Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

Daniel L E Waters, Catherine J. Nock, Ryuji Ishikawa, Nicole Rice, Robert J. Henry

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of AustralianO. rufipogon and O.meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The AustralianO. rufipogon may be a perennial form of O.meridionalis.

Original languageEnglish
Pages (from-to)211-217
Number of pages7
JournalEcology and Evolution
Volume2
Issue number1
DOIs
Publication statusPublished - 2012

Fingerprint

wild rice
chloroplast
Oryza sativa
rice
genome
Oryza rufipogon
Oryza australiensis
Oryza
single nucleotide polymorphism
germplasm
chloroplasts
wild population
chloroplast genome
polymorphism
sampling

Cite this

Waters, Daniel L E ; Nock, Catherine J. ; Ishikawa, Ryuji ; Rice, Nicole ; Henry, Robert J. / Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. In: Ecology and Evolution. 2012 ; Vol. 2, No. 1. pp. 211-217.
@article{c6bf55be863749109bec1658631da011,
title = "Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice",
abstract = "Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of AustralianO. rufipogon and O.meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The AustralianO. rufipogon may be a perennial form of O.meridionalis.",
keywords = "Chloroplast genome, Oryza meridionalis, Oryza rufipogon, Oryza sativa, Wild rice",
author = "Waters, {Daniel L E} and Nock, {Catherine J.} and Ryuji Ishikawa and Nicole Rice and Henry, {Robert J.}",
year = "2012",
doi = "10.1002/ece3.66",
language = "English",
volume = "2",
pages = "211--217",
journal = "Ecology and Evolution",
issn = "2045-7758",
publisher = "John Wiley & Sons",
number = "1",

}

Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. / Waters, Daniel L E; Nock, Catherine J.; Ishikawa, Ryuji; Rice, Nicole; Henry, Robert J.

In: Ecology and Evolution, Vol. 2, No. 1, 2012, p. 211-217.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

AU - Waters, Daniel L E

AU - Nock, Catherine J.

AU - Ishikawa, Ryuji

AU - Rice, Nicole

AU - Henry, Robert J.

PY - 2012

Y1 - 2012

N2 - Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of AustralianO. rufipogon and O.meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The AustralianO. rufipogon may be a perennial form of O.meridionalis.

AB - Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of AustralianO. rufipogon and O.meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The AustralianO. rufipogon may be a perennial form of O.meridionalis.

KW - Chloroplast genome

KW - Oryza meridionalis

KW - Oryza rufipogon

KW - Oryza sativa

KW - Wild rice

UR - http://www.scopus.com/inward/record.url?scp=84871201714&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84871201714&partnerID=8YFLogxK

U2 - 10.1002/ece3.66

DO - 10.1002/ece3.66

M3 - Article

AN - SCOPUS:84871201714

VL - 2

SP - 211

EP - 217

JO - Ecology and Evolution

JF - Ecology and Evolution

SN - 2045-7758

IS - 1

ER -