A Draft Sequence of the Rice Genome (
            <i>Oryza sativa</i>
            L. ssp.
            <i>indica</i>
            )

Goff, Stephen A.; Ricke, Darrell O.; Lan, Tian; Presting, Gernot G.; Wang, Ronglin; Dunn, Mary; Glazebrook, Jane; Sessions, Allen; Oeller, Paul W.; Varma, Hemant; Hadley, David; Hutchison, Don; Martin, Chris; Katagiri, Fumiaki; Lange, B. Markus; Moughamer, Todd; Xia, Yu; Budworth, Paul; Zhong, Jingping; Miguel, Trini; Paszkowski, Uta; Zhang, Shiping; Colbert, Michelle; Sun, Weilin; Chen, Runsheng; Cooper, Bret; Park, Sylvia; Wood, Todd Charles; Mao, Long; Quail, Peter H.; Wing, Rod A.; Dean, Ralph A.; Yu, Yeisoo; Zharkikh, Andrey; Shen, Richard; Sahasrabudhe, Sudhir; Thomas, Alun; Cannings, Rob; Gutin, Alexander; Pruss, Dmitry; Reid, Julia; Tavtigian, Sean V.; Mitchell, Jeff T.; Eldredge, Glenn; Scholl, Terri; Miller, Rose Mary; Bhatnagar, S. K.; Adey, Nils B.; Rubano, Todd; Tusneem, Nadeem; Robinson, Rosann; Feldhaus, Jane; Macalma, Teresita; Oliphant, Arnold; Briggs, Steven P.

doi:10.1126/science.1068037

Cited by 3,199 publications

(1,241 citation statements)

References 97 publications

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“…We identified all CDPK and CRK gene family members in six plant species ( H. brasiliensis , A. thaliana , O. sativa , P. trichocarpa , M. esculenta , and R. communis ) from their published genome sequences 33, 34, 35, 36, 37, 38, 39. The latest genome and protein sequences of these species were downloaded from Phytozome v10.…”

Section: Resultsmentioning

confidence: 99%

The calcium‐dependent protein kinase (CDPK) and CDPK‐related kinase gene families in Hevea brasiliensis—comparison with five other plant species in structure, evolution, and expression

et al. 2016

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Calcium‐dependent protein kinases (CDPKs or CPKs) play important roles in various physiological processes of plants, including growth and development, stress responses and hormone signaling. Although the CDPK gene family has been characterized in several model plants, little is known about this gene family in Hevea brasiliensis (the Para rubber tree). Here, we characterize the entire H. brasiliensis CDPK and CDPK‐related kinase (CRK) gene families comprising 30 CDPK genes (HbCPK1 to 30) and nine CRK genes (HbCRK1 to 9). Structure and phylogeny analyses of these CDPK and CRK genes demonstrate evolutionary conservation in these gene families across H. brasiliensis and other plant species. The expression of HbCPK and HbCRK genes was investigated via Solexa sequencing in a range of experimental conditions (different tissues, phases of leaf development, ethylene treatment, and various abiotic stresses). The results suggest that HbCPK and HbCRK genes are important components in growth, development, and stress responses of H. brasiliensis. Parallel studies on the CDPK and CRK gene families were also extended to five other plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Manihot esculenta, and Ricinus communis). The CDPK and CRK genes from different plant species that exhibit similar expression patterns tend to cluster together, suggesting a coevolution of gene structure and expression behavior in higher plants. The results serve as a foundation to further functional studies of these gene families in H. brasiliensis as well as in the whole plant kingdom.

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Section: Resultsmentioning

confidence: 99%

The calcium‐dependent protein kinase (CDPK) and CDPK‐related kinase gene families in Hevea brasiliensis—comparison with five other plant species in structure, evolution, and expression

et al. 2016

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“…It was a milestone in plant biology and made Arabidopsis one of the most popular species for basic plant research. Rice, a staple food in most of the world, was the second available plant genome in 2002 [4,5]. Rapid progress in the development of new sequencing technology and bioinformatic tools in recent years has allowed faster and more efficient sequencing, and assembly of genomes at lower cost.…”

Section: Plant Genomes: Current Statusmentioning

confidence: 99%

“…As many as 20 plant genomes have been sequenced and assembled in the last two years [6-25]. Genome sequences of plants belonging to different groups, such as two plants from the early land plant clades (a moss Physcomitrella patens and a spikemoss Selaginella moellendorffii ) and numerous economically important monocots (Box 1), such as rice, maize, sorghum, and so on, have now been decoded [4,5,25-28] (Figure 1). Eudicots (Box 1), the largest group in flowering plants, are composed of two major clades, the Eurosids and Euasterids.…”

Section: Plant Genomes: Current Statusmentioning

confidence: 99%

The tomato genome: implications for plant breeding, genomics and evolution

Ranjan¹,

Ichihashi²,

Sinha³

2012

Genome Biol

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“…Afterwards, sequencing of the rice ( O. sativa L. ssp. indica ) genome more than a decade ago 73 allowed the identification of a family of rice nshb genes and a single copy of the rice thb gene (see subsection below).…”

Section: Introductionmentioning

confidence: 99%

Rice (Oryza) hemoglobins

2014

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Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice ( Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit an extremely high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs.

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A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. indica )

Cited by 3,199 publications

References 97 publications

The calcium‐dependent protein kinase (CDPK) and CDPK‐related kinase gene families in Hevea brasiliensis—comparison with five other plant species in structure, evolution, and expression

The calcium‐dependent protein kinase (CDPK) and CDPK‐related kinase gene families in Hevea brasiliensis—comparison with five other plant species in structure, evolution, and expression

The tomato genome: implications for plant breeding, genomics and evolution

Rice (Oryza) hemoglobins

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