[HTML][HTML] Homoeologs: what are they and how do we infer them?

NM Glover, H Redestig, C Dessimoz - Trends in plant science, 2016 - cell.com
The evolutionary history of nearly all flowering plants includes a polyploidization event.
Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs' …

[HTML][HTML] The rubber tree genome reveals new insights into rubber production and species adaptation

C Tang, M Yang, Y Fang, Y Luo, S Gao, X Xiao, Z An… - Nature plants, 2016 - nature.com
Abstract The Para rubber tree (Hevea brasiliensis) is an economically important tropical tree
species that produces natural rubber, an essential industrial raw material. Here we present a …

Large-scale analyses of angiosperm nucleotide-binding site-leucine-rich repeat genes reveal three anciently diverged classes with distinct evolutionary patterns

ZQ Shao, JY Xue, P Wu, YM Zhang, Y Wu… - Plant …, 2016 - academic.oup.com
Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant
disease resistance gene family (R genes), with hundreds of copies occurring in individual …

ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression

Y Aoki, Y Okamura, S Tadaka, K Kinoshita… - Plant and Cell …, 2016 - academic.oup.com
Abstract ATTED-II (http://atted. jp) is a coexpression database for plant species with parallel
views of multiple coexpression data sets and network analysis tools. The user can efficiently …

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

MA Hardigan, E Crisovan, JP Hamilton, J Kim… - The Plant …, 2016 - academic.oup.com
Clonally reproducing plants have the potential to bear a significantly greater mutational load
than sexually reproducing species. To investigate this possibility, we examined the breadth …

A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

MR McKain, H Tang, JR McNeal… - Genome biology and …, 2016 - academic.oup.com
Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy
characterized by large intragenomic syntenic blocks. Three such whole-genome duplication …

SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species

D Veltri, MM Wight, JA Crouch - Nucleic Acids Research, 2016 - academic.oup.com
Defining syntenic relationships among orthologous gene clusters is a frequent undertaking
of biologists studying organismal evolution through comparative genomic approaches. With …

Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa

F Cheng, C Sun, J Wu, J Schnable… - New …, 2016 - Wiley Online Library
Subgenome dominance is an important phenomenon observed in allopolyploids after whole
genome duplication, in which one subgenome retains more genes as well as contributes …

[HTML][HTML] Genome-wide identification, characterization and expression analysis of the chalcone synthase family in maize

Y Han, T Ding, B Su, H Jiang - International journal of molecular sciences, 2016 - mdpi.com
Members of the chalcone synthase (CHS) family participate in the synthesis of a series of
secondary metabolites in plants, fungi and bacteria. The metabolites play important roles in …

Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration

M Kavas, MC Baloğlu, ES Atabay, UT Ziplar… - Molecular genetics and …, 2016 - Springer
Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial
roles in response to stress. Though, most eukaryotes carry the proteins of this family …