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Sequence variability at the mitochondrial ND 1, ND 6, cyt b and D ‐loop segments in tench ( T inca tinca L .)
Author(s) -
Lo Presti R.,
Kohlmann K.,
Kersten P.,
Lisa C.,
Di Stasio L.
Publication year - 2014
Publication title -
journal of applied ichthyology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.392
H-Index - 62
eISSN - 1439-0426
pISSN - 0175-8659
DOI - 10.1111/jai.12423
Subject(s) - biology , haplotype , haplogroup , d loop , genbank , indel , mitochondrial dna , phylogenetic tree , genetics , restriction fragment length polymorphism , cytochrome b , single nucleotide polymorphism , gene , polymerase chain reaction , allele , genotype
Summary The authors' previous PCR ‐ RFLP studies on ND 1, ND 6, cyt b and D‐loop segments of mt DNA in tench revealed the existence of nine composite haplotypes, named H1‐H9. As cyt b is the only mt DNA segment whose variability has been widely studied in tench, the same four segments were sequenced in 29 individuals from 17 populations covering all nine haplotypes, with the aim of providing additional data on tench mt DNA variation. Ninety‐six polymorphic sites were identified and all differences were single nucleotide substitutions, except for six indels found in the D‐loop. The observed polymorphisms gave origin to five different ND 1 sequences, seven ND 6 sequences, six cyt b sequences and 17 D‐loop sequences. Comparison with data in GenBank revealed that none of the five ND 1 sequences were as yet reported, nor the one for cyt b or sixteen for the D‐loop; concerning ND 6, the data were the first contribution on the variability of this segment. The combination of the haplotypes at the single segments determined 20 composite haplotypes: seven (H1a–H1g) had been classified as H1 and six (H2a–H2f) as H2 with the PCR ‐ RFLP analysis, while for the other haplotypes previously identified (H3–H9) no additional variability was found. The analysis of phylogenetic trees showed that each segment was informative enough to clearly identify the two highly divergent haplogroups already reported in tench, but only the D‐loop gave a good resolution of the tree branching because of its high variability. The Median‐Joining network, constructed using the composite haplotypes, indicated H1a as the founder node for haplogroup A and the haplotypes H2a‐H2f as ancestral with respect to H7–H9. The new data on the variability of mt DNA can contribute to a better understanding of the between and within population diversity in tench.