Characterization of cetacean Numt and its application into cetacean phylogeny

Ko, Young-Joon; Yang, Eun Chan; Lee, Jae-Hak; Lee, Kyeong Won; Jeong, Jae Yeon; Park, Kiejung; Chung, Oksung; Bhak, Jong; Lee, Jung-Hyun; Yim, Hyung-Soon

doi:10.1007/s13258-015-0353-7

Cited by 13 publications

(17 citation statements)

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“…Furthermore, when integrating all of the neighboring hits within 10 kb into one single event, the hit count ranged from 562 in A. thaliana to 9,022 in V. vinifera . This implies that the transposition of mitochondrial DNA of plants into chromosomal DNA is more preferable than in whale species [ 19 ].…”

Section: Resultsmentioning

confidence: 99%

“…In the previous whale Numt study [ 19 ], they also performed a Numt size distribution analysis. The average whale genome size is 2.5 Gb, and the average mitochondrial genome size is 16 kb.…”

Section: Resultsmentioning

confidence: 99%

“…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 ].…”

Section: Introductionmentioning

confidence: 99%

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Analysis of Nuclear Mitochondrial DNA Segments of Nine Plant Species: Size, Distribution, and Insertion Loci

Kim

2016

Genomics Inform

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Nuclear mitochondrial DNA segment (Numt) insertion describes a well-known phenomenon of mitochondrial DNA transfer into a eukaryotic nuclear genome. However, it has not been well understood, especially in plants. Numt insertion patterns vary from species to species in different kingdoms. In this study, the patterns were surveyed in nine plant species, and we found some tip-offs. First, when the mitochondrial genome size is relatively large, the portion of the longer Numt is also larger than the short one. Second, the whole genome duplication event increases the ratio of the shorter Numt portion in the size distribution. Third, Numt insertions are enriched in exon regions. This analysis may be helpful for understanding plant evolution.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Analysis of Nuclear Mitochondrial DNA Segments of Nine Plant Species: Size, Distribution, and Insertion Loci

Kim

2016

Genomics Inform

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“…Bu genlerinin oluşma mekanizmaları ve tarihsel süreçleri üzerine yapılan araştırmalar ökaryotik genomların evrimini anlamamıza büyük ölçüde katkı sağlamaktadır [57]. Bu durum taksonların evrimsel geçmişi ve filogenetik ilişkileri hakkında bilgi verir [52,[63][64]. Bu çalışmada PZR, dizileme ve hizalama aşamaları sonucunda bir numt (ncBT) bölgesinin varlığı ilk kez Bombus cinsinde saptanmıştır.…”

Section: Ncbt: Yalancı Gen öZellikleriunclassified

Genetic structuring of Anatolian Bombus lapidarius L. (Apidae: Hymenoptera) populations

Altun

Korkmaz

Basibuyuk

2018

ANADOLU UNIVERSITY JOURNAL OF SCIENCE AND TECHNOLOGY –C Life Sciences and Biotechnology

