title: HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data.
abstract: Characterization of homoeallelic base-identity in allopolyploids is difficult since homeologous subgenomes are closely related and becomes further challenging if diploid-progenitor data is missing. We present HANDS2, a next-generation sequencing-based tool that enables highly accurate (>90%) genome-wide discovery of homeolog-specific base-identity in allopolyploids even in the absence of a diploid-progenitor. We applied HANDS2 to the transcriptomes of various cruciferous plants belonging to genus Brassica. Our results suggest that the three C genomes in Brassica are more similar to each other than the three A genomes, and provide important insights into the relationships between various Brassica tetraploids and their diploid-progenitors at a single-base resolution.
authors.affiliation: Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), D.H.A., Lahore 54792, Pakistan.
authors.forename: Amina
authors.initials: A
authors.lastname: Khan
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Belfield
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom.
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Harberd
authors.affiliation: Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), D.H.A., Lahore 54792, Pakistan.
authors.forename: Aziz
authors.initials: A
authors.lastname: Mithani
mesh_terms: D000483:Alleles; D001937:Brassica / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D011123:Polyploidy