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The Evolution and Utility of Ribosomal ITS Sequences in Bambusinae and Related Species: Divergence, Pseudogenes, and Implications for Phylogeny

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The Evolution and Utility of Ribosomal ITS Sequences in Bambusinae and Related Species: Divergence, Pseudogenes, and Implications for Phylogeny c Indian Academy of Sciences RESEARCH ARTICLE The evolution and utility of ribosomal ITS sequences in Bambusinae and related species: divergence, pseudogenes, and implications for phylogeny HUI-XING SONG, SU-PING GAO, MING-YAN JIANG, GUANG-LI LIU, XIAO-FANG YU and QI-BING CHEN∗ School of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People’s Republic of China Abstract Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evo- lution. Concerted evolution leads to intragenomic uniformity of repeats even between loci on nonhomologous chromosomes. However, a number of studies have shown that the ITS polymorphism within individuals is quite common. The molecu- lar systematics of Bambusinae and related species were recently assessed by different teams using independently generated ITS sequences, and the results disagreed in some remarkable features. Here we compared the ITS sequences of the mem- bers of Bambusa s. l., the genera Dendrocalamus, Dinochloa, Gigantochloa, Guadua, Melocalamus, Monocladus, Oxytenan- thera, Thyrsostachys, Pleioblastus, Pseudosasa and Schizostachyum. We have reanalysed the ITS sequences used by different research teams to reveal the underlying patterns of their different results. After excluding the sequences suspected to repre- sent paralogous loci, a phylogenetic analysis of the subtribe Bambusinae species were performed using maximum parsimony and maximum-likelihood methods. The implications of the findings are discussed. The risk of incorporating ITS paralogues in plant evolutionary studies that can distort the phylogenetic signal should caution molecular systematists. [Song H.-X., Gao S.-P., Jiang M.-Y., Liu G.-L., Yu X.-F. and Chen Q.-B. 2012 The evolution and utility of ribosomal ITS sequences in Bambusinae and related species: divergence, pseudogenes, and implications for phylogeny. J. Genet. 91, 129–139] Introduction expected, and ITS polymorphism within individuals is quite common (Baldwin et al. 1995; Wendel et al. 1995;Muir The ribosomal internal transcribed spacer (ITS) sequences and Schlötterer 1999; Denduangboripant and Cronk 2000; have been used successfully in studying phylogenetic and Mayol and Rosselló 2001; Rosselló et al. 2006, 2007; Nieto- genomic relationships of plants at lower taxonomic levels Feliner and Rossselló 2007; Zhang and Ge 2007;Kimet al. (Hamby and Zimmer 1992;Baldwin1993;Baldwinet al. 2008; Göer and Grimm 2008; Grimm and Denk 2008; Pilotti 1995;Hsiaoet al. 1995;Sanget al. 1995; Wendel et al. 1995; et al. 2009). In that case, if only one cloned sequence is used Zhang and Sang 1999; Volkov et al. 1999; Feliner et al. 2004; as the representative of the ITS sequence of one individual, Liu et al. 2006). There are multiple copies of this ribosomal some polymorphism will be absent and the resulting phylo- array in the genome, but they appear to undergo rapid con- genetic analysis will be suspect. These results underline that certed evolution and all copies appear to be virtually iden- the use of ITS as a universal marker should be evaluated on tical (Wendel et al. 1995;Baldwinet al. 1995; Álvarez and a case-by-case basis. Wendel 2003; Nieto-Feliner and Rossselló 2007). Therefore, Bambusinae is a woody bamboo subtribe placed in the in many studies, the rDNA is treated as a single gene, and tribe Bambuseae subfamily Bambusoideae of grass family both direct sequencing and cloning of PCR products were Poaceae (Ohrnberger 1999). The subtribe comprises 10 to 13 used for ITS analysis, with only one clone for each individual genera, found mostly in the tropical and subtropical regions sequenced even if PCR products were cloned (Hsiao et al. of the Old World, many of which are economically exploited 1995;Liuet al. 2006;Yanget al. 2008; Silva et al. 2012). by the communities in South and South-East Asia. Because However, in recent years a number of studies have shown of the long time period before flowering in woody bamboos, that the concerted evolution of rDNA is not completely as vegetative characters such as culm sheath, ligule, blade, branching and rhizome have often been used to classify these ∗ For correspondence. E-mail: [email protected]. species instead of flowers. It has been difficult to relate these Keywords. Bambusinae; internal transcribed spacer; phylogenetic analysis; pseudogenes; evolution. Journal of Genetics, Vol. 91, No. 2, August 2012 129 Hui-Xing Song et al. characteristics to floral distinctions, which is one cause of analysis. The consensus sequence for each group was