The chromosome-level genome sequence and karyotypic evolution
of Megadenia pygmaea (Brassicaceae)

J 2021

The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae)

YANG, W.J., L. ZHANG, Terezie MANDÁKOVÁ, L. HUANG, T. LI et. al.

Základní údaje

Originální název

The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae)

Autoři

YANG, W.J., L. ZHANG, Terezie MANDÁKOVÁ (203 Česká republika, domácí), L. HUANG, T. LI, J.B. JIANG, Y.Z. YANG, Martin LYSÁK (203 Česká republika, garant, domácí), J.Q. LIU a Q.J. HU

Vydání

Molecular Ecology Resources, HOBOKEN, WILEY, 2021, 1755-098X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 8.678

Kód RIV

RIV/00216224:14740/21:00121242

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1111/1755-0998.13291

UT WoS

000594666000001

Klíčová slova anglicky

Brassicaceae; descending dysploidy; genome assembly; karyotype and chromosome evolution; Qinghai-Tibet Plateau

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 1. 2022 13:57, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was assembled for Megadenia pygmaea using Nanopore long reads and high-throughput chromosome conformation capture (Hi-C). The assembled genome is 215.2 Mb and is anchored on six pseudochromosomes. We annotated a total of 25,607 high-confidence protein-coding genes and corroborated the phylogenetic affinity of Megadenia with the Brassicaceae expanded lineage II, containing numerous agricultural crops. We dated the divergence of Megadenia from its closest relatives to 27.04 (19.11-36.60) million years ago. A reconstruction of the chromosomal composition of the species was performed based on the de novo assembled genome and comparative chromosome painting analysis. The karyotype structure of M. pygmaea is very similar to the previously inferred proto-Calepineae karyotype (PCK; n = 7) of the lineage II. However, an end-to-end translocation between two ancestral chromosomes reduced the chromosome number from n = 7 to n = 6 in Megadenia. Our reference genome provides fundamental information for karyotypic evolution and evolutionary study of this genus.

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

YANG, W.J., L. ZHANG, Terezie MANDÁKOVÁ, L. HUANG, T. LI, J.B. JIANG, Y.Z. YANG, Martin LYSÁK, J.Q. LIU a Q.J. HU. The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae). Molecular Ecology Resources. HOBOKEN: WILEY, 2021, roč. 21, č. 3, s. 871-879. ISSN 1755-098X. Dostupné z: https://dx.doi.org/10.1111/1755-0998.13291.

@article{1752938,
   author = {Yang, W.J. and Zhang, L. and Mandáková, Terezie and Huang, L. and Li, T. and Jiang, J.B. and Yang, Y.Z. and Lysák, Martin and Liu, J.Q. and Hu, Q.J.},
   article_location = {HOBOKEN},
   article_number = {3},
   doi = {http://dx.doi.org/10.1111/1755-0998.13291},
   keywords = {Brassicaceae; descending dysploidy; genome assembly; karyotype and chromosome evolution; Qinghai-Tibet Plateau},
   language = {eng},
   issn = {1755-098X},
   journal = {Molecular Ecology Resources},
   title = {The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae)},
   url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13291},
   volume = {21},
   year = {2021}
}

TY  - JOUR
ID  - 1752938
AU  - Yang, W.J. - Zhang, L. - Mandáková, Terezie - Huang, L. - Li, T. - Jiang, J.B. - Yang, Y.Z. - Lysák, Martin - Liu, J.Q. - Hu, Q.J.
PY  - 2021
TI  - The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae)
JF  - Molecular Ecology Resources
VL  - 21
IS  - 3
SP  - 871-879
EP  - 871-879
PB  - WILEY
SN  - 1755098X
KW  - Brassicaceae
KW  - descending dysploidy
KW  - genome assembly
KW  - karyotype and chromosome evolution
KW  - Qinghai-Tibet Plateau
UR  - https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13291
N2  - Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was assembled for Megadenia pygmaea using Nanopore long reads and high-throughput chromosome conformation capture (Hi-C). The assembled genome is 215.2 Mb and is anchored on six pseudochromosomes. We annotated a total of 25,607 high-confidence protein-coding genes and corroborated the phylogenetic affinity of Megadenia with the Brassicaceae expanded lineage II, containing numerous agricultural crops. We dated the divergence of Megadenia from its closest relatives to 27.04 (19.11-36.60) million years ago. A reconstruction of the chromosomal composition of the species was performed based on the de novo assembled genome and comparative chromosome painting analysis. The karyotype structure of M. pygmaea is very similar to the previously inferred proto-Calepineae karyotype (PCK; n = 7) of the lineage II. However, an end-to-end translocation between two ancestral chromosomes reduced the chromosome number from n = 7 to n = 6 in Megadenia. Our reference genome provides fundamental information for karyotypic evolution and evolutionary study of this genus.
ER  -

YANG, W.J., L. ZHANG, Terezie MANDÁKOVÁ, L. HUANG, T. LI, J.B. JIANG, Y.Z. YANG, Martin LYSÁK, J.Q. LIU a Q.J. HU. The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae). \textit{Molecular Ecology Resources}. HOBOKEN: WILEY, 2021, roč.~21, č.~3, s.~871-879. ISSN~1755-098X. Dostupné z: https://dx.doi.org/10.1111/1755-0998.13291.

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