TY  - JOUR
A1  - Fukushima, Kenji
A1  - Pollock, David D.
T1  - Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution
JF  - Nature Communications
N2  - The origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamate 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminates project-specific biases, and expression shifts are reconstructed using gene-family-wise phylogenetic Ornstein-Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties than shifts without gene duplication. The expression properties are tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs are nonrandom, forming modular connections that are reshaped by gene duplication. Thus, if expression shifts, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. Regardless of whether the shifts are adaptive or not, this supports a major role for what might be termed preadaptive pathways of gene expression evolution.
KW  - phylogenetic trees
KW  - adaptive conflict
KW  - divergence times
KW  - duplicate genes
KW  - recent origin
KW  - package
KW  - selection
KW  - alignmen
KW  - rates
KW  - biology
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230468
VL  - 11,
ER  - 
TY  - JOUR
A1  - Zhang, Yonghong
A1  - Zheng, Lanlan
A1  - Zheng, Yan
A1  - Zhou, Chao
A1  - Huang, Ping
A1  - Xiao, Xiao
A1  - Zhao, Yongheng
A1  - Hao, Xincai
A1  - Hu, Zhubing
A1  - Chen, Qinhua
A1  - Li, Hongliang
A1  - Wang, Xuanbin
A1  - Fukushima, Kenji
A1  - Wang, Guodong
A1  - Li, Chen
T1  - Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum
JF  - Frontiers in Plant Science
N2  - Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue, and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance.
KW  - genome assembly
KW  - resveratrol biosynthesis
KW  - whole-genome duplication
KW  - medicinal plant
KW  - stress tolerance
KW  - Polygonum  cuspidatum
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-189279
SN  - 1664-462X
VL  - 10
ER  -