A multi gene sequence-based phylogeny of the Musaceae (banana) family

Christelová, Pavla; Valárik, Miroslav; Hřibová, Eva; Langhe, Edmond De; Doležel, Jaroslav

doi:10.1186/1471-2148-11-103

Cited by 64 publications

(76 citation statements)

References 75 publications

(111 reference statements)

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“…The highest similarity of repeats within the groups of M. beccarii / M. textilis and M. acuminata / M. ornata or M. acuminata / M. ornata / M. balbisiana are in agreement with previous results that showed close phylogenetic relationships of these species [6], [8], [46] and support the new taxonomy of Musaceae [9]. In general, sequence and quantitative differences were proportional to diversification of species of the Musaceae family (compare Fig.…”

Section: Discussionsupporting

confidence: 91%

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

et al. 2014

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BackgroundThe banana family (Musaceae) includes genetically a diverse group of species and their diploid and polyploid hybrids that are widely cultivated in the tropics. In spite of their socio-economic importance, the knowledge of Musaceae genomes is basically limited to draft genome assemblies of two species, Musa acuminata and M. balbisiana. Here we aimed to complement this information by analyzing repetitive genome fractions of six species selected to represent various phylogenetic groups within the family.ResultsLow-pass sequencing of M. acuminata, M. ornata, M. textilis, M. beccarii, M. balbisiana, and Ensete gilletii genomes was performed using a 454/Roche platform. Sequence reads were subjected to analysis of their overall intra- and inter-specific similarities and, all major repeat families were quantified using graph-based clustering. Maximus/SIRE and Angela lineages of Ty1/copia long terminal repeat (LTR) retrotransposons and the chromovirus lineage of Ty3/gypsy elements were found to make up most of highly repetitive DNA in all species (14–34.5% of the genome). However, there were quantitative differences and sequence variations detected for classified repeat families as well as for the bulk of total repetitive DNA. These differences were most pronounced between species from different taxonomic sections of the Musaceae family, whereas pairs of closely related species (M. acuminata/M. ornata and M. beccarii/M. textilis) shared similar populations of repetitive elements.ConclusionsThis study provided the first insight into the composition and sequence variation of repetitive parts of Musaceae genomes. It allowed identification of repetitive sequences specific for a single species or a group of species that can be utilized as molecular markers in breeding programs and generated computational resources that will be instrumental in repeat masking and annotation in future genome assembly projects.

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Section: Discussionsupporting

confidence: 91%

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

et al. 2014

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“…Judging from the cluster analysis based on Neighbor Joining method, there are no A or B genome-specific satellite units in Musa (Figure 2B). These findings indicate that both satellites originated before the divergence of the section Eumusa (∼28 Mya) [66] and that their sequences remained conserved during speciation. Unfortunately, our observation means that the satellites are not suitable as FISH probes to discriminate A and B genome chromosomes and hence cannot help in characterizing genomic constitution in interspecific Musa hybrids.…”

Section: Discussionmentioning

confidence: 71%

Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)

et al. 2013

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Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.

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“…Otherwise, it is difficult to ascertain whether the similarity observed in the pair of sequences is an inherited trait from a common ancestor, or a homoplasy [14,19]. The level of substitution saturation in rpo genes was measured by comparing the number of transitions and transversions with the size of the genetic distance for each pair of sequences (Figure 3).…”

Section: Resultsmentioning

confidence: 99%

The Uneven Rate of the Molecular Evolution of Gene Sequences of DNA-Dependent RNA Polymerase I of the Genus Lamium L.

Krawczyk

Sawicki

2013

IJMS

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RNA polymerase type I (plastid-encoded polymerase, PEP) is one of the key chloroplast enzymes. However, the rpo genes that encode its subunits (rpoA, rpoB, rpoC1 and rpoC2) are relatively rapidly evolving sequences. The aim of this study was to investigate the rate of the molecular evolution of rpo genes and to evaluate them as phylogenetic markers on the example of the genus Lamium L. (Lamiaceae). The analyzed genes were shown to differ in the level of variation, rate of intragenic mutations, phylogenetic informativeness, and in the impact of these mutations on the properties of encoded peptides. Destabilizing effects of the positive pressure were observed in all genes examined coding for PEP enzyme. We have demonstrated the relationship between mutations fixed by positive selection and the separation of phylogenetic lines within the genus Lamium. The study showed also that the rpo genes were reliable phylogenetic markers, useful in the reconstruction of interconnections of species belonging to the same genus. Of the four tested genes, the most promising phylogenetic marker was rpoA gene, while the least useful gene appeared to be rpoC1.

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A multi gene sequence-based phylogeny of the Musaceae (banana) family

Cited by 64 publications

References 75 publications

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)

The Uneven Rate of the Molecular Evolution of Gene Sequences of DNA-Dependent RNA Polymerase I of the Genus Lamium L.

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