Project description:Transcriptomics comparative analysis of the Japanese inshore hagfish, Eptatretus burgeri, the Artic lamprey, Lethenteron camtschaticum, and the cloudy catshark, Scyliorhinus torazame
Project description:In the Japanese hagfish Eptatretus burgeri, 16 chromosomes (eliminated [E]-chromosomes) have been lost in somatic cells (2n = 36), which is equivalent to approx. 21% of the genomic DNA in germ cells (2n = 52). At least seven of the 12 eliminated repetitive DNA families isolated in eight hagfish species were selectively amplified in the germline genome of this species. One of them, EEEb1 (eliminated element of E. burgeri 1) is exclusively localized on all E-chromosomes. Herein, we identified four novel eliminated repetitive DNA families (named EEEb3-6) through PCR amplification and suppressive subtractive hybridization (SSH) combined with Southern-blot hybridization. EEEb3 was mosaic for 5S rDNA and SINE elements. EEEb4 was GC-rich repeats and has one pair of direct and inverted repeats, whereas EEEb5 and EEEb6 were AT-rich repeats with one pair and two pairs of sub-repeats, respectively. Interestingly, all repeat classes except EEEb3 were transcribed in the testes, although no open reading frames (ORF) were identified. We conducted fluorescence in situ hybridization (FISH) to examine the chromosomal localizations of EEEb3-6 and EEEb2, which was previously isolated from the germline genome of E. burgeri. All sequences were only found on all EEEb1-positive E-chromosomes. Copy number estimation of the repeated elements by slot-blot hybridization revealed that (i) the EEEb1-6 family members occupied 39.9% of the total eliminated DNA, and (ii) a small number of repeats were retained in somatic cells, suggesting that there is incomplete elimination of the repeated elements. These results provide new insights into the mechanisms involved in the chromosome elimination and the evolution of E-chromosomes.
Project description:The fishery of inshore hagfish (Eptatretus burgeri) is particularly important from the perspective of the eel-skin leather industry in the northwest Pacific. In order to reveal the genetic diversity and population structure of E. burgeri in the northwest Pacific, we analyzed partial nucleotide sequences of three mitochondrial DNA regions (523 bp in COI, 712 bp in ND4 and 617 bp in Cytb) based on specimens collected from six locations in Korea and Japan. The genetic diversities of E. burgeri were higher in Korean locations compared to Japanese ones. AMOVA showed that E. burgeri was completely separated into two groups (group A: southern coast of Korea and western coast of Japan vs. group B: eastern coast of Japan). Furthermore, groups A and B were divided into each two lineages (lineage I: west southern coast of Korea, lineage II: east southern coast of Korea and western coast of Japan, lineage III and IV: eastern coast of Japan). Our molecular results suggest that these two groups and lineages of E. burgeri may be different evolutionary significant unit and management unit, respectively.
