BackgroundThe rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses.ResultsWe report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies.ConclusionsThe MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates.ReviewersThis article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.
This study reports trends in rural low-skill employment in the 1990s and their impact on the rural workforce. The share of rural jobs classified as low-skill fell by 2.2 percentage points between 1990 and 2000, twice the decline of the urban low-skill employment share, but much less than the decline of the 1980s. Employment shifts from low-skill to skilled occupations within industries, rather than changes in industry mix, explain virtually all of the decline in the rural low-skill employment share. The share decline was particularly large for rural Black women, many of whom moved out of low-skill blue-collar work into service occupations, while the share of rural Hispanics who held low-skill jobs increased.
"Migrants are generally assumed to gather specific information about the destination primarily through physical contact, or through family, friends, and acquaintances. In this paper, I propose an additional source of information: similarities between origin and destination labor markets. Data from the 1983-1987 PSID [Panel Study of Income Dynamics] are used in a two-stage least squares model of postmove search duration in the U.S. Rural-to-urban migrants (except for rural Southerners) exhibit significantly lower search duration than other groups, controlling for productivity-related characteristics and postmove earnings. In addition, employment growth differences between origin and destination are found to be better predictors of search duration than are differences in average earnings."
E ducation is a key determinant of economic well-being for both individuals and places. Despite overall improvements, however, rural residents still have significantly lower educational attainment than urban residents. Improving the quality of education and encouraging students to stay in school is one possible strategy for reducing poverty and raising local well-being. A better-educated workforce should have higher incomes. Partridge and Rickman showed that both education levels and increases in attainment explained spatial variation in poverty reduction.Outmigration to metro areas is a potential obstacle to this strategy, however. Migration from rural areas occurs because of the lack of demand for a better-educated rural workforce and the necessity of leaving rural areas to attend college (Gibbs). Outmigration may prevent local human capital levels from reaching the threshold required to attract new industry or encourage expansion in the existing economic base. Even where robust rural job growth exists, the lower skill levels and wages offered by rural employers, on average, both dampen the poverty-reducing power of education and hinder long-term development prospects associated with an increasingly high-skill economy.This study documents a direct effect of education on householder poverty, but does not find an indirect effect through migration. Data from the Panel Study of Income Dynamics (PSID) is used to obtain a sample of 708 working-age (25-64 years of age) household heads that lived in a nonmetro county in 1993.
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