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Article ; Online: Tracing the history of chromosome evolution in legumes using genomics.

Wojciechowski, Martin F

2019 Volume 223, Issue 4, Page(s) 1693–1695

MeSH term(s)	Chromosomes ; Fabaceae ; Genome ; Genomics
Language	English
Publishing date	2019-06-07
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.15926
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Article ; Online: Characterization and comparative analysis of the complete plastid genomes of four Astragalus species.

Moghaddam, Mahtab / Wojciechowski, Martin F / Kazempour-Osaloo, Shahrokh

PloS one

2023 Volume 18, Issue 5, Page(s) e0286083

Abstract: Astragalus is the largest flowering plant genus. We assembled the plastid genomes of four Astragalus species (Astragalus iranicus, A. macropelmatus, A. mesoleios, A. odoratus) using next-generation sequencing and analyzed their plastomes including genome ...

Abstract	Astragalus is the largest flowering plant genus. We assembled the plastid genomes of four Astragalus species (Astragalus iranicus, A. macropelmatus, A. mesoleios, A. odoratus) using next-generation sequencing and analyzed their plastomes including genome organization, codon usage, nucleotide diversity, prediction of RNA editing and etc. The total length of the newly sequenced Astragalus plastomes ranged from 121,050 bp to 123,622 bp, with 110 genes comprising 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Comparative analysis of the chloroplast genomes of Astragalus revealed several hypervariable regions comprising three non-coding sites (trnQ(UUG)-accD, rps7 -trnV(GAC) and trnR(ACG)-trnN(GUU)) and four protein-coding genes (ycf1, ycf2, accD and clpP), which have potential as molecular markers. Positive selection signatures were found in five genes in Astragalus species including rps11, rps15, accD, clpP and ycf1. The newly sequenced species, A. macropelmatus, has an approximately 13-kb inversion in IR region. Phylogenetic analysis based on 75 protein-coding gene sequences confirmed that Astragalus form a monophyletic clade within the tribe Galegeae and Oxytropis is sister group to the Coluteoid clade. The results of this study may helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Astragalus and IRLC levels and investigating the phylogenetic relationships. Moreover, the newly plastid genomes sequenced have been increased the plastome data resources on Astragalus that can be useful in further phylogenomic studies.
MeSH term(s)	Phylogeny ; Genome, Plastid ; Astragalus Plant ; Genome, Chloroplast ; Fabaceae
Language	English
Publishing date	2023-05-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0286083
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Article ; Online: Remarkably rapid, recent diversification of Cochemiea and Mammillaria in the Baja California, Mexico region.

Breslin, Peter B / Wojciechowski, Martin F / Majure, Lucas C

American journal of botany

2022 Volume 109, Issue 9, Page(s) 1472–1487

Abstract: Premise: The Cactaceae of northwestern Mexico and the southwestern United States constitute a major component of the angiosperm biodiversity of the region. The Mammilloid clade, (Cactaceae, tribe Cacteae), composed of the genera Cochemiea, Coryphantha, ... ...

