Rapid diversification of five Oryza AA genomes associated with rice adaptation.

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.

[Compound amino acid combined with vitamin E for idiopathic asthenospermia].

Objective: To study the therapeutic efficacy of compound amino acid combined with vitamin E in the treatment of idiopathic asthenospermia. Methods: This study included 120 cases of idiopathic asthenospermia treated in the Outpatient Department of our hospital between February 2014 and January 2015. We randomized the patients into a treatment group( n = 70,aged23- 43 [mean 32. 5] years) and a control group( n = 50,aged 23- 44 [mean 31. 7] years),the former treated with compound amino acid plus vitamin E while the latter with vitamin E only. After 90 days of medication, we evaluated the therapeutic effects by comparing the total sperm motility( progressive motility + non-progressive motility, PR + NP),the percentage of progressively motile sperm( PR),and the pregnancy rate between the two groups. Results: Before treatment, PR + NP and PR were(26. 24 ± 6. 56) %and(24. 65 ± 6. 43) % in the treatment group and(15. 13 ± 5. 68) % and(14. 73 ± 6. 16) in the control, with no statistically significant differences between the two groups( P > 0. 05). After 90 days of medication, PR + NP and PR were( 49. 63 ± 9. 78) % and(33. 33 ± 5. 64)% in the former and(37. 67 ± 7. 98)% and(27. 23 ± 6. 46)% in the latter, remarkably increased in both groups as compared with the baseline( P < 0. 05),but significantly more in the treatment than in the control group( P < 0. 05). Four pregnancies(5. 71%) were achieved in the former group but only 1(2. 00%) in the latter. The total rate of effectiveness was markedly higher in the treatment group than in the control(74. 28% vs 44. 00%,P < 0. 05). No adverse reactions were observed in either group. Conclusion: Compound amino acid combined with vitamin E can safely and effectively improve sperm motility in idiopathic asthenospermia patients.

LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes.

The amplification and recombination of long terminal repeat (LTR) retrotransposons have proven to determine the size, organization, function, and evolution of most host genomes, especially very large plant genomes. However, the limitation of tools for an efficient discovery of structural complexity of LTR retrotransposons and the nested insertions is a great challenge to confront ever-growing amount of genomic sequences for many organisms. Here we developed a novel software, called as LTRtype, to characterize different types of structurally complex LTR retrotransposon elements as well as nested events. This system is capable of rapidly scanning large-scale genomic sequences and appropriately characterizing the five complex types of LTR retrotransposon elements. After testing on the Arabidopsis thaliana genome, we found that this program is able to properly annotate a large number of structurally complex elements as well as the nested insertions. Thus, LTRtype can be employed as an automatic and efficient tool that will help to reconstruct the evolutionary history of LTR retrotransposons and better understand the evolution of host genomes. LTRtype is publicly available at: http://www.plantkingdomgdb.com/LTRtype/index.html.

The complete chloroplast genome sequence of American bird pepper (Capsicum annuum var. glabriusculum).

The complete chloroplast genome sequence of American bird pepper (Capsicum annuum var. glabriusculum) is reported and characterized in this study. The genome size is 156,612 bp, containing a pair of inverted repeats (IRs) of 25,776 bp separated by a large single-copy region of 87,213 bp and a small single-copy region of 17,851 bp. The chloroplast genome harbors 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. A total of 18 of these genes are duplicated in the inverted repeat regions, 16 genes contain 1 intron, and 2 genes and one ycf have 2 introns.

Full transcription of the chloroplast genome in photosynthetic eukaryotes.

Prokaryotes possess a simple genome transcription system that is different from that of eukaryotes. In chloroplasts (plastids), it is believed that the prokaryotic gene transcription features govern genome transcription. However, the polycistronic operon transcription model cannot account for all the chloroplast genome (plastome) transcription products at whole-genome level, especially regarding various RNA isoforms. By systematically analyzing transcriptomes of plastids of algae and higher plants, and cyanobacteria, we find that the entire plastome is transcribed in photosynthetic green plants, and that this pattern originated from prokaryotic cyanobacteria - ancestor of the chloroplast genomes that diverged about 1 billion years ago. We propose a multiple arrangement transcription model that multiple transcription initiations and terminations combine haphazardly to accomplish the genome transcription followed by subsequent RNA processing events, which explains the full chloroplast genome transcription phenomenon and numerous functional and/or aberrant pre-RNAs. Our findings indicate a complex prokaryotic genome regulation when processing primary transcripts.