Genomes, repeatomes and interphase chromosome organization in
the meadowfoam family (Limnanthaceae, Brassicales)

J 2022

Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales)

ZUO, Sheng, Terezie MALÍK MANDÁKOVÁ, Michaela KUBOVÁ and Martin LYSÁK

Basic information

Original name

Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales)

Authors

ZUO, Sheng (156 China, belonging to the institution), Terezie MALÍK MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Michaela KUBOVÁ (203 Czech Republic, belonging to the institution) and Martin LYSÁK (203 Czech Republic, guarantor, belonging to the institution)

Edition

PLANT JOURNAL, ENGLAND, WILEY, 2022, 0960-7412

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10611 Plant sciences, botany

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 7.200

RIV identification code

RIV/00216224:14740/22:00125618

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1111/tpj.15750

UT WoS

000787376300001

Keywords in English

Brassicales chromosomes DNA repeats interphase Limnanthes meadowfoam Rabl repeatome

Abstract

V originále

The meadowfoam family (Limnanthaceae) is one of the smallest and genomically underexplored families of the Brassicales. The Limnanthaceae harbor about seven species in the genus Limnanthes (meadowfoam) and Floerkea proserpinacoides (false mermaidweed), all native to North America. Because all Limnanthes and Floerkea species have only five chromosome pairs, i.e., a chromosome number rare in Brassicales and shared with Arabidopsis thaliana (Arabidopsis), we examined the Limnanthaceae genomes as a potential model system. Using low-coverage whole-genome sequencing data, we reexamined phylogenetic relationships and characterized the repeatomes of Limnanthaceae genomes. Phylogenies based on complete chloroplast and 35S rDNA sequences corroborated the sister relationship between Floerkea and Limnanthes and two major clades in the latter genus. The genome size of Limnanthaceae species ranges from 1.5 to 2.1 Gb, apparently due to the large increase in DNA repeats, which constitute 60-70% of their genomes. Repeatomes are dominated by long terminal repeat retrotransposons, while tandem repeats represent only less than 0.5% of the genomes. The average chromosome size in Limnanthaceae species (340-420 Mb) is more than 10 times larger than in Arabidopsis (32 Mb). A three-dimensional fluorescence in situ hybridization analysis demonstrated that the five chromosome pairs in interphase nuclei of Limnanthes species adopt the Rabl-like configuration.

Links

EF19_073/0016943, research and development project

Name: Interní grantová agentura Masarykovy univerzity

GA18-20134S, research and development project

Name: Organizace interfázních chromosomů a časné meiotické párování chromosomů u brukvovitých

Investor: Czech Science Foundation

LM2018140, research and development project

Name: e-Infrastruktura CZ (Acronym: e-INFRA CZ)

Investor: Ministry of Education, Youth and Sports of the CR

90129, large research infrastructures

Name: Czech-BioImaging II

90132, large research infrastructures

Name: NCMG II

Citovat

ZUO, Sheng, Terezie MALÍK MANDÁKOVÁ, Michaela KUBOVÁ and Martin LYSÁK. Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales). PLANT JOURNAL. ENGLAND: WILEY, 2022, vol. 110, No 5, p. 1462-1475. ISSN 0960-7412. Available from: https://dx.doi.org/10.1111/tpj.15750.

@article{1845119,
   author = {Zuo, Sheng and Malík Mandáková, Terezie and Kubová, Michaela and Lysák, Martin},
   article_location = {ENGLAND},
   article_number = {5},
   doi = {http://dx.doi.org/10.1111/tpj.15750},
   keywords = {Brassicales chromosomes DNA repeats interphase Limnanthes meadowfoam Rabl repeatome},
   language = {eng},
   issn = {0960-7412},
   journal = {PLANT JOURNAL},
   title = {Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales)},
   url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15750},
   volume = {110},
   year = {2022}
}

TY  - JOUR
ID  - 1845119
AU  - Zuo, Sheng - Malík Mandáková, Terezie - Kubová, Michaela - Lysák, Martin
PY  - 2022
TI  - Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales)
JF  - PLANT JOURNAL
VL  - 110
IS  - 5
SP  - 1462-1475
EP  - 1462-1475
PB  - WILEY
SN  - 09607412
KW  - Brassicales chromosomes DNA repeats interphase Limnanthes meadowfoam Rabl repeatome
UR  - https://onlinelibrary.wiley.com/doi/10.1111/tpj.15750
N2  - The meadowfoam family (Limnanthaceae) is one of the smallest and genomically underexplored families of the Brassicales. The Limnanthaceae harbor about seven species in the genus Limnanthes (meadowfoam) and Floerkea proserpinacoides (false mermaidweed), all native to North America. Because all Limnanthes and Floerkea species have only five chromosome pairs, i.e., a chromosome number rare in Brassicales and shared with Arabidopsis thaliana (Arabidopsis), we examined the Limnanthaceae genomes as a potential model system. Using low-coverage whole-genome sequencing data, we reexamined phylogenetic relationships and characterized the repeatomes of Limnanthaceae genomes. Phylogenies based on complete chloroplast and 35S rDNA sequences corroborated the sister relationship between Floerkea and Limnanthes and two major clades in the latter genus. The genome size of Limnanthaceae species ranges from 1.5 to 2.1 Gb, apparently due to the large increase in DNA repeats, which constitute 60-70% of their genomes. Repeatomes are dominated by long terminal repeat retrotransposons, while tandem repeats represent only less than 0.5% of the genomes. The average chromosome size in Limnanthaceae species (340-420 Mb) is more than 10 times larger than in Arabidopsis (32 Mb). A three-dimensional fluorescence in situ hybridization analysis demonstrated that the five chromosome pairs in interphase nuclei of Limnanthes species adopt the Rabl-like configuration.
ER  -

ZUO, Sheng, Terezie MALÍK MANDÁKOVÁ, Michaela KUBOVÁ and Martin LYSÁK. Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales). \textit{PLANT JOURNAL}. ENGLAND: WILEY, 2022, vol.~110, No~5, p.~1462-1475. ISSN~0960-7412. Available from: https://dx.doi.org/10.1111/tpj.15750.

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