PMID- 33440692
OWN - NLM
STAT- MEDLINE
DCOM- 20210406
LR  - 20210406
IS  - 1422-0067 (Electronic)
IS  - 1422-0067 (Linking)
VI  - 22
IP  - 2
DP  - 2021 Jan 11
TI  - Plastid Genomes of the Early Vascular Plant Genus Selaginella Have Unusual Direct 
      Repeat Structures and Drastically Reduced Gene Numbers.
LID - 10.3390/ijms22020641 [doi]
LID - 641
AB  - The early vascular plants in the genus Selaginella, which is the sole genus of 
      the Selaginellaceae family, have an important place in evolutionary history, 
      along with ferns, as such plants are valuable resources for deciphering plant 
      evolution. In this study, we sequenced and assembled the plastid genome 
      (plastome) sequences of two Selaginella tamariscina individuals, as well as 
      Selaginella stauntoniana and Selaginella involvens. Unlike the inverted repeat 
      (IR) structures typically found in plant plastomes, Selaginella species had 
      direct repeat (DR) structures, which were confirmed by Oxford Nanopore long-read 
      sequence assembly. Comparative analyses of 19 lycophytes, including two Huperzia 
      and one Isoetes species, revealed unique phylogenetic relationships between 
      Selaginella species and related lycophytes, reflected by structural 
      rearrangements involving two rounds of large inversions that resulted in dynamic 
      changes between IR and DR blocks in the plastome sequence. Furthermore, we 
      present other uncommon characteristics, including a small genome size, drastic 
      reductions in gene and intron numbers, a high GC content, and extensive RNA 
      editing. Although the 16 Selaginella species examined may not fully represent the 
      genus, our findings suggest that Selaginella plastomes have undergone unique 
      evolutionary events yielding genomic features unparalleled in other lycophytes, 
      ferns, or seed plants.
FAU - Shim, Hyeonah
AU  - Shim H
AD  - Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding 
      Institute, Research Institute of Agriculture and Life Sciences, College of 
      Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 
      Seoul 08826, Korea.
FAU - Lee, Hyeon Ju
AU  - Lee HJ
AD  - Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding 
      Institute, Research Institute of Agriculture and Life Sciences, College of 
      Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 
      Seoul 08826, Korea.
FAU - Lee, Junki
AU  - Lee J
AD  - Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding 
      Institute, Research Institute of Agriculture and Life Sciences, College of 
      Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 
      Seoul 08826, Korea.
AD  - Phyzen Genomics Institute, Seongnam 13558, Korea.
FAU - Lee, Hyun-Oh
AU  - Lee HO
AD  - Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding 
      Institute, Research Institute of Agriculture and Life Sciences, College of 
      Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 
      Seoul 08826, Korea.
AD  - Phyzen Genomics Institute, Seongnam 13558, Korea.
FAU - Kim, Jong-Hwa
AU  - Kim JH
AD  - Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea.
FAU - Yang, Tae-Jin
AU  - Yang TJ
AUID- ORCID: 0000-0002-9676-8801
AD  - Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding 
      Institute, Research Institute of Agriculture and Life Sciences, College of 
      Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 
      Seoul 08826, Korea.
FAU - Kim, Nam-Soo
AU  - Kim NS
AD  - Department of Molecular Bioscience, Kangwon National University, Chuncheon 24341, 
      Korea.
LA  - eng
GR  - Project No. PJ013238/Cooperative Research Program for Agriculture Science & 
      Technology Development, Rural Development Administration, Republic of Korea/
GR  - MSIP(NRF-2015M3A9A5030733)/Bio & Medical Technology Development Program of the 
      NRF funded by the Korean government/
PT  - Journal Article
DEP - 20210111
PL  - Switzerland
TA  - Int J Mol Sci
JT  - International journal of molecular sciences
JID - 101092791
SB  - IM
MH  - Base Composition
MH  - Gene Expression Regulation, Plant
MH  - Genes, Plant
MH  - Genome Size
MH  - *Genome, Plant
MH  - *Genome, Plastid
MH  - *Genomics/methods
MH  - Introns
MH  - Phylogeny
MH  - RNA Editing
MH  - Selaginellaceae/classification/*genetics
PMC - PMC7827865
OTO - NOTNLM
OT  - RNA editing
OT  - Selaginella
OT  - direct repeats
OT  - lycophytes
OT  - plastomes
COIS- The authors declare no conflict of interest.
EDAT- 2021/01/15 06:00
MHDA- 2021/04/07 06:00
PMCR- 2021/01/11
CRDT- 2021/01/14 01:01
PHST- 2020/11/16 00:00 [received]
PHST- 2021/01/06 00:00 [revised]
PHST- 2021/01/08 00:00 [accepted]
PHST- 2021/01/14 01:01 [entrez]
PHST- 2021/01/15 06:00 [pubmed]
PHST- 2021/04/07 06:00 [medline]
PHST- 2021/01/11 00:00 [pmc-release]
AID - ijms22020641 [pii]
AID - ijms-22-00641 [pii]
AID - 10.3390/ijms22020641 [doi]
PST - epublish
SO  - Int J Mol Sci. 2021 Jan 11;22(2):641. doi: 10.3390/ijms22020641.