Phylogenomics and genome size evolution in Amomum s. s.
(Zingiberaceae): Comparison of traditional and modern
sequencing methods

J 2023

Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods

HLAVATÁ, Kristýna, Jana LEONG-ŠKORNIČKOVÁ, Eliška ZÁVESKÁ, Otakar ŠÍDA, Mark NEWMAN et. al.

Basic information

Original name

Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods

Authors

HLAVATÁ, Kristýna, Jana LEONG-ŠKORNIČKOVÁ, Eliška ZÁVESKÁ, Otakar ŠÍDA, Mark NEWMAN, Terezie MALÍK MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Martin LYSÁK (203 Czech Republic, belonging to the institution), Karol MARHOLD and Tomáš FÉR (guarantor)

Edition

Molecular Phylogenetics and Evolution, Elsevier, 2023, 1055-7903

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: 4.100 in 2022

RIV identification code

RIV/00216224:14740/23:00132764

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1016/j.ympev.2022.107666

UT WoS

000929726100005

Keywords in English

Chromosome counts; cpDNA; Elettariopsis; Hyb-Seq; ITS; Polyploidy

Abstract

V originále

Background and Aims: A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. Methods: In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted. Key Results: Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54-8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. Conclusions: Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.

Links

LM2018140, research and development project

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

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

90267, large research infrastructures

Name: NCMG III

Citovat

HLAVATÁ, Kristýna, Jana LEONG-ŠKORNIČKOVÁ, Eliška ZÁVESKÁ, Otakar ŠÍDA, Mark NEWMAN, Terezie MALÍK MANDÁKOVÁ, Martin LYSÁK, Karol MARHOLD and Tomáš FÉR. Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods. Molecular Phylogenetics and Evolution. Elsevier, 2023, vol. 178, January, p. 1-14. ISSN 1055-7903. Available from: https://dx.doi.org/10.1016/j.ympev.2022.107666.

@article{2355899,
   author = {Hlavatá, Kristýna and LeongandŠkorničková, Jana and Záveská, Eliška and Šída, Otakar and Newman, Mark and Malík Mandáková, Terezie and Lysák, Martin and Marhold, Karol and Fér, Tomáš},
   article_number = {January},
   doi = {http://dx.doi.org/10.1016/j.ympev.2022.107666},
   keywords = {Chromosome counts; cpDNA; Elettariopsis; Hyb-Seq; ITS; Polyploidy},
   language = {eng},
   issn = {1055-7903},
   journal = {Molecular Phylogenetics and Evolution},
   title = {Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods},
   url = {https://doi.org/10.1016/j.ympev.2022.107666},
   volume = {178},
   year = {2023}
}

TY  - JOUR
ID  - 2355899
AU  - Hlavatá, Kristýna - Leong-Škorničková, Jana - Záveská, Eliška - Šída, Otakar - Newman, Mark - Malík Mandáková, Terezie - Lysák, Martin - Marhold, Karol - Fér, Tomáš
PY  - 2023
TI  - Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods
JF  - Molecular Phylogenetics and Evolution
VL  - 178
IS  - January
SP  - 1-14
EP  - 1-14
PB  - Elsevier
SN  - 10557903
KW  - Chromosome counts
KW  - cpDNA
KW  - Elettariopsis
KW  - Hyb-Seq
KW  - ITS
KW  - Polyploidy
UR  - https://doi.org/10.1016/j.ympev.2022.107666
N2  - Background and Aims: A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. Methods: In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted. Key Results: Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54-8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. Conclusions: Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.
ER  -

HLAVATÁ, Kristýna, Jana LEONG-ŠKORNIČKOVÁ, Eliška ZÁVESKÁ, Otakar ŠÍDA, Mark NEWMAN, Terezie MALÍK MANDÁKOVÁ, Martin LYSÁK, Karol MARHOLD and Tomáš FÉR. Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods. \textit{Molecular Phylogenetics and Evolution}. Elsevier, 2023, vol.~178, January, p.~1-14. ISSN~1055-7903. Available from: https://dx.doi.org/10.1016/j.ympev.2022.107666.

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