The meso-octoploid Heliophila variabilis genome sheds a new
light on the impact of polyploidization and diploidization on
the diversity of the Cape flora

J 2023

The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora

HUANG, Yile, Xinyi GUO, Kang ZHANG, Terezie MALÍK MANDÁKOVÁ, Feng CHENG et. al.

Basic information

Original name

The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora

Authors

HUANG, Yile (156 China, belonging to the institution), Xinyi GUO (156 China, belonging to the institution), Kang ZHANG, Terezie MALÍK MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Feng CHENG and Martin LYSÁK (203 Czech Republic, guarantor, belonging to the institution)

Edition

Plant Journal, Wiley, 2023, 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 in 2022

RIV identification code

RIV/00216224:14740/23:00132880

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1111/tpj.16383

UT WoS

001037076300001

Keywords in English

genome assembly; octoploidy; polyploidy; whole-genome duplication; genome diploidization; chromosomal rearrangements; adaptive evolution; southern Africa; Brassicaceae

Abstract

V originále

Although the South African Cape flora is one of the most remarkable biodiversity hotspots, its high diversity has not been associated with polyploidy. Here, we report the chromosome-scale genome assembly of an ephemeral cruciferous species Heliophila variabilis (~334 Mb, n = 11) adapted to South African semiarid biomes. Two pairs of differently fractionated subgenomes suggest an allo-octoploid origin of the genome at least 12 million years ago. The ancestral octoploid Heliophila genome (2n = 8x = ~60) has probably originated through hybridization between two allotetraploids (2n = 4x = ~30) formed by distant, intertribal, hybridization. Rediploidization of the ancestral genome was marked by extensive reorganization of parental subgenomes, genome downsizing, and speciation events in the genus Heliophila. We found evidence for loss-of-function changes in genes associated with leaf development and early flowering, and over-retention and sub/neofunctionalization of genes involved in pathogen response and chemical defense. The genomic resources of H. variabilis will help elucidate the role of polyploidization and genome diploidization in plant adaptation to hot arid environments and origin of the Cape flora. The sequenced H. variabilis represents the first chromosome-scale genome assembly of a meso-octoploid representative of the mustard family.

Links

GA19-07487S, research and development project

Name: Polyploidní minulost a diploidní současnost: evoluce a diversifikace jihoafrického rodu Heliophila

Investor: Czech Science Foundation, The polyploid past versus diploid present: evolution and diversification of the southern African Heliophila

MUNI/A/1200/2022, interní kód MU

Name: Specifický výzkum s využitím přístupů funkční genomiky a proteomiky

Investor: Masaryk University, Specific research using functional genomics and proteomics approaches

MUNI/R/1268/2022, interní kód MU

Name: Understanding the genomic impact of apomixis in Boechera

Investor: Masaryk University, Understanding the genomic impact of apomixis in Boechera, CAREER RESTART

90254, large research infrastructures

Name: e-INFRA CZ II

Citovat

HUANG, Yile, Xinyi GUO, Kang ZHANG, Terezie MALÍK MANDÁKOVÁ, Feng CHENG and Martin LYSÁK. The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora. Plant Journal. Wiley, 2023, vol. 116, No 2, p. 446-466. ISSN 0960-7412. Available from: https://dx.doi.org/10.1111/tpj.16383.

@article{2358539,
   author = {Huang, Yile and Guo, Xinyi and Zhang, Kang and Malík Mandáková, Terezie and Cheng, Feng and Lysák, Martin},
   article_number = {2},
   doi = {http://dx.doi.org/10.1111/tpj.16383},
   keywords = {genome assembly; octoploidy; polyploidy; whole-genome duplication; genome diploidization; chromosomal rearrangements; adaptive evolution; southern Africa; Brassicaceae},
   language = {eng},
   issn = {0960-7412},
   journal = {Plant Journal},
   title = {The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora},
   url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.16383},
   volume = {116},
   year = {2023}
}

TY  - JOUR
ID  - 2358539
AU  - Huang, Yile - Guo, Xinyi - Zhang, Kang - Malík Mandáková, Terezie - Cheng, Feng - Lysák, Martin
PY  - 2023
TI  - The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora
JF  - Plant Journal
VL  - 116
IS  - 2
SP  - 446-466
EP  - 446-466
PB  - Wiley
SN  - 09607412
KW  - genome assembly
KW  - octoploidy
KW  - polyploidy
KW  - whole-genome duplication
KW  - genome diploidization
KW  - chromosomal rearrangements
KW  - adaptive evolution
KW  - southern Africa
KW  - Brassicaceae
UR  - https://onlinelibrary.wiley.com/doi/10.1111/tpj.16383
N2  - Although the South African Cape flora is one of the most remarkable biodiversity hotspots, its high diversity has not been associated with polyploidy. Here, we report the chromosome-scale genome assembly of an ephemeral cruciferous species Heliophila variabilis (~334 Mb, n = 11) adapted to South African semiarid biomes. Two pairs of differently fractionated subgenomes suggest an allo-octoploid origin of the genome at least 12 million years ago. The ancestral octoploid Heliophila genome (2n = 8x = ~60) has probably originated through hybridization between two allotetraploids (2n = 4x = ~30) formed by distant, intertribal, hybridization. Rediploidization of the ancestral genome was marked by extensive reorganization of parental subgenomes, genome downsizing, and speciation events in the genus Heliophila. We found evidence for loss-of-function changes in genes associated with leaf development and early flowering, and over-retention and sub/neofunctionalization of genes involved in pathogen response and chemical defense. The genomic resources of H. variabilis will help elucidate the role of polyploidization and genome diploidization in plant adaptation to hot arid environments and origin of the Cape flora. The sequenced H. variabilis represents the first chromosome-scale genome assembly of a meso-octoploid representative of the mustard family.
ER  -

HUANG, Yile, Xinyi GUO, Kang ZHANG, Terezie MALÍK MANDÁKOVÁ, Feng CHENG and Martin LYSÁK. The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora. \textit{Plant Journal}. Wiley, 2023, vol.~116, No~2, p.~446-466. ISSN~0960-7412. Available from: https://dx.doi.org/10.1111/tpj.16383.

Detailed Information on Publication Record