Abstract
In the past hundreds of millions of years, from green algae to land plants, cell walls have developed into a highly complex structure that is essential for plant growth and survival. Plant cell wall diversity and evolution can be directly investigated by chemically profiling polysaccharides and lignins in the cell walls of diverse plants and algae. With the increasingly low cost and high throughput of DNA sequencing technologies, cell wall evolution can also be studied by bioinformatics analysis of the occurrence of cell wall synthesis-related enzymes in the genomes and transcriptomes of different species. This chapter presents a bioinformatics workflow running on a Linux platform to process genomic data for such gene occurrence analysis. As a case study, cellulose synthase (CesA) and CesA-like (Csl) protein families are mined for in two newly sequenced organisms: the charophyte green alga Klebsormidium flaccidum (renamed as Klebsormidium nitens) and the fern Lygodium japonicum.
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Acknowledgments
E.F. is supported by the Research & Artistry Award of Northern Illinois University and partially supported by the National Institutes of Health (1R15GM114706) to Y.Y. R.B. was a University Honors Program Undergraduate Student of Northern Illinois University. We acknowledge the Department of Computer Science of NIU for providing free access to the Linux computing cluster Gaea and the Yin lab members for helpful discussions.
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Fitzek, E., Balazic, R., Yin, Y. (2020). Bioinformatics Analysis of Plant Cell Wall Evolution. In: Popper, Z. (eds) The Plant Cell Wall. Methods in Molecular Biology, vol 2149. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0621-6_27
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DOI: https://doi.org/10.1007/978-1-0716-0621-6_27
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