cre- controversy in the classification of bamboo genera. A sound ated with BioEdit (Hall 1999) and aligned with CLUSTAL taxonomy is needed for conservation and management of the W (Thompson et al. 1994) to show the major difference of woody bamboos belonging to this subtribe. the types. The recent availability of molecular data enabled tax- The phylogenetic analyses based on the reduced sequence onomists to review the phylogeny of the Bambusinae. Some matrix were conducted using parsimony and distance meth- studies on taxa of Bambusinae based on ITS nuclear rDNA ods with PAUP* 4.0 (Swofford 1998). We first carried out sequences have been undertaken such as for Bambusa (Sun a NJ analysis using the Kimura two parameter distance esti- et al. 2005) and major groups of the paleotropical woody mates (Kimura 1980). Maximum parsimony (MP) analyses bamboos (Yang et al. 2008). However, only limited species were performed by heuristic search, tree bisection reconnec- were sampled in previous molecular studies, and only one tion (TBR) branch swapping, and RANDOM stepwise addi- ITS sequence was typically cloned to represent the mul- tion with 100 replicates. To find the evolutionary model that tiple copies of each plant ribosomal array. As a result, fits best for given data, we subjected the alignment of the the phylogenetic relationships of the genera were not well sequences to Modeltest (Posada and Crandall 1998) v3.7. resolved. The parameters of the best fit model were then used as input The present paper examines the ITS polymorphism within for a ML analysis. Topological robustness was assessed by and among the species of the subtribe Bambusinae and the bootstrap analysis with 500 replicates (Felsenstein 1985). In related species, assessing nucleotide diversity among homol- all analyses the functional outgroup (FOG) (Watrous and ogous ITS repeats, and infer the molecular phylogeny of the Wheeler 1981)usedwasP. heteroclada. related genera based on all of the published ITS sequences Some sequences in Bambusinae were closely related. available. Specifically, the objectives of this study were To detect the lineage relationships among these closely to (i) evaluate the utility of ITS sequence in the subtribe related sequences in subtribe Bambusinae, a phylogenetic Bambusinae; and (ii) reveal relationships of the Bambusinae network reconstruction method was used to study relation- species. ships among the 44 sequences which belong to 34 species within Bambusinae group. We conducted clone genealogy by coalescent simulations using the Median-Joining model Materials and methods as implemented in the Network v4.0 software (Bandelt et al. 1999). The ITS sequences of the members of broad concept Bam- busa and the related species of Dendrocalamus, Dinochloa, Gigantochloa, Guadua, Melocalamus, Monocladus, Oxy- Results tenanthera, Thyrsostachys, Pleioblastus, Pseudosasa and Polymorphism of ITS sequences and phylogenetic analysis Schizostachyum by different research teams were obtained from GenBank (http://www.ncbi.nlm.nih.gov/genbank/). A A total of 99 sequences belonging to 72 species were species of temperate woody bamboo, Phyllostachys hetero- included in this study. The aligned sequences revealed three clada, was used as outgroup. The species name, clone number, distinctly different sequence types, which have a high level GenBank accession number and the authors are listed in table 1. of variation in length and in sequence composition. Based Sequences were aligned with CLUSTALW (Thompson on the alignment result combining with the sequence infor- et al. 1994) and the alignment was manually refined using mation in GenBank, we ascertained the uniform boundary Genedoc (Nicholas et al. 1997). The aligned matrix was sub- for each sequence type respectively. The sequences ranged jected to a neighbour-joining (NJ) analysis using the Kimura from 541 to 667 bp. The NJ tree (figure 1) showed three well two parameter distance estimates (Kimura 1980). Constant supported clades also recovered from phylogenetic analysis, sites were subsequently removed from the alignments. Then labelled as I, II and III, respectively. In clade I, the sequences the matrix was first subjected to a maximum-likelihood were clustered matching the genera in general, different (ML) analysis, searching for the appropriate evolutionary clones belonging to one or two genera were grouped together model using Modeltest (Posada and Crandall 1998), and as subclades. However, species were mixed in clades II and then inputting the appropriate model(s) obtained from the III. Unexpectedly, the sequences from same species (i.e. likelihood ratio tests and the Akaike information crite- Bambusa bambos, B. multiplex, B. vulgaris, Dendrocalamus rion (AIC), into the ML analysis. All analyses were car- strictus, etc.) were scattered into different
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