Citrus is a large genus that includes several major cultivated species, including C. sinensis (sweet orange), Citrus reticulata (tangerine and mandarin), Citrus limon (lemon), Citrus grandis (pummelo) and Citrus paradisi (grapefruit). In 2009, the global citrus acreage was 9 million hectares and citrus production was 122.3 million tons (FAO statistics, see URLs), which is the top ranked among all the fruit crops. Among the 10.9 million tons (valued at $9.3 billion) of citrus products traded in 2009, sweet orange accounted for approximately 60% of citrus production for both fresh fruit and processed juice consumption (FAO statistics, see URLs). Moreover, citrus fruits and juice are the prime human source of vitamin C, an important component of human nutrition.Citrus fruits also have some unique botanical features, such as nucellar embryony (nucellus cells can develop into apomictic embryos that are genetically identical to mother plant). Consequently, somatic embryos grow much more vigorously than the zygotic embryos in seeds such that seedlings are essentially clones of the maternal parent. Such citrus-unique characteristics have hindered the study of citrus genetics and breeding improvement 1,2 . Complete genome sequences would provide valuable genetic resources for improving citrus crops.Citrus is believed to be native to southeast Asia 3-5 , and cultivation of fruit crops occurred at least 4,000 years ago 3,6 . The genetic origin of the sweet orange is not clear, although there are some speculations that sweet orange might be derived from interspecific hybridization of some primitive citrus species 7,8 . Citrus is also in the order Sapindales, a sister order to the Brassicales in the Malvidae, making it valuable for comparative genomics studies with the model plant Arabidopsis.We aimed to sequence the genome of Valencia sweet orange (C. sinensis cv. Valencia), one of the most important sweet orange varieties cultivated worldwide and grown primarily for orange juice production. Normal sweet oranges are diploids, with nine pairs of chromosomes and an estimated genome size of ~367 Mb 9 . To reduce the complexity of the sequenced genome, we obtained a doublehaploid (dihaploid) line derived from the anther culture of Valencia sweet orange 10 . We first generated whole-genome shotgun pairedend-tag sequence reads from the dihaploid genomic DNA and built a de novo assembly as the citrus reference genome; we then produced shotgun sequencing reads from the parental diploid DNA and mapped the sequences to the haploid reference genome to obtain the complete genome information for Valencia sweet orange. In addition, we conducted comprehensive transcriptome sequencing analyses for four representative tissues using shotgun RNA sequencing (RNA-Seq) to capture all transcribed sequences and paired-end-tag RNA sequencing (RNA-PET) to demarcate the 5′ and 3′ ends of all transcripts. On the basis of the DNA and RNA sequencing data, we characterized the orange genome for its gene content, heterozygosity and evolutionary features. ...

Interspecific hybridization and allopolyploidization contribute to the origin of many important crops. Synthetic Brassica is a widely used model for the study of genetic recombination and "fixed heterosis" in allopolyploids. To investigate the effects of the cytoplasm and genome combinations on meiotic recombination, we produced digenomic diploid and triploid hybrids and trigenomic triploid hybrids from the reciprocal crosses of three Brassica diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC). The chromosomes in the resultant hybrids were doubled to obtain three allotetraploids (B. juncea, AA.BB; B. napus, AA.CC; B. carinata, BB.CC). Intra-and intergenomic chromosome pairings in these hybrids were quantified using genomic in situ hybridization and BAC-FISH. The level of intra-and intergenomic pairings varied significantly, depending on the genome combinations and the cytoplasmic background and/or their interaction. The extent of intragenomic pairing was less than that of intergenomic pairing within each genome. The extent of pairing variations within the B genome was less than that within the A and C genomes, each of which had a similar extent of pairing. Synthetic allotetraploids exhibited nondiploidized meiotic behavior, and their chromosomal instabilities were correlated with the relationship of the genomes and cytoplasmic background. Our results highlight the specific roles of the cytoplasm and genome to the chromosomal behaviors of hybrids and allopolyploids.

