Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.

Sato, Shusei; Hirakawa, Hideki; Isobe, Sachiko; Fukai, Eigo; Watanabe, Akïharu; Kato, Midori; Kawashima, Kumiko; Minami, Chiharu; Muraki, Akiko; Nakazaki, Naomi; Takahashi, Chika; Nakayama, Shinobu; Kishida, Yoshie; Kohara, Mitsuyo; Yamada, Manabu; Tsuruoka, Hisano; Sasamoto, Shigemi; Tabata, Satoshi; Aizu, Tomoyuki; Toyoda, Atsushi; Shin-I, Tadasu; Minakuchi, Yohei; Kohara, Yuji; Fujiyama, Asao; Tsuchimoto, Suguru; Kajiyama, Shin’ichiro; Makigano, Eri; Ohmido, Nobuko; Shibagaki, Nakako; Cartagena, Joyce A.; Wada, Naoki; Kohinata, Tsutomu; Alipour, Atefeh; Yuasa, Shota; Matsunaga, Sachihiro; Fukui, Kiichi

doi:10.1093/dnares/dsq030

Cited by 279 publications

(244 citation statements)

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“…Constrained portions of the cassava genome were identified by quantifying rejected substitutions (strength of purifying selection) with the GERP++ program 16 . Multiple whole-genome sequence alignment was carried out for the seven species in the Malpighiales clade of the plant kingdom, including cassava, rubber (H. brasiliensis) 39 , jatropha (Jatropha curcas) 40 , castor bean (Ricinus communis) 41 , willow (Salix purpurea) 42 , flax (Linum usitatissimum) 43 , and poplar (Populus trichocarpa) 44 . Whole-genome alignment was carried out with the Large-Scale Genome Alignment Tool (LASTZ) 45 .…”

Section: Alignment Of Reads and Variant Calling Of Cassava Haplotype mentioning

confidence: 99%

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

et al. 2017

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Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America; however, ubiquitous deleterious mutations may severely decrease its fitness. To evaluate these deleterious mutations, we constructed a cassava haplotype map through deep sequencing 241 diverse accessions and identified >28 million segregating variants. We found that (i) although domestication has modified starch and ketone metabolism pathways to allow for human consumption, the concomitant bottleneck and clonal propagation have resulted in a large proportion of fixed deleterious amino acid changes, increased the number of deleterious alleles by 26%, and shifted the mutational burden toward common variants; (ii) deleterious mutations have been ineffectively purged, owing to limited recombination in the cassava genome; (iii) recent breeding efforts have maintained yield by masking the most damaging recessive mutations in the heterozygous state but have been unable to purge the mutation burden; such purging should be a key target in future cassava breeding.For millions of people in the tropics, cassava is the third most consumed carbohydrate source, after rice and maize 1 . Even though cassava was domesticated in Latin America 2,3 , it has spread widely and has become a major staple crop in Africa. Although its wild progenitor, M. esculenta sp. falbellifolia, reproduces by seed 4 , cultivated cassava is notably almost exclusively clonally propagated via stem cutting 5 . The limited number of recombination events in such vegetatively propagated crops may result in an accumulation of deleterious alleles throughout the genome 6 . Thus, mutation burden in cassava is expected to be more severe than that in sexually propagated species. Deleterious mutations are considered to be at the heart of inbreeding depression 7 . Even in elite cassava accessions, inbreeding depression is extremely severe, and a single generation of inbreeding may result in a >60% decrease in fresh root yield 8,9 . In this study, we sought to identify deleterious mutations in cassava populations, with the goal of accelerating cassava breeding by allowing breeders to purge deleterious mutations more efficiently.We conducted a comprehensive characterization of genetic variation by whole-genome sequencing (WGS) of 241 cassava accessions ( Fig. 1, Supplementary Fig. 1 and Supplementary Table 1). On average, more than 30× coverage was generated for each accession. To ensure high-quality variant discovery, variants from low-copynumber regions of the cassava genome 10,11 were identified to develop the cassava haplotype map II (HapMapII) (Supplementary Fig. 2), containing 25.9 million SNPs and 1.9 million insertions/deletions (indels) (Supplementary Table 2), of which nearly 50% were rare (minor-allele frequency <0.05) (Supplementary Fig. 3). The error rate of variant calling, i.e., the proportion of segregating sites in the reference accession, was 0.01%. The correlation between read depth and the proportion of SNP heterozygosity was extremely low (r 2 = 6 × 10...