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ÖZETAnadolu, Avrupa'nın günümüz biyoçeşitliliğine önemli derecede katkı sağlayan bölgelerden birisidir. Bazı günümüz orta ve kuzey Avrupa popülasyonlarının buzul dönemlerinde Anadolu'da barınmış popülasyonlardan giden öncülerce oluşturulduğu savunulmaktadır. Soğuk tercih eden hayvanlar yayılış örüntülerinde buzul dönemlerinde genişleme buzullar arası dönemlerde ise daralma sergiledikleri için model organizmalar olarak kabul edilmektedir. Bu kapsamda Anadolu'nun, tarihsel biyocoğrafyası ve genetik çeşitliliği konusunda bilgi edinmek amacıyla Karadeniz bölgesinde yayılış gösteren Bombus lapidarius'un 14 kadar popülasyonundan COI ve nCTB gen bölgeleri çalışılmıştır. Her iki belirteç açısından da haplotip çeşitliliği ve özgün haplotip sayısı yüksek olup, popülasyonlar arasında anlamlı bir genetik farklılaşma saptanmıştır. Özellikle Doğu-Batı farklılaşması Karadeniz boyunca desteklenmektedir. Tüm analizlerde Doğu4 ve Doğu5 popülasyonlarının diğer popülasyonlardan belirgin olarak farklı olduğu görülmektedir. Bu farklılaşma popülasyonların coğrafik yayılış örüntüleri ile doğrudan ilişkilidir. Aynı zamanda bu popülasyonlar ayrı bir soy hattı oluşturmaktadır. Ayrıca Batı popülasyonları son türemiş popülasyonlar olarak görülmektedir.Anahtar Kelimeler: mtDNA, NUMT, Anadolu, Filocoğrafya, Genetik yapı, Coğrafik genetik yapılanma GENETIC STRUCTURING OF ANATOLIAN BOMBUS LAPIDARIUS L. (APIDAE: HYMENOPTERA) POPULATIONS ABSTRACTAnatolia is one of the important regions which have contributed to current biodiversity of Europe. It is suggested that some of the current central and northern populations of Europe have been originated from populations took refuge during glacial ages. Cold preferring animals are accepted as model organisms because they exhibit range expansion and range contraction patterns during glacial and interglacial periods, respectively. In order to improve our knowledge on biogeography and genetic diversity of Anatolia, the distribution pattern of Bombus lapidarius were investigated in the Black Sea region using COI and nCTB genes from 14 populations. High numbers of unique and diverse haplotypes were observed in both markers, suggesting genetic differentiations among populations. East-West differentiation is particularly supported throughout the Black Sea region. All analyses indicate that the East4 and East5 populations exhibit significantly differentiation from other populations. This differentiation is directly related to the geographical distribution patterns of populations. These populations constitute a separate lineage at the same time. In addition, Western populations can be accepted as recently derived populations.

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“…rates and sequence diversity of the plant mitochondrial genome (Christensen, 2013). As large 253 mitochondrial sequences are often transferred to the nucleus (Ko et al, 2015;Lopez et al, 1996;254 Michalovova et al, 2013;Richly & Leister, 2004;Noutsos et al, 2005;Bensasson et al, 2001;255 Stupar et al, 2001), looking into the relationship between Numts and orphan genes may prove 256 fruitful in understanding de novo gene evolution. 257…”

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Mitochondrial fostering: the mitochondrial genome may play a role in plant orphan gene evolution

O’Conner

2020

Preprint

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9Plant mitochondrial genomes exhibit odd evolutionary patterns. They have a high 10 rearrangement but low mutation rate, and a large size. Based on massive 11 mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique 12 evolutionary traits, we propose a "Mitochondrial Fostering" theory where the organelle 13 genome plays an integral role in the arrival and development of orphan genes (genes with 14 no homologues in other lineages). Two approaches were used to test this theory: 15 1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial 16originating DNA that has migrated to the nucleus) at the genome level, and 172) bioinformatic analysis of particular orphan sequences present in both the mitochondrial 18 genome and the nuclear genome of Arabidopsis thaliana. One study example is given about 19 one orphan sequence that codes for two unique orphan genes: one in the mitochondrial 20 genome and another one in the nuclear genome. DNA alignments show regions of this A. 21 thaliana orphan sequence exist scattered throughout other land plant mitochondrial 22 genomes. This is consistent with the high recombination rates of mitochondrial genomes in 23 land plants. This may also enable the creation of novel coding sequences within the orphan 24 loci, which can then be transferred to the nuclear genome and become exposed to new 25 evolutionary pressures. Our study also reveals a high correlation between mitochondrial 26 DNA rate transferred to the nuclear genome and number of orphan genes in land plants. 27All the data suggests the mitochondrial genome may play a role in nuclear orphan gene 28 evolution in land plants. 29 30

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Characterization of cetacean Numt and its application into cetacean phylogeny

Cited by 13 publications

References 46 publications

Analysis of Nuclear Mitochondrial DNA Segments of Nine Plant Species: Size, Distribution, and Insertion Loci

Analysis of Nuclear Mitochondrial DNA Segments of Nine Plant Species: Size, Distribution, and Insertion Loci

Genetic structuring of Anatolian Bombus lapidarius L. (Apidae: Hymenoptera) populations

Mitochondrial fostering: the mitochondrial genome may play a role in plant orphan gene evolution

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