Abstract	Premise: The Cactaceae of northwestern Mexico and the southwestern United States constitute a major component of the angiosperm biodiversity of the region. The Mammilloid clade, (Cactaceae, tribe Cacteae), composed of the genera Cochemiea, Coryphantha, Cumarinia, Mammillaria, and Pelecyphora is especially species rich. We sought to understand the timing, geographical and climate influences correlated with expansion of the Mammilloid clade, through the Sonoran Desert into Baja California. Methods: We reconstructed the historical biogeography of the Mammilloid clade, using Bayesian and maximum likelihood methods, based on a strongly supported molecular phylogeny. We also estimated divergence times, the timing of emergence of key characters, and diversification rates and rate shifts of the Mammilloid clade. Results: We found that the most recent common ancestor of Cochemiea arrived in the Cape region of Baja California from the Sonoran Desert region approximately 5 million years ago, coinciding with the timing of peninsular rifting from the mainland, suggesting dispersal and vicariance as causes of species richness and endemism. The diversification rate for Cochemiea is estimated to be approximately 12 times that of the mean background diversification rate for angiosperms. Divergence time estimation shows that many of the extant taxa in Cochemiea and Baja California Mammillaria emerged from common ancestors 1 million to 200,000 years ago, having a mid-Pleistocene origin. Conclusions: Cochemiea and Mammillaria of the Baja California region are examples of recent, rapid diversification. Geological and climatic forces at multiple spatial and temporal scales are correlated with the western distributions of the Mammilloid clade.
MeSH term(s)	Bayes Theorem ; Cactaceae/genetics ; Geography ; Mexico ; Phylogeny
Language	English
Publishing date	2022-09-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.16048
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Article: Insights into Species Delimitation of Selected Species in the Flowering Plant Genus Medicago Section Buceras (Leguminosae)

Steier, Julia E. / Mandáková, Terezie / Wojciechowski, Martin F. / Steele, Kelly P.

Systematic botany. 2022 June 14, v. 47, no. 2

2022

Abstract: The genus Medicago (Leguminosae, Papilionoideae) contains about 90 species including the important forage crop alfalfa Medicago sativa and the genomic model Medicago truncatula. Despite intensive research on the genus because of its agricultural ... ...

Abstract	The genus Medicago (Leguminosae, Papilionoideae) contains about 90 species including the important forage crop alfalfa Medicago sativa and the genomic model Medicago truncatula. Despite intensive research on the genus because of its agricultural importance, there is a relative lack of information about chromosome number and genome size in some Medicago species, especially those from Medicago section Buceras that were formerly placed in the sister genus Trigonella, and are paraphyletic to the remainder of the genus Medicago. Past studies revealed that previous species delimitations did not conform well with complex patterns of morphological or genetic variation. Some published chromosome numbers, e.g. 2n = 28 and 2n = 44, differ from those of the rest of the genus, which are mostly 2n = 16 or polyploids thereof, although some cases of aneuploid reduction or dysploidy (e.g. 2n = 14) do exist. Here we estimated phylogenetic relationships of 42 accessions corresponding to 14 currently recognized Medicago species that are paraphyletic to the remainder of Medicago with a focus on Medicago monantha; for a number of those accessions we obtained estimates of genome size (39) and chromosome number (14). We can confirm the delimitation of two species within M. section Buceras and our data suggest that there are at least two entities with distinct geographic distributions within the currently recognized species M. monantha, which differ in chromosome number and genome size. Our data also suggest that polyploidy and post-polyploid descending dysploidy played a significant role in genome evolution within M. section Buceras. Our data provide a strong foundation for whole-genome sequencing projects and further in-depth research of these paraphyletic lineages.
Keywords	Medicago sativa ; Medicago truncatula ; Trigonella ; alfalfa ; aneuploidy ; chromosome number ; chromosomes ; forage crops ; genetic variation ; genome ; genomics ; models ; paraphyly ; polyploidy
Language	English
Dates of publication	2022-0614
Size	p. 431-440.
Publishing place	American Society of Plant Toxonomists
Document type	Article
ZDB-ID	2052625-8
ISSN	1548-2324 ; 0363-6445
ISSN (online)	1548-2324
ISSN	0363-6445
DOI	10.1600/036364422X16512564801533
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Article ; Online: Remarkably rapid, recent diversification of Cochemiea and Mammillaria in the Baja California, Mexico region

Breslin, Peter B. / Wojciechowski, Martin F. / Majure, Lucas C.

American Journal of Botany. 2022 Sept., v. 109, no. 9 p.1472-1487

2022

Abstract: PREMISE: The Cactaceae of northwestern Mexico and the southwestern United States constitute a major component of the angiosperm biodiversity of the region. The Mammilloid clade, (Cactaceae, tribe Cacteae), composed of the genera Cochemiea, Coryphantha, ... ...

