PMC:5056902 / 866-3068 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5056902","sourcedb":"PMC","sourceid":"5056902","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5056902","text":"Introduction\nFrom the beginning of endosymbiosis between the origin eukaryote cell and alphaproteobacteria, the phenomenon of mitochondrial gene transfer to the host cell is still an ongoing evolutionary process [12]. It is termed nuclear mitochondrial DNA (Numt), pronounced \"new might\" [3]. In general, the mutation rate of nuclear DNA is lower than that of the mitochondrial genome. For this reason, Numt is often called a molecular fossil and is used as a molecular marker for speciation events in evolution [45]. While Numt insertion is a well-known phenomenon, the mechanism of DNA insertion into the nuclear genome is not clear. One of the strongly supported hypotheses is that during the process of double-strand break repair, an absorbed mitochondrial DNA fragment is inserted into the nuclear genome via a non-homologous end joining event [6789].\nAfter whole-genome sequencing was finished, Numt analysis was performed in various species: cat, cattle, dog, fruit fly, gorilla, grasshopper, goose, horse, horseshoe bat, honeybee, human, maize, squirrel, and whale [1011121314151617]. One review paper summarized all existences of Numt in complete genome sequences [18]. In the case of whale, a phylogenetic analysis of Numts with six whale species was carried out, establishing Numt as an evolutionary marker in speciation events [19]. In plant, a recent study discovered that Numt insertion is dispersed throughout the periphery of the centromere [20]. But, there are many barriers in plant Numt analyses. Genomic complexity is a big problem in not only the nuclear genome but also the mitochondrial genome [212223].\nIn this article, Numts of two green algae (Chlamydomonas reinhardtii and Coccomyxa subellipsoidea), three monocots (Oryza sativa, Sorghum bicolor, and Zea mays), and four eudicots (Vitis vinifera, Glycine max, Brassica rapa, and Arabidopsis thaliana), for which whole-genome nuclear and mitochondrial sequences are publically available, were detected using the nucleotide-nucleotide Basic Local Alignment Search Tool (BLASTN) searches and subjected to a basic analysis for their fundamental properties, which will be required in further comparative genome analyses in plants.","divisions":[{"label":"Title","span":{"begin":0,"end":12}}],"tracks":[{"project":"2_test","denotations":[{"id":"27729838-19014347-44844976","span":{"begin":213,"end":214},"obj":"19014347"},{"id":"27729838-14735123-44844977","span":{"begin":213,"end":215},"obj":"14735123"},{"id":"27729838-7932781-44844978","span":{"begin":289,"end":290},"obj":"7932781"},{"id":"27729838-19578158-44844979","span":{"begin":513,"end":514},"obj":"19578158"},{"id":"27729838-21237827-44844980","span":{"begin":513,"end":515},"obj":"21237827"},{"id":"27729838-10573425-44844981","span":{"begin":850,"end":851},"obj":"10573425"},{"id":"27729838-8754225-44844982","span":{"begin":850,"end":852},"obj":"8754225"},{"id":"27729838-2165219-44844983","span":{"begin":850,"end":853},"obj":"2165219"},{"id":"27729838-18949041-44844984","span":{"begin":850,"end":854},"obj":"18949041"},{"id":"27729838-20540682-44844985","span":{"begin":1074,"end":1076},"obj":"20540682"},{"id":"27729838-17404397-44844986","span":{"begin":1074,"end":1078},"obj":"17404397"},{"id":"27729838-17868078-44844987","span":{"begin":1074,"end":1080},"obj":"17868078"},{"id":"27729838-25991039-44844988","span":{"begin":1074,"end":1082},"obj":"25991039"},{"id":"27729838-25194325-44844989","span":{"begin":1074,"end":1084},"obj":"25194325"},{"id":"27729838-22412894-44844990","span":{"begin":1074,"end":1086},"obj":"22412894"},{"id":"27729838-18202357-44844991","span":{"begin":1074,"end":1088},"obj":"18202357"},{"id":"27729838-10723741-44844992","span":{"begin":1074,"end":1090},"obj":"10723741"},{"id":"27729838-20168995-44844993","span":{"begin":1174,"end":1176},"obj":"20168995"},{"id":"27729838-23715017-44844994","span":{"begin":1458,"end":1460},"obj":"23715017"},{"id":"27729838-24681310-44844995","span":{"begin":1618,"end":1620},"obj":"24681310"},{"id":"27729838-23431381-44844996","span":{"begin":1618,"end":1622},"obj":"23431381"},{"id":"27729838-24651721-44844997","span":{"begin":1618,"end":1624},"obj":"24651721"}],"attributes":[{"subj":"27729838-19014347-44844976","pred":"source","obj":"2_test"},{"subj":"27729838-14735123-44844977","pred":"source","obj":"2_test"},{"subj":"27729838-7932781-44844978","pred":"source","obj":"2_test"},{"subj":"27729838-19578158-44844979","pred":"source","obj":"2_test"},{"subj":"27729838-21237827-44844980","pred":"source","obj":"2_test"},{"subj":"27729838-10573425-44844981","pred":"source","obj":"2_test"},{"subj":"27729838-8754225-44844982","pred":"source","obj":"2_test"},{"subj":"27729838-2165219-44844983","pred":"source","obj":"2_test"},{"subj":"27729838-18949041-44844984","pred":"source","obj":"2_test"},{"subj":"27729838-20540682-44844985","pred":"source","obj":"2_test"},{"subj":"27729838-17404397-44844986","pred":"source","obj":"2_test"},{"subj":"27729838-17868078-44844987","pred":"source","obj":"2_test"},{"subj":"27729838-25991039-44844988","pred":"source","obj":"2_test"},{"subj":"27729838-25194325-44844989","pred":"source","obj":"2_test"},{"subj":"27729838-22412894-44844990","pred":"source","obj":"2_test"},{"subj":"27729838-18202357-44844991","pred":"source","obj":"2_test"},{"subj":"27729838-10723741-44844992","pred":"source","obj":"2_test"},{"subj":"27729838-20168995-44844993","pred":"source","obj":"2_test"},{"subj":"27729838-23715017-44844994","pred":"source","obj":"2_test"},{"subj":"27729838-24681310-44844995","pred":"source","obj":"2_test"},{"subj":"27729838-23431381-44844996","pred":"source","obj":"2_test"},{"subj":"27729838-24651721-44844997","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#eca093","default":true}]}]}}