Identification of common molecular subsequences

Smith, Temple F.; Waterman, Michael S.

doi:10.1016/0022-2836(81)90087-5

Cited by 8,500 publications

(5,143 citation statements)

References 6 publications

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“…Indels identified as gaps surrounded by one-to-one alignments with at least 100 bp in both ends were retained. We used EMBOSS Water 67 based on the standard Smith-Waterman algorithm 68 to revise the retained indel set by redoing the alignments of regions that contain multiple indels. Putative functional effects of SNPs and indels were annotated using the ANNOVAR package 69 .…”

Section: Competing Financial Interestsmentioning

confidence: 99%

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

et al. 2014

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Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

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Section: Competing Financial Interestsmentioning

confidence: 99%

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

et al. 2014

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“…9 Hits within chromosome X were found for all SNPs except 2.3(476). After carrying out this process, it was noticed that one SNP, 1.1(635), resides within the 30-base pair repeat sequence.…”

Section: Variants Typedmentioning

confidence: 99%

A unique demographic history exists for the MAO-A gene in Polynesians

et al. 2012

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Variation in the human monoamine oxidase A (MAO-A) gene can influence neurotransmittor levels and is thought to have a role in many behavioral traits. The genetic architecture of MAO-A is known to vary across different geographic subgroups. Previous studies have reported evidence for positive selection within the MAO-A gene region in seven ethnic groups: Pygmy, Aboriginal Taiwanese, Chinese, Japanese, Mexican and Russian. Polynesian populations have not been tested and repeated founder effects due to the island-hopping voyages of Polynesians across the South Pacific suggest a unique demographic history exists at the MAO-A gene, perhaps including selective effects. To explore this, we genotyped 13 key single-nucleotide polymorphisms (SNPs) spanning MAO-A gene as well as the functional polymorphism (MAO-A-uVNTR) in 47 unrelated Maori individuals. A comparison of genetic variation between Maori and non-Maori groups found a substantial reduction in genetic diversity at the MAO-A gene locus and an increase in the frequency of the most common MAO-A gene variant in the Maori group. Results of this study support previous findings and also point toward a 5-SNP haplotype that may have been influenced by selective effects in the Maori population. Full-sequence data for MAO-A in a large cohort are now required to conclusively determine whether MAO-A has undergone positive selection in Polynesians. Overall, these new data describe a unique demographic history for the MAO-A gene in the Maori population and will be helpful for studies wishing to investigate MAO-A as a candidate gene for influencing behavioral traits in the Polynesians.

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“…An alignment score (Smith & Waterman, 1981) greater than or equal to 100 and miRNA:mRNA Minimum Free Energy (MFE, ∆G) less than −20 kcal/mol were considered as putative target genes. The targets were further annotated against NCBI‐RefSeq invertebrate protein database and Gene Ontology (GO) terms were assigned (using Blast‐2‐GO) based on the annotation.…”

Section: Methodsmentioning

confidence: 99%

Genome‐wide identification, expression profiling, and target gene analysis of microRNAs in the Onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae)

Rebijith

Asokan

Hande

et al. 2018

Ecology and Evolution

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Thrips tabaci Lindeman is an important polyphagous insect pest species estimated to cause losses of more than U.S. $1 billion worldwide annually. Chemical insecticides are of limited use in the management of T. tabaci due to the thigmokinetic behavior and development of resistance to insecticides. There is an urgent need to find alternative management strategies. Small noncoding RNAs (sncRNAs) especially microRNAs (miRNAs) hold great promise as key regulators of gene expression in a wide range of organisms. MiRNAs are a group of endogenously originated sncRNA known to regulate gene expression in animals, plants, and protozoans. In this study, we explored these RNAs in T. tabaci using deep sequencing to provide a basis for future studies of their biological and physiological roles in governing gene expression. Apart from snoRNAs and piRNAs, our study identified nine novel and 130 known miRNAs from T. tabaci. Functional classification of the targets for these miRNAs predicted that majority are involved in regulating transcription, translation, signal transduction and genetic information processing. The higher expression of few miRNAs (such as tta‐miR‐281, tta‐miR‐184, tta‐miR‐3533, tta‐miR‐N1, tta‐miR‐N7, and tta‐miR‐N9) in T. tabaci pupal and adult stages reflected their possible role in larval and adult development, metamorphosis, parthenogenesis, and reproduction. This is the first exploration of the miRNAome in T. tabaci, which not only provides insights into their possible role in insect metamorphosis, growth, and development but also offer an important resource for future pest management strategies.

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Identification of common molecular subsequences

Cited by 8,500 publications

References 6 publications

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

A unique demographic history exists for the MAO-A gene in Polynesians

Genome‐wide identification, expression profiling, and target gene analysis of microRNAs in the Onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae)

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