PMID- 27185400
OWN - NLM
STAT- MEDLINE
DCOM- 20171121
LR  - 20181113
IS  - 2160-1836 (Electronic)
IS  - 2160-1836 (Linking)
VI  - 6
IP  - 7
DP  - 2016 Jul 7
TI  - Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus 
      vulgaris).
PG  - 2091-101
LID - 10.1534/g3.116.028761 [doi]
AB  - Transposons are ubiquitous genomic components that play pivotal roles in plant 
      gene and genome evolution. We analyzed two genome sequences of common bean 
      (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. 
      The family is extremely abundant, as more than 12,000 pvCACTA1 elements were 
      found. To our knowledge, this is the most abundant CACTA family reported thus 
      far. The computational and fluorescence in situ hybridization (FISH) analyses 
      indicated that the pvCACTA1 elements were concentrated in terminal regions of 
      chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, 
      WWW, W is A or T). Comparative analysis of the common bean genomes from two 
      domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 
      elements occurred after the divergence of the two common beans, and some of the 
      polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 
      elements were detected in related species but not outside the Phaseolus genus. We 
      calculated the molecular evolutionary rate of pvCACTA1 transposons using 
      orthologous elements that indicated that most transposition events likely 
      occurred before the divergence of the two gene pools. These results reveal unique 
      features and evolution of this new transposon family in the common bean genome.
CI  - Copyright (c) 2016 Gao et al.
FAU - Gao, Dongying
AU  - Gao D
AD  - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 
      30602.
FAU - Zhao, Dongyan
AU  - Zhao D
AD  - Department of Horticulture, Michigan State University, East Lansing, Michigan 
      48824.
FAU - Abernathy, Brian
AU  - Abernathy B
AD  - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 
      30602.
FAU - Iwata-Otsubo, Aiko
AU  - Iwata-Otsubo A
AD  - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 
      30602.
FAU - Herrera-Estrella, Alfredo
AU  - Herrera-Estrella A
AD  - Laboratorio Nacional de Genomica para la Biodiversidad, Cinvestav Sede Irapuato, 
      Mexico 36821.
FAU - Jiang, Ning
AU  - Jiang N
AD  - Department of Horticulture, Michigan State University, East Lansing, Michigan 
      48824.
FAU - Jackson, Scott A
AU  - Jackson SA
AD  - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 
      30602 sjackson@uga.edu.
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20160707
PL  - England
TA  - G3 (Bethesda)
JT  - G3 (Bethesda, Md.)
JID - 101566598
RN  - 0 (DNA Transposable Elements)
RN  - 0 (Plant Proteins)
SB  - IM
MH  - Base Sequence
MH  - Chromosome Mapping
MH  - *DNA Transposable Elements
MH  - *Genetic Speciation
MH  - *Genome, Plant
MH  - In Situ Hybridization, Fluorescence
MH  - Phaseolus/classification/*genetics
MH  - *Phylogeny
MH  - Plant Proteins/*genetics
MH  - Sequence Alignment
MH  - Sequence Homology, Nucleic Acid
PMC - PMC4938662
OTO - NOTNLM
OT  - CACTA
OT  - DNA transposon
OT  - Phaseolus
OT  - common bean
OT  - genome evolution
EDAT- 2016/05/18 06:00
MHDA- 2017/11/29 06:00
PMCR- 2016/05/16
CRDT- 2016/05/18 06:00
PHST- 2016/05/18 06:00 [entrez]
PHST- 2016/05/18 06:00 [pubmed]
PHST- 2017/11/29 06:00 [medline]
PHST- 2016/05/16 00:00 [pmc-release]
AID - g3.116.028761 [pii]
AID - GGG_028761 [pii]
AID - 10.1534/g3.116.028761 [doi]
PST - epublish
SO  - G3 (Bethesda). 2016 Jul 7;6(7):2091-101. doi: 10.1534/g3.116.028761.