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Satsuma (Citrus unshiu Marc.) is one of the most abundantly produced mandarin varieties of citrus, known for its seedless fruit production and as a breeding parent of citrus. De novo assembly of the heterozygous diploid genome of Satsuma (“Miyagawa Wase”) was conducted by a hybrid assembly approach using short-read sequences, three mate-pair libraries, and a long-read sequence of PacBio by the PLATANUS assembler. The assembled sequence, with a total size of 359.7 Mb at the N50 length of 386,404 bp, consisted of 20,876 scaffolds. Pseudomolecules of Satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of Clementine, pummelo, and sweet orange. Gene prediction by modeling with MAKER-P proposed 29,024 genes and 37,970 mRNA; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. BUSCO scores for the assembled scaffold and predicted transcripts, and another analysis by BAC end sequence mapping indicated the assembled genome consistency was close to those of the haploid Clementine, pummel, and sweet orange genomes. The number of repeat elements and long terminal repeat retrotransposon were comparable to those of the seven citrus genomes; this suggested no significant failure in the assembly at the repeat region. A resequencing application using the assembled sequence confirmed that both kunenbo-A and Satsuma are offsprings of Kishu, and Satsuma is a back-crossed offspring of Kishu. These results illustrated the performance of the hybrid assembly approach and its ability to construct an accurate heterozygous diploid genome.
citrus, Satsuma, draft genome assembly, gene prediction, genome synteny, gibberellic acid biosynthesis, carotenoid biosynthesis, parentage analysis
Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach
Tokurou Shimizu,1,* Yasuhiro Tanizawa,2 Takako Mochizuki,2 Hideki Nagasaki,2,† Terutaka Yoshioka,1 Atsushi Toyoda,3 Asao Fujiyama,3 Eli Kaminuma,2 and Yasukazu Nakamura2
Seven protein-binding sites on the immunoglobulin heavy-chain (IgH) enhancer element have been identified by exonuclease III protection and gel retardation assays. It appears that the seven sites bind a minimum of four separate proteins. Three of these proteins also bind to other enhancers or promoters, but one protein seems to recognize exclusively IgH enhancer sequences. A complex of four binding sites, recognized by different proteins, is located within one 80-base-pair region of IgH enhancer DNA. Close juxtaposition of enhancer proteins may allow protein-protein interactions or be part of a mechanism for modulating enhancer protein activity. All IgH enhancer-binding proteins identified in this study were found in extracts from nonlymphoid as well as lymphoid cells. These data provide the first direct evidence that multiple proteins bind to enhancer elements and that while some of these proteins recognize common elements of many enhancers, others have more limited specificities.
Binding in vitro of multiple cellular proteins to immunoglobulin heavy-chain enhancer DNA.
C L Peterson, K Orth, and K L Calame
OBJECTIVE: We examine the relationship between health insurance status and access to care among low-income persons 65 years of age and under, taking into account their social demographic characteristics and health care needs. DATA SOURCES AND STUDY SETTING. Study groups consist of the subsamples of persons with incomes between 100 and 150 percent of the federal poverty level and those below the federal poverty level interviewed in the 1983, 1984, and 1986 Health Interview Surveys (HIS) of the National Center for Health Statistics. Sample sizes range from about 6,000 to 11,000 depending on the proportion of each study group administered the insurance supplement. STUDY DESIGN. Annual visits and whether hospitalized during a year are used as measures of access to medical care. The analysis consists of identifying predictors of use of services (i.e., health status and social characteristics) and, taking them into account, examining the relationship of insurance status to access to care. This was first undertaken on the 1983 survey; the models obtained then are replicated on the other two years of data. DATA COLLECTION/EXTRACTION METHODS. The HIS utilizes in-person interviews to gather health and medical history information from a stratified random sample of the U.S. population. Data were obtained through public use tapes distributed by the National Center for Health Statistics. PRINCIPAL FINDINGS. Results are consistent for all three years among persons in poverty. Being covered by Medicaid, in contrast to having private insurance or being without health insurance, is related to use of both ambulatory care and hospital care. The access differences for persons in poverty, regardless of their vulnerability or “risk” of requiring medical care, are marked and generally statistically significant. Among the near-poor the same findings occur, although the differences are less sharp and less often statistically significant. CONCLUSIONS. The most obvious explanation is that the poor, and to a considerable extent the near-poor, have limited access because of copayments and deductibles that are typically part of private insurance coverage. The findings raise policy questions regarding the utility of either “play or pay” employer-provided insurance or income tax deductions to increase access.
Insurance status and access to health services among poor persons.
H E Freeman and C R Corey