Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species
Kyung-Hee Kim,Sang Choon Lee,Junki Lee,Yeisoo Yu,Kiwoung Yang,Kiwoung Yang,Beom-Soon Choi,Hee-Jong Koh,Nomar Espinosa Waminal,Hong Il Choi,Nam-Hoon Kim,Woojong Jang,Hyun-Seung Park,Jonghoon Lee,Hyun Oh Lee,Ho Jun Joh,Hyeon Ju Lee,Jee Young Park,Sampath Perumal,Murukarthick Jayakodi,Yun Sun Lee,Backki Kim,Dario Copetti,Soonok Kim,Sunggil Kim,Ki-Byung Lim,Young-Dong Kim,Jungho Lee,Kwang Su Cho,Beom Seok Park,Rod A. Wing,Tae-Jin Yang +31 more
TLDR
A high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence is introduced, clarifying three ambiguous but important issues in the evolution of wild Oryza species.Abstract:
Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.read more
Citations
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The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses.
Yanjun Zhang,Liuwen Du,Ao Liu,Jianjun Chen,Li Wu,Weiming Hu,Wei Zhang,Kyung-Hee Kim,Kyung-Hee Kim,Sang Choon Lee,Tae-Jin Yang,Ying Wang +11 more
TL;DR: Phylogenetic relationships among the five Epimedium species based on their cp genomes showed accordance with the updated system of the genus on the whole, but reminded that the evolutionary relationships and the divisions of the species need further investigation applying more evidences.
Journal ArticleDOI
PACVr: plastome assembly coverage visualization in R
Michael Gruenstaeudl,Nils Jenke +1 more
TL;DR: ’PACVr’ is introduced, an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as the individual plastome genes and confirms sequence equality of and visualizes gene synteny between, the inverted repeat regions of the input genome.
Journal ArticleDOI
Practical considerations for plant phylogenomics.
TL;DR: The most recent advances in plant phylogenomic methods are reviewed and recommendations for project‐dependent best practices and considerations are made, focusing on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address.
Journal ArticleDOI
A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions
Jeffery M. Saarela,Sean V. Burke,William P. Wysocki,Matthew D. Barrett,Matthew D. Barrett,Lynn G. Clark,Joseph M. Craine,Paul M. Peterson,Robert J. Soreng,Maria S. Vorontsova,Melvin R. Duvall +10 more
TL;DR: resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
Journal ArticleDOI
Genome and evolution of the shade-requiring medicinal herb Panax ginseng.
Nam-Hoon Kim,Murukarthick Jayakodi,Sang Choon Lee,Beom-Soon Choi,Woojong Jang,Junki Lee,Hyun Hee Kim,Nomar Espinosa Waminal,Nomar Espinosa Waminal,Meiyappan Lakshmanan,Binh van Nguyen,Yun Sun Lee,Hyun-Seung Park,Hyun Jo Koo,Jee Young Park,Sampath Perumal,Ho Jun Joh,Hana Lee,Jin-Kyung Kim,In Seo Kim,Kyung-Hee Kim,Lokanand Koduru,Kyo Bin Kang,Sang Hyun Sung,Yeisoo Yu,Daniel S. Park,Doil Choi,Eunyoung Seo,Seungill Kim,Young-Chang Kim,Dong Yun Hyun,Youn-Il Park,Changsoo Kim,Tae-Ho Lee,Hyun Uk Kim,Moon Soo Soh,Yi Lee,Jun Gyo In,Heui Soo Kim,Yong-Min Kim,Deok-Chun Yang,Rod A. Wing,Dong-Yup Lee,Dong-Yup Lee,Andrew H. Paterson,Tae-Jin Yang +45 more
TL;DR: Functional and evolutionary analyses suggest that production of pharmacologically important dammarane‐type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light.
References
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TL;DR: A map-based, finished quality sequence that covers 95% of the 389 Mb rice genome, including virtually all of the euchromatin and two complete centromeres, and finds evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes.