The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).
Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.
Ming
Ray
R
Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA.
Hou
Shaobin
S
Feng
Yun
Y
Yu
Qingyi
Q
Dionne-Laporte
Alexandre
A
Saw
Jimmy H
JH
Senin
Pavel
P
Wang
Wei
W
Ly
Benjamin V
BV
Lewis
Kanako L T
KL
Salzberg
Steven L
SL
Feng
Lu
L
Jones
Meghan R
MR
Skelton
Rachel L
RL
Murray
Jan E
JE
Chen
Cuixia
C
Qian
Wubin
W
Shen
Junguo
J
Du
Peng
P
Eustice
Moriah
M
Tong
Eric
E
Tang
Haibao
H
Lyons
Eric
E
Paull
Robert E
RE
Michael
Todd P
TP
Wall
Kerr
K
Rice
Danny W
DW
Albert
Henrik
H
Wang
Ming-Li
ML
Zhu
Yun J
YJ
Schatz
Michael
M
Nagarajan
Niranjan
N
Acob
Ricelle A
RA
Guan
Peizhu
P
Blas
Andrea
A
Wai
Ching Man
CM
Ackerman
Christine M
CM
Ren
Yan
Y
Liu
Chao
C
Wang
Jianmei
J
Wang
Jianping
J
Na
Jong-Kuk
JK
Shakirov
Eugene V
EV
Haas
Brian
B
Thimmapuram
Jyothi
J
Nelson
David
D
Wang
Xiyin
X
Bowers
John E
JE
Gschwend
Andrea R
AR
Delcher
Arthur L
AL
Singh
Ratnesh
R
Suzuki
Jon Y
JY
Tripathi
Savarni
S
Neupane
Kabi
K
Wei
Hairong
H
Irikura
Beth
B
Paidi
Maya
M
Jiang
Ning
N
Zhang
Wenli
W
Presting
Gernot
G
Windsor
Aaron
A
Navajas-Pérez
Rafael
R
Torres
Manuel J
MJ
Feltus
F Alex
FA
Porter
Brad
B
Li
Yingjun
Y
Burroughs
A Max
AM
Luo
Ming-Cheng
MC
Liu
Lei
L
Christopher
David A
DA
Mount
Stephen M
SM
Moore
Paul H
PH
Sugimura
Tak
T
Jiang
Jiming
J
Schuler
Mary A
MA
Friedman
Vikki
V
Mitchell-Olds
Thomas
T
Shippen
Dorothy E
DE
dePamphilis
Claude W
CW
Palmer
Jeffrey D
JD
Freeling
Michael
M
Paterson
Andrew H
AH
Gonsalves
Dennis
D
Wang
Lei
L
Alam
Maqsudul
M
D017360:Arabidopsis / Q000235:genetics; D029441:Carica / Q000235:genetics*; D020451:Contig Mapping; D030541:Databases, Genetic; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D030821:Plants, Genetically Modified / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics; D014329:Tropical Climate
D014157:Transcription Factors