Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae)
TLDR
A bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus across the milkweed genus, Asclepias is presented and is applicable to other taxa and other high- copy regions characterized by low coverage genome sequencing (genome skimming).Abstract:
Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom perl script Low frequency polymorphisms existed in all individuals (mean = 58%) Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming)read more
Citations
More filters
Modern Applied Statistics With S
TL;DR: The modern applied statistics with s is universally compatible with any devices to read, and is available in the digital library an online access to it is set as public so you can download it instantly.
Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database.
TL;DR: The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants and found a non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression.
Journal ArticleDOI
Phylogeny and photosynthesis of the grass tribe Paniceae
TL;DR: The recovered phylogeny and ancestral state reconstructions support between four and seven independent origins of C4 photosynthesis within the Paniceae and indicate which species are potentially the closest C3 sister taxa of each of these events.
Journal ArticleDOI
Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes.
David S. Gernandt,Xitlali Aguirre Dugua,Alejandra Vázquez-Lobo,Ann Willyard,Alejandra Moreno Letelier,Jorge A. Pérez de la Rosa,Daniel Piñero,Aaron Liston +7 more
TL;DR: A phylogenetic hypothesis is presented in which mostly hierarchical relationships are overlain by gene flow in Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance.
References
More filters
Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
BookDOI
Modern Applied Statistics with S
W. N. Venables,Brian D. Ripley +1 more
TL;DR: A guide to using S environments to perform statistical analyses providing both an introduction to the use of S and a course in modern statistical methods.
Journal ArticleDOI
APE: Analyses of Phylogenetics and Evolution in R language
TL;DR: UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics that provides both utility functions for reading and writing data and manipulating phylogenetic trees.
Related Papers (5)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more