Distribution of nuclear mitochondrial pseudogenes in three pollinator fig wasps associated with Ficus pumila |
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| Institution: | 1. School of Resources and Environmental Sciences, Tiantong National Station of Forest Ecosystem, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Dongchuan Road 500, Shanghai 200241, China;2. Ecological Security and Protection Key laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, China;3. School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom;1. Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic;2. Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovakia;3. Department of Plant Ecology and Environmental Conservation, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-096 Warsaw, Poland;1. Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China;2. Extreme Stress Resistance and Biotechnology Laboratory, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China;1. NSERC/UQAT/UQAM Industrial Chair in Sustainable Forest Management, Université du Québec en Abitibi-Témiscamingue, 445, boulevard de l''Université, Rouyn-Noranda, Québec J9X 5E4, Canada;2. Institut des sciences de la forêt tempérée, Université du Québec en Outaouais, 58, rue Principale, Ripon, Québec, J0V 1V0, Canada;1. Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;2. Invasive Species Programme, South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa;1. Department of Biology, Faculty of Science, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan;2. Biodiversity Division, National Institute for Agro-Environmental Sciences, Kannondai 3-1-3, Tsukuba 305-8604, Japan |
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| Abstract: | Nuclear mitochondrial pseudogenes (NUMTs) are nuclear sequences transferred from mitochondrial genomes. Although widespread, their distribution patterns among populations or closely related species are rarely documented. We amplified and sequenced the mitochondrial cytochrome b (Cytb) gene to check for NUMTs in three fig wasp species that pollinate Ficus pumila (Wiebesia sp. 1, 2 and 3) in Southeastern China using direct and cloned sequencing. Unambiguous sequences (332) of 487 bp in length belonging to 33 haplotypes were found by direct sequencing. Their distribution was highly concordant with those of cytochrome c oxidase subunit I (COI). Obvious signs of co-amplification of NUMTs were indicated by their uneven distribution. NUMTs were observed in all individuals of 12 populations of Wiebesia sp. 3, and 13 individuals of three northern populations of Wiebesia sp. 1. Sequencing clones of potential co-amplification products confirmed that they were NUMTs. These NUMTs either clustered as NUMT clades basal to mtDNA Cytb clades (basal NUMTs), or together with Cytb haplotypes. Basal NUMTs had either stop codons or frame-shifting mutations resulting from deletion of a 106 bp fragment. In addition, no third codon or synonymous substitutions were detected within each NUMT clade. The phylogenetic tree indicated that basal NUMTs had been inserted into nuclei before divergence of the three species. No significant pairwise differences were detected in their ratios of third codon substitutions, suggesting that these NUMTs originated from one transfer event, with duplication in the nuclear genome resulting in the coexistence of the 381 bp copy. No significant substitution differences were detected between Cytb haplotypes and NUMTs that clustered with Cytb haplotypes. However, these NUMTs coexisted with Cytb haplotypes in multiple populations, suggesting that these NUMT haplotypes were recently inserted into the nuclear genome. Both basal and recently inserted NUMTs were rare events, and were absent in most populations of Wiebesia sp. 1 and 2. Further studies are needed to distinguish between mechanisms potentially generating this rarity, such as purifying selection, genetic drift or amplification failure. |
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| Keywords: | Creeping fig NUMTs Southeastern China |
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