Discovery Function Labels Based On Numerical Features Of MicroRNA Found In Plant

MicroRNAs(miRNAs),are a class of small endogenous non-coding RNAs that play Important post-transcriptional regulation role by degrading targeted mRNAs or repressing mRNA translation. We screened 84 miRNAs belonging to 21 conserved family from 4014 miRNAs in miRBase database which distributed in 47 plant species. Of the predicted 274 target genes,42 GO terms were found in the Gene Ontology. With the 135 numerical features which extracted by perl program, the difference significantly result of ANOVA (P<0.001) and multiple comparison show that the function labels G…,GC content and Helix in biological process, cellular component and biological function, respectively. Our result have suggested a potential connection between numerical features of miRNAs and the function of target genes of miRNAs.

LTR_retriever: a highly accurate and sensitive program for identification of LTR retrotransposons

ABSTRACTLong terminal-repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. Identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the well-conserved structure, multiple programs were developed for de novo identification of LTR-RTs; however, these programs are associated with low specificity and high false discovery rate (FDR). Here we report LTR_retriever, a multithreading empowered Perl program that identifies LTR-RTs and generates high-quality LTR libraries from genomic sequences. LTR_retriever demonstrated significant improvements by achieving high levels of sensitivity (91.8%), specificity (94.7%), accuracy (94.3%), and precision (90.6%) in model plants. LTR_retriever is also compatible with long sequencing reads. With 40k self-corrected PacBio reads equivalent to 4.5X genome coverage in Arabidopsis, the constructed LTR library showed excellent sensitivity and specificity. In addition to canonical LTR-RTs with 5'-TG..CA-3' termini, LTR_retriever also identifies non-canonical LTR-RTs (non-TGCA), which have been largely ignored in genome-wide studies. We identified seven types of non-canonical LTRs from 42 out of 50 plant genomes. The majority of non-canonical LTRs are Copia elements, with which the LTR is four times shorter than that of other Copia elements, which may be a result of their target specificity. Strikingly, non-TGCA Copia elements are often located in genic regions and preferentially insert nearby or within genes, indicating their impact on the evolution of genes and potential as mutagenesis tools.

EMBEDDED WH-QUESTIONS IN L2 ENGLISH IN INDIA

This corpus study brings a second language (L2) research perspective, insights from generative grammar, and new empirical evidence to bear on a long-accepted claim in the World Englishes literature—namely, that inversion with wh-movement in colloquial Indian English is obligatory in embedded clauses and impossible in main clauses. It is argued that this register of Indian English is a L2 variety, functioning as part of a multilingual code repertoire, but that syntactic universals apply to first and second languages alike. Despite recent attempts at formalization, this distribution should be unattested, as such a grammar would fall outside the constraints of Universal Grammar and would contradict proposed discourse-pragmatic principles of natural language. A Perl program was created to search the Indian subcorpus of the International Corpus of English (Greenbaum, 1996) for relevant distributional patterns. Results reveal that wh-inversion in Indian English operates in the same way as in other varieties: It is robustly attested in main clauses and appears only occasionally in embedded clauses where syntactic and pragmatic conditions allow; it is obligatory only with interrogative complementizer deletion. Thus, contrary to the standard account but commensurate with recent corpus studies, users of English in India exhibit knowledge of universal constraints in this domain.