Sequencing of 30 Citrus accessions

Overview
Analysis NameSequencing of 30 Citrus accessions
MethodIllumina HiSeq2500 (NA)
SourceNCBI SRP095606
Date performed2016-11-15

Mikeal Roose and Yoko Eck from the University of California, Riverside sequenced 30 Citrus accessions for the development of a SNP array for Citrus.  The data was deposited in NCBI under the BioProject PRJNA357637, and SRP095606. The Roose lab provided the BAM files of each of the 30 accessions aligned to the Citrus clementina v1.0 genome by Albert Wu (JGI).  The data is available for visualization in the C. clementina v1.0 JBrowse.  The BAM and BAI files are available to download on the CGD FTP site.   Below is a table that explains what the three letter abbreviations stand for for the file names.

This data was also used in Genomics of the origin and evolution of Citrus (Wu et al, 2018).

 

Abbreviation Scientific Name Common Name
MXL Citrus aurantiifolia Mexican lime
AFL Citrus australasica Red pulp finger lime
ARL Citrus australis Australian round lime
ADL Citrus glauca Australian desert lime
HYS Citrus hystrix Mauritius papeda
JAM Citrus jambhiri Schaub rough lemon
FOR Citrus japonica var. margarita Nagami kumquat
KSH Citrus kinokuni Kishu mandarin
LSB Citrus limon Frost Lisbon lemon
CPP Citrus maxima Cariappa pummelo
HUP Citrus maxima Hunan pummelo
KPP Citrus maxima Kao Phuang pummelo
MBP Citrus maxima Mato Buntan pummelo
TAP Citrus maxima Tahitian pummelo
TDP Citrus maxima Thong Dee pummelo
BUD Citrus medica Buddha's Hand citron
ETH Citrus medica Ethrog citron
QIN Citrus medica Qinlong citron
YUN Citrus medica Yunnanese citron
MIC Citrus micrantha Small-fruited papeda
CLP Citrus reshni Cleopatra mandarin
CSM Citrus reticulata Changsha mandarin
DNC Citrus reticulata Dancy mandarin
SCM Citrus reticulata Sun Chu Sha Kat mandarin
SNK Citrus sunki Sunki mandarin
TBM Citrus tachibana Tachibana orange
FDT Citrus trifoliata Flying Dragon trifoliate
PON Citrus trifoliata Pomeroy trifoliate
DUN Citrus x paradisi Duncan grapefruit
TRM Citrus x paradisi Triumph grapefruit