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The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes.

ABSTRACT: The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.

SUBMITTER: Sawicki J

PROVIDER: S-EPMC7140840 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes.

Sawicki Jakub J Bączkiewicz Alina A Buczkowska Katarzyna K Górski Piotr P Krawczyk Katarzyna K Mizia Patryk P Myszczyński Kamil K Ślipiko Monika M Szczecińska Monika M

Genes 20200312 3

The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of <i>Conocephalum, Riccia and Sphaerocarpos</i> species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the ...[more]

PMID: 32178248

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Project description:BackgroundAngelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. Angelica species are found on all continents of the Northern Hemisphere, and East Asia hosts the highest number of species. Morphological characters such as fruit anatomy, leaf morphology and subterranean structures of Angelica species show extreme diversity. Consequently, the taxonomic classification of Angelica species is complex and remains controversial, as the classifications proposed by previous studies based on morphological data and molecular data are highly discordant. In addition, the phylogenetic relationships of major clades in the Angelica group, particularly in the Angelica s. s. clade, remain unclear. Chloroplast (cp) genome sequences have been widely used in phylogenetic studies and for evaluating genetic diversity.ResultsIn this study, we sequenced and assembled 28 complete cp genomes from 22 species, two varieties and two cultivars of Angelica. Combined with 36 available cp genomes in GenBank from representative clades of the subfamily Apioideae, the characteristics and evolutionary patterns of Angelica cp genomes were studied, and the phylogenetic relationships of Angelica species were resolved. The Angelica cp genomes had the typical quadripartite structure including a pair of inverted repeats (IRs: 5836-34,706 bp) separated by a large single-copy region (LSC: 76,657-103,161 bp) and a small single-copy region (SSC: 17,433-21,794 bp). Extensive expansion and contraction of the IR region were observed among cp genomes of Angelica species, and the pattern of the diversification of cp genomes showed high consistency with the phylogenetic placement of Angelica species. Species of Angelica were grouped into two major clades, with most species grouped in the Angelica group and A. omeiensis and A. sinensis grouped in the Sinodielsia with Ligusticum tenuissimum.ConclusionsOur results further demonstrate the power of plastid phylogenomics in enhancing the phylogenetic reconstructions of complex genera and provide new insights into plastome evolution across Angelica L.

Project description:Understanding the biogeographical and diversification processes explaining current diversity patterns of subcosmopolitan-distributed groups is challenging. We aimed at disentangling the historical biogeography of the subcosmopolitan liverwort genus Lejeunea with estimation of ancestral areas of origin and testing if sexual system and palaeotemperature variations can be factors of diversification. We assembled a dense taxon sampling for 120 species sampled throughout the geographical distribution of the genus. Lejeunea diverged from its sister group after the Paleocene-Eocene boundary (52.2 Ma, 95% credibility intervals 50.1-54.2 Ma), and the initial diversification of the crown group occurred in the early to middle Eocene (44.5 Ma, 95% credibility intervals 38.5-50.8 Ma). The DEC model indicated that (1) Lejeunea likely originated in an area composed of the Neotropics and the Nearctic, (2) dispersals through terrestrial land bridges in the late Oligocene and Miocene allowed Lejeunea to colonize the Old World, (3) the Boreotropical forest covering the northern regions until the late Eocene did not facilitate Lejeunea dispersals, and (4) a single long-distance dispersal event was inferred between the Neotropics and Africa. Biogeographical and diversification analyses show the Miocene was an important period when Lejeunea diversified globally. We found slight support for higher diversification rates of species with both male and female reproductive organs on the same individual (monoicy), and a moderate positive influence of palaeotemperatures on diversification. Our study shows that an ancient origin associated with a dispersal history facilitated by terrestrial land bridges and not long-distance dispersals are likely to explain the subcosmopolitan distribution of Lejeunea. By enhancing the diversification rates, monoicy likely favoured the colonisations of new areas, especially in the Miocene that was a key epoch shaping the worldwide distribution.

Dataset Information

The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes.

Publications

The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes.

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