Abstract	PREMISE: The Cactaceae of northwestern Mexico and the southwestern United States constitute a major component of the angiosperm biodiversity of the region. The Mammilloid clade, (Cactaceae, tribe Cacteae), composed of the genera Cochemiea, Coryphantha, Cumarinia, Mammillaria, and Pelecyphora is especially species rich. We sought to understand the timing, geographical and climate influences correlated with expansion of the Mammilloid clade, through the Sonoran Desert into Baja California. METHODS: We reconstructed the historical biogeography of the Mammilloid clade, using Bayesian and maximum likelihood methods, based on a strongly supported molecular phylogeny. We also estimated divergence times, the timing of emergence of key characters, and diversification rates and rate shifts of the Mammilloid clade. RESULTS: We found that the most recent common ancestor of Cochemiea arrived in the Cape region of Baja California from the Sonoran Desert region approximately 5 million years ago, coinciding with the timing of peninsular rifting from the mainland, suggesting dispersal and vicariance as causes of species richness and endemism. The diversification rate for Cochemiea is estimated to be approximately 12 times that of the mean background diversification rate for angiosperms. Divergence time estimation shows that many of the extant taxa in Cochemiea and Baja California Mammillaria emerged from common ancestors 1 million to 200,000 years ago, having a mid‐Pleistocene origin. CONCLUSIONS: Cochemiea and Mammillaria of the Baja California region are examples of recent, rapid diversification. Geological and climatic forces at multiple spatial and temporal scales are correlated with the western distributions of the Mammilloid clade.
Keywords	Bayesian theory ; Coryphantha ; Mammillaria ; Pelecyphora ; ancestry ; biogeography ; botany ; climate ; indigenous species ; phylogeny ; species richness ; statistical analysis ; Mexico ; Sonoran Desert
Language	English
Dates of publication	2022-09
Size	p. 1472-1487.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.16048
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Article: Projected climate change threatens significant range contraction of

Breslin, Peter B / Wojciechowski, Martin F / Albuquerque, Fabio

Ecology and evolution

2020 Volume 10, Issue 23, Page(s) 13211–13224

Abstract: Aim: Threats faced by narrowly distributed endemic plant species in the face of the Earth's sixth mass extinction and climate change exposure are especially severe for taxa on islands. We investigated the current and projected distribution and range ... ...

Abstract	Aim: Threats faced by narrowly distributed endemic plant species in the face of the Earth's sixth mass extinction and climate change exposure are especially severe for taxa on islands. We investigated the current and projected distribution and range changes of Location: The island archipelago in Bahía Magdalena on the Pacific coast, Baja California Sur, Mexico. Methods: We used temperature and precipitation variables at 30-arc second resolution and soil type, employing multiple species distribution modeling methods, to identify important climate and soil conditions driving current habitat suitability. The best model of current suitability is used to predict possible effects of four climate change scenarios based on best-case to worst-case representative concentration pathways, with projected climate data from two general circulation models, over two time periods. Main conclusions: The occurrence of the species is found to be strongly correlated with ultramafic soils. The most important climate predictor for habitat suitability is annual temperature range. The species is predicted to undergo range contractions from 21% to 53%, depending on the severity and duration of exposure to climate change. The broader implications for a wide range of narrowly adapted, threatened, and endemic plant species indicate an urgent need for threat assessment based on habitat suitability and climate change modeling.
Language	English
Publishing date	2020-10-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.6914
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Article ; Online: In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae).

Choi, In-Su / Wojciechowski, Martin F / Ruhlman, Tracey A / Jansen, Robert K

Molecular phylogenetics and evolution

2021 Volume 163, Page(s) 107236

Abstract: Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage ... ...