Trigenomic Brassica allohexaploids synthesized from three crossing strategies showed diploidized and non-diploidized meiotic behaviors and produced both euploid and aneuploid progenies during successive generations, revealing the distinct subgenome stabilities (B > A> C). Three cultivated allotetraploid Brassica species (Brassica napus, B. juncea, B. carinata) represent the model system of speciation through interspecific hybridization and allopolyploidization, but no Brassica species at higher ploidy level exists in nature. In this study, Brassica allohexaploids (2n = 54, AABBCC) were artificially synthesized using three crossing strategies, and had combinations of the genomes from the extant allotetraploids and diploids (B. rapa, B. oleracea and B. nigra). The chromosome numbers and complements of these allohexaploids and the self-pollinated progenies of successive generations (S0-S7) were determined using multicolor fluorescent in situ hybridization that distinguished the chromosomes of three constituent genomes from each other. Both euploid and aneuploid progenies were identified. The most aneuploids maintained all B- and A-genome chromosomes and variable number of C-genome chromosomes, suggesting that genome stability was B > A > C. In the extreme case, loss of whole set of C-genome chromosomes led to the production of B. juncea-type progeny. Some aneuploid progenies had the same number of chromosomes (2n = 54) as the euploid, but the simultaneous loss and gain of A- and C-genome chromosomes. The diploidized and non-diploidized meiotic behaviors co-occurred in all allohexaploid individuals of consecutive generations. The aberrant chromosome pairing and segregation mainly involved the chromosomes of A and C genomes, which resulted in aneuploidy in self-pollinated progenies. The mechanisms for the differential stability of three genomes and the stabilization of the new allohexaploids are discussed.

Intragenomic chromosome homology in the B genome of Brassica nigra and their homoeology with the chromosomes of the A-genome of B. rapa and C-genome of B. oleracea was investigated in triploids (ABC, n = 27) of different origins obtained following hybridizations between natural B. napus (AACC, 2n = 38) x B. nigra (BB, 2n = 16) [AC.B], synthetic B. napus x B. nigra [A.C.B] and B. carinata (BBCC, 2n = 34) x B. rapa (AA, 2n = 20) [BC.A]. A relatively high percentage of pollen mother cells (PMCs) with at least one B-genome chromosome paired allosyndetically with A/C chromosomes was evident in all three combinations. A maximum of three B-genome chromosomes undergoing allosyndesis per cell was observed in AC.B and A.C.B combinations. A maximum of two autosyndetic bivalents within the B genome appeared at diakinesis in all combinations. The accurate analyses of auto- and allo-syndetic pairing for B genome in trigenomic combinations provided further evidence for the hypothesis that the three basic diploid genomes of the cultivated Brassica species evolved from one common ancestral genome with a lower chromosome number. The results showed that Brassica diploids may not be ancient polyploids but may have undergone chromosomal duplications instead of whole-genome duplication. The relevance of these results along with genetic changes of progenitor genomes which occurred during the evolution of Brassica polyploids is discussed.

SummaryOilseed rape (Brassica napus L.), which has yellow flowers, is both an important oil crop and a traditional tourism resource in China, whereas the Orychophragmus violaceus, which has purple flowers, likely possesses a candidate gene or genes to alter the flower colour of oilseed rape. A previously established B. napus line has a particular pair of O. violaceus chromosomes (M4) and exhibits slightly red petals. In this study, the transcriptomic analysis of M4, B. napus (H3), and O. violaceus with purple petals (OvP) and with white petals (OvW) revealed that most anthocyanin biosynthesis genes were up‐regulated in both M4 and OvP. Read assembly and sequence alignment identified a homolog of AtPAP2 in M4, which produced the O. violaceus transcript (OvPAP2). The overexpression of OvPAP2 via the CaMV35S promoter in Arabidopsis thaliana led to different levels of anthocyanin accumulation in most organs, including the petals. However, the B. napus overexpression plants showed anthocyanin accumulation primarily in the anthers, but not the petals. However, when OvPAP2 was driven by the petal‐specific promoter XY355, the transgenic B. napus plants produced red anthers and red petals. The results of metabolomic experiments showed that specific anthocyanins accumulated to high levels in the red petals. This study illustrates the feasibility of producing red‐flowered oilseed rape, thereby enhancing its ornamental value, via the ectopic expression of the OvPAP2 gene. Moreover, the practical application of this study for insect pest management in the crop is discussed.