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Section: Alignment Of Reads and Variant Calling Of Cassava Haplotype mentioning

confidence: 99%

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

et al. 2017

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“…e details of the plant material used in this study, a J. curcas line originating from the Palawan Island in the Philippines, were described in our previous report (Sato et al 2011).…”

Section: Plant Materialsmentioning

confidence: 99%

“…e strategy used to accumulate shotgun genomic sequences generated by an Illumina-solexa GAII sequencer is described in the previous report (Sato et al 2011). e following four paired-end runs, two of which had been used in the previous study and deposited to DDBJ Sequence Read Archive (DRA), were used for the assembly: 36/36 bp (DRA000305), 50/31 bp (DRA000306), 51/51 bp, and 76/76 bp.…”

Section: Genome Sequencing and Assemblymentioning

confidence: 99%

Upgraded genomic information of <i>Jatropha curcas</i> L.

Hirakawa

Tsuchimoto

Sakai

et al. 2012

Plant Biotechnology

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In order to upgrade the genome sequence information of J. curcas L., we integrated de novo assembly of a total of 537 million paired-end reads generated from the Illumina sequencing platform into the current genome assembly which was obtained by a combination of the conventional Sanger method and the Roche/454 sequencing platform. e total length of the upgraded genome sequences thus obtained was 297,661,187 bp consisting of 39,277 contigs. e average and N50 lengths of the generated contigs were 7,579 bp and 15,950 bp, both of which were increased fourfold from the previous genome assembly. Along with genome sequence upgrading, the currently available transcriptome data were collected from the public databases and assembled into 19,454 tentative consensus sequences. Based on a comparison between these tentative consensus sequences of transcripts and the predictions of computer programs, a total of 30,203 complete and partial structures of protein-encoding genes were deduced. e number of genes with complete structures was increased about threefold from the previous genome annotation. By applying the upgraded genome sequence and predicted proteincoding gene information, the number and features of the tandemly arrayed genes, syntenic relations between Jatropha and other plant genomes, and structural features of transposable elements were investigated. e detailed information on the updated J. curcas genome is available at http://www.kazusa.or.jp/jatropha/. Key words:Jatropha curcas, genome sequencing, transcriptome sequences, tentative consensus sequence, tandem gene duplication, database.Jatropha curcas L. is a perennial small tree or large shrub that belongs to the Euphorbiaceae family. J. curcas is endemic to central America but is distributed throughout the tropics and subtropics of Asia and Africa. J. curcas is an important non-edible oilseed crop with great potential for the production of biodiesel fuel. Since J. curcas is an undomesticated plant, its positive attributes in terms of breeding and utilization are not fully understood.In order to accelerate its genetic improvement, it is desirable to understand the genome information of J. curcas. With this goal in mind, we have analyzed the genome sequence of J. curcas by applying combined sequencing methods, and have made the obtained sequence information available through the public and web databases.e accumulated genome information (JAT_r3.0) was 285,858,490 bp consisting of 120,586 contigs and 29,831 singlets, and this accounted for approximately 95% of the gene-containing regions. A total of 40,929 complete and partial structures of proteinencoding genes have been deduced on the accumulated genome sequences. However, the majority of the predicted genes were partially predicted ones as the contig lengths were relatively short in JAT_r3.0. Further improvement of the genome sequence information is therefore needed.Along with the genome sequence approach, several transcriptome analyses have been attempted. Natarajan et al. have reported 12,084 ESTs using...

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“…Large scale single-pass sequencing of cDNAs from different plants has provided a large repository of genes whose tissuespecific expression can be evaluated for the cloning of genes in addition to the development of markers for map-based cloning (White et al 2000). In J. curcas, volumes of genomic data that include the whole genome (Sato et al 2011) and seed transcriptome information have been generated in the last few years (King et al 2011). A total of 12,084 expressed sequence tags (ESTs), from developing J. curcas seeds were sequenced and they represented genes coding for diverse biological functions (Natarajan et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

Chandran

Sankararamasubramanian

Kumar

et al. 2014

Physiol Mol Biol Plants

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Jatropha curcas has been widely studied at the molecular level due to its potential as an alternative source of fuel. Many of the reports till date on this plant have focussed mainly on genes contributing to the accumulation of oil in its seeds. A suppression subtractive hybridization strategy was employed to identify genes which are differentially expressed in the mid maturation stage of J. curcas seeds. Random expressed sequence tag sequencing of the cDNA subtraction library resulted in 385 contigs and 1,428 singletons, with 591 expressed sequence tags mapping for enzymes having catalytic roles in various metabolic pathways. Differences in transcript levels in early and mid-to-late maturation stages of seeds were also investigated using sequence information obtained from the cDNA subtraction library. Seven out of 12 transcripts having putative roles in central carbon metabolism were up regulated in early seed maturation stage while lipid metabolism related transcripts were detected at higher levels in the later stage of seed maturation. Interestingly, 4 of the transcripts revealed putative alternative splice variants that were specifically present or up regulated in the early or late maturation stage of the seeds. Transcript expression patterns from the current study using maturing seeds of J. curcas reveal a subtle balancing of oil accumulation and utilization, which may be influenced by their energy requirements.

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Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.

Cited by 279 publications

References 50 publications

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Upgraded genomic information of <i>Jatropha curcas</i> L.

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

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