Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus Musa

Li, Linfeng; Häkkinen, Markku; Yuan, Yong–Ming; Hao, Gang; Ge, Xue‐Jun

doi:10.1016/j.ympev.2010.06.021

Cited by 70 publications

(97 citation statements)

References 34 publications

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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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“…In line with the results of Liu et al [50], who studied ITS and chloroplast loci, our analyses showed monophyletic origin of Musaceae. Both BI and NJ phylogenetic trees showed close relationships of species belonging to sections Australimusa and Callimusa and sections Eumusa and Rhodochlamys , thus confirming previous findings [39], [41], [42], [49], [50]. At the same time, both trees showed reverse positions of the Ensete / Musella clade and Australimusa / Callimusa clade, probably due to the use of only one genomic locus (ITS) in the present work.…”

Section: Discussionsupporting

confidence: 91%

“…Nwakanma et al , [48] noted that a specific restriction pattern of the ITS region enabled differentiation between diploid AA and BB genomes as well as between the triploid AAA intraspecific hybrid clones and those that carry the B genome (AAB and ABB). More recently, the nucleotide information of the ITS region was used to study relationships of wild species of Musaceae [49], [50]. Nevertheless, there has been a lack of detailed knowledge on the ITS region in Musa and its potential for the analysis of genetic diversity and phylogenetic relationship remains unexplored.…”

Section: Introductionmentioning

confidence: 99%

The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

et al. 2011

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Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades – Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes.

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“…The Callimusa section, however, did not form a separate cluster, which reflects its controversial position and agrees with its previously reported close relationship to the Australimusa species (Jarret and Gawel 1995; Wong et al 2001 b , 2002). Also, the close relationship between Rhodochlamys and M. acuminata species (Wong et al 2002; Bartoš et al 2005; Li et al 2010; Liu et al 2010) was confirmed. The marker set enabled distinction to the level of individual subgroup/subspecies.…”

Section: Discussionmentioning

confidence: 66%