PMID- 37639389
OWN - NLM
STAT- MEDLINE
DCOM- 20230831
LR  - 20230904
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 18
IP  - 8
DP  - 2023
TI  - Bioinformatic and fine-scale chromosomal mapping reveal the nature and evolution 
      of eliminated chromosomes in the Japanese hagfish, Eptatretus burgeri, through 
      analysis of repetitive DNA families.
PG  - e0286941
LID - 10.1371/journal.pone.0286941 [doi]
LID - e0286941
AB  - In the Japanese hagfish, Eptatretus burgeri, approximately 21% of the genomic DNA 
      in germ cells (2n = 52) consists of 16 chromosomes (eliminated [E]-chromosomes) 
      that are eliminated from presumptive somatic cells (2n = 36). To uncover the 
      eliminated genome (E-genome), we have identified 16 eliminated repetitive DNA 
      families from eight hagfish species, with 11 of these repeats being selectively 
      amplified in the germline genome of E. burgeri. Furthermore, we have demonstrated 
      that six of these sequences, namely EEEb1-6, are exclusively localized on all 16 
      E-chromosomes. This has led to the hypothesis that the eight pairs of 
      E-chromosomes are derived from one pair of ancestral chromosomes via multiple 
      duplication events over a prolonged evolutionary period. NGS analysis has 
      recently facilitated the re-assembly of two distinct draft genomes of E. burgeri, 
      derived from the testis and liver. This advancement allows for the prediction of 
      not only nonrepetitive eliminated sequences but also over 100 repetitive and 
      eliminated sequences, accomplished through K-mer-based analysis. In this study, 
      we report four novel eliminated repetitive DNA sequences (designated as EEEb7-10) 
      and confirm the relative chromosomal localization of all eliminated repeats 
      (EEEb1-10) by fluorescence in situ hybridization (FISH). With the exception of 
      EEEb10, all sequences were exclusively detected on EEEb1-positive chromosomes. 
      Surprisingly, EEEb10 was detected as an intense signal on EEEb1-positive 
      chromosomes and as a scattered signal on other chromosomes in germ cells. The 
      study further divided the eight pairs of E-chromosomes into six groups based on 
      the signal distribution of each DNA family, and fiber-FISH experiments showed 
      that the EEEb2-10 family was dispersed in the EEEb1-positive extended chromatin 
      fiber. These findings provide new insights into the mechanisms underlying 
      chromosome elimination and the evolution of E-chromosomes, supporting our 
      previous hypothesis.
CI  - Copyright: (c) 2023 Nagao et al. This is an open access article distributed under 
      the terms of the Creative Commons Attribution License, which permits unrestricted 
      use, distribution, and reproduction in any medium, provided the original author 
      and source are credited.
FAU - Nagao, Kohei
AU  - Nagao K
AD  - Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, 
      Japan.
FAU - Tanaka, Yoshiki
AU  - Tanaka Y
AD  - Department of Life Science and Technology, School of Life Science and Technology, 
      Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
FAU - Kajitani, Rei
AU  - Kajitani R
AD  - Department of Life Science and Technology, School of Life Science and Technology, 
      Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
FAU - Toyoda, Atsushi
AU  - Toyoda A
AUID- ORCID: 0000-0002-0728-7548
AD  - Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 
      Japan.
AD  - Comparative Genomics Laboratory, National Institute of Genetics, Mishima, 
      Shizuoka, Japan.
FAU - Itoh, Takehiko
AU  - Itoh T
AD  - Department of Life Science and Technology, School of Life Science and Technology, 
      Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
FAU - Kubota, Souichirou
AU  - Kubota S
AD  - Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, 
      Japan.
FAU - Goto, Yuji
AU  - Goto Y
AUID- ORCID: 0009-0008-2636-4335
AD  - Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, 
      Japan.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20230828
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 9007-49-2 (DNA)
RN  - 0 (Euchromatin)
SB  - IM
MH  - Animals
MH  - Male
MH  - Computational Biology
MH  - DNA
MH  - Euchromatin
MH  - *Hagfishes/genetics
MH  - In Situ Hybridization, Fluorescence
PMC - PMC10461843
COIS- The authors have declared that no competing interests exist.
EDAT- 2023/08/28 18:41
MHDA- 2023/08/31 06:41
PMCR- 2023/08/28
CRDT- 2023/08/28 13:32
PHST- 2023/05/26 00:00 [received]
PHST- 2023/08/14 00:00 [accepted]
PHST- 2023/08/31 06:41 [medline]
PHST- 2023/08/28 18:41 [pubmed]
PHST- 2023/08/28 13:32 [entrez]
PHST- 2023/08/28 00:00 [pmc-release]
AID - PONE-D-23-16202 [pii]
AID - 10.1371/journal.pone.0286941 [doi]
PST - epublish
SO  - PLoS One. 2023 Aug 28;18(8):e0286941. doi: 10.1371/journal.pone.0286941. 
      eCollection 2023.