Transcriptional analysis of phloem-associated cells of potato

BMC Genomics
Tian LinDavid J Hannapel

Abstract

Numerous signal molecules, including proteins and mRNAs, are transported through the architecture of plants via the vascular system. As the connection between leaves and other organs, the petiole and stem are especially important in their transport function, which is carried out by the phloem and xylem, especially by the sieve elements in the phloem system. The phloem is an important conduit for transporting photosynthate and signal molecules like metabolites, proteins, small RNAs, and full-length mRNAs. Phloem sap has been used as an unadulterated source to profile phloem proteins and RNAs, but unfortunately, pure phloem sap cannot be obtained in most plant species. Here we make use of laser capture microdissection (LCM) and RNA-seq for an in-depth transcriptional profile of phloem-associated cells of both petioles and stems of potato. To expedite our analysis, we have taken advantage of the potato genome that has recently been fully sequenced and annotated. Out of the 27 k transcripts assembled that we identified, approximately 15 k were present in phloem-associated cells of petiole and stem with greater than ten reads. Among these genes, roughly 10 k are affected by photoperiod. Several RNAs from this day length-regulated gr...Continue Reading

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Citations

Jan 14, 2017·Plant Molecular Biology·Tejashree H GhateAnjan K Banerjee
Jan 27, 2017·Annual Review of Plant Biology·Byung-Kook Ham, William J Lucas
Nov 7, 2017·The New Phytologist·Muluneh TamiruMathew G Lewsey
Apr 12, 2021·Nitric Oxide : Biology and Chemistry·Ming-Yue WeiHai-Lei Zheng

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Methods Mentioned

BETA
heterografting
laser capture microdissection
RNA-seq
three-hybrid
HT-seq
laser
HTseq

Software Mentioned

MEME
intersectBed
GOseq
AmiGO
GSNAP
BEDTools
QuasiSeq
R package “ QuasiSeq ”
PALM
Blast2GO

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