Abstract	Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.
MeSH term(s)	Evolution, Molecular ; Fabaceae/genetics ; Genome, Mitochondrial ; Introns/genetics ; Phylogeny
Language	English
Publishing date	2021-06-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2021.107236
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Article: Molecular phylogeny of the Mammilloid clade (Cactaceae) resolves the monophyly of Mammillaria

Breslin, Peter B. / Wojciechowski, Martin F. / Majure, Lucas C.

Taxon. 2021 Apr., v. 70, no. 2

2021

Abstract: To resolve more than 150 years of taxonomic confusion regarding the genus Mammillaria, the molecular phylogeny of the Mammilloid clade, including the genera Cochemiea, Coryphantha, Cumarinia, Escobaria, Mammillaria, Neolloydia, and Ortegocactus, is ... ...

Abstract	To resolve more than 150 years of taxonomic confusion regarding the genus Mammillaria, the molecular phylogeny of the Mammilloid clade, including the genera Cochemiea, Coryphantha, Cumarinia, Escobaria, Mammillaria, Neolloydia, and Ortegocactus, is reconstructed. We included broad sampling of genera as well as a regionally nearly complete taxon sampling of Mammillaria and Cochemiea from the Baja California region. Employing the large single‐copy region of the plastid genome as sequence data, we conducted maximum likelihood, maximum parsimony and Bayesian inference to reconstruct a molecular phylogeny of the clade. The molecular phylogenetic topology was further supported by reconstructing the ancestral states of 10 characters, from which three traditionally taxonomically important characters for the sampled taxa were selected. Results from our analyses clarify the evolutionary relationships of these closely related taxa, providing high resolution with strongly supported clades and subclades. The genus Mammillaria as currently circumscribed is non‐monophyletic, and thus, we propose a recircumscription of the Mammilloid clade yielding three monophyletic genera, Mammillaria s.str., Cochemiea s.l. and Coryphantha. We herein make appropriate combinations to accommodate our circumscription of these genera.
Keywords	Bayesian theory ; Coryphantha ; Escobaria ; Mammillaria ; Neolloydia ; monophyly ; plastid genome ; statistical analysis ; topology ; Mexico
Language	English
Dates of publication	2021-04
Size	p. 308-323.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	204216-2
ISSN	0040-0262
ISSN	0040-0262
DOI	10.1002/tax.12451
Database	NAL-Catalogue (AGRICOLA)

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Article: In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae)

Choi, In-Su / Wojciechowski, Martin F. / Ruhlman, Tracey A. / Jansen, Robert K.

Molecular phylogenetics and evolution. 2021 Oct., v. 163

2021

Abstract: Plant specific mitoviruses in the ‘genus’ Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage ... ...

Abstract	Plant specific mitoviruses in the ‘genus’ Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.
Keywords	Acacia ; Mitovirus ; RNA ; Trifolium ; genomics ; introns ; legumes ; mitochondria ; mitochondrial genome ; nerve tissue ; phylogeny ; transposons
Language	English
Dates of publication	2021-10
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2021.107236
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Article: Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae)

Choi, In‐Su / Wojciechowski, Martin F. / Steele, Kelly P. / Hunter, Sarah G. / Ruhlman, Tracey A. / Jansen, Robert K.

plant journal. 2022 Apr., v. 110, no. 2

2022

Abstract: Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily ... ...

Abstract	Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post‐IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10‐like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6–3.0% of total genomic DNA, a value approximately three‐fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10‐like sequence coverage level was 691.5–7198‐fold higher in M. polymorpha and closely related species. In addition to the post‐IGT amplification, our analysis identified the canonical telomeric repeat and the species‐specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10‐like tandem repeat family in the M. polymorpha clade is discussed.
Keywords	DNA ; Medicago polymorpha ; chromosomal instability ; gene transfer ; genes ; mitochondria ; mitochondrial genome ; nuclear genome ; satellites ; telomeres
Language	English
Dates of publication	2022-04
Size	p. 389-406.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.15676
Database	NAL-Catalogue (AGRICOLA)

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