-0 and BoKIN2-0, the introns of which were spliced completely, were analyzed in various organs and young leaves treated by abiotic stresses. Our data indicated that BoKIN1-0 is highly expressed in various organs, whereas BoKIN2-0 is expressed exclusively in the stamen. Our study also suggested that BoKIN1-0 was upregulated significantly in young leaves of plants exposed to abscisic acid treatment, and cold and heat stress. BoKIN1 and BoKIN2 had differential AS and APA patterns in pre-mRNA processing, and showed differences in their expression patterns and transcript levels. BoKIN1 participates widely in organ development and responds to diverse abiotic stresses, whereas BoKIN2 plays a main role in stamen development in the CMS cabbage.

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Comparative analysis of the variable 3′ UTR and gene expression of the KIN and KIN-homologous LEA genes in Capsella bursa-pastoris

Cited by 8 publications

References 35 publications

Genomic limitations to RNA sequencing expression profiling

Genomic limitations to RNA sequencing expression profiling

Beta‐thymosin gene polymorphism associated with freshwater invasiveness of alewife (Alosa pseudoharengus)

Comparative analysis of alternative splicing, alternative polyadenylation and the expression of the two KIN genes from cytoplasmic male sterility cabbage (Brassica oleracea L. var. capitata L.)

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