來自中國科學(xué)院昆明植物研究所等處的研究人員利用新一代測序技術(shù)Illumina完成了六種木本竹子葉綠體基因組全序列的測定,，為分析木本竹子的機(jī)制機(jī)理以及系統(tǒng)發(fā)育學(xué)研究提供了參考。這項(xiàng)研究獲得了中國科學(xué)院知識創(chuàng)新工程（KSCX-YW-N-029）、國家自然科學(xué)基金項(xiàng)目（30990244）和云南省創(chuàng)新團(tuán)隊(duì)的資助,，研究成果公布在《公共科學(xué)圖書館—綜合》（PLoS ONE）雜志上。
這項(xiàng)研究由李德銖研究員領(lǐng)導(dǎo)張韻潔和馬朋飛等人完成，李德銖研究員現(xiàn)任中國科學(xué)院昆明植物研究所所長，研究員,，博士生導(dǎo)師。曾于1997年獲國家杰出青年科學(xué)基金資助,，同年入選中國科學(xué)院“百人計(jì)劃”,，2004年入選首批“新世紀(jì)百千萬人才工程”國家級人選。
竹亞科（Bambusoideae）隸屬于禾本科（Poaceae）,，全世界共分布有一千余種,。木本竹子因種類數(shù)目多，形態(tài)性狀復(fù)雜多變及多年生一次性開花等原因而成為系統(tǒng)發(fā)育學(xué)研究難點(diǎn),。隨著新一代測序技術(shù)的興起,，系統(tǒng)發(fā)育基因組學(xué)為解決這類困難類群的系統(tǒng)發(fā)育關(guān)系帶來了曙光。
中國科學(xué)院昆明植物研究所李德銖研究組對木本竹子的研究有較好的研究基礎(chǔ),。最近,，該研究組選取1種熱帶竹子和5種溫帶竹子，利用新一代測序技術(shù)Illumina測定了這些種的葉綠體基因組全序列,。通過與已知的2種竹子葉綠體基因組序列比對發(fā)現(xiàn)竹亞科植物的葉綠體基因組非常保守,，具有良好的共線性和較低的分子進(jìn)化速率，并證實(shí)了通過改良高鹽低pH法直接分離葉綠體DNA并測序這一方法的可行性,。
基于24種禾本科植物葉綠體基因全序列,，該研究組還構(gòu)建了禾本科的系統(tǒng)發(fā)育樹。在BEP分支中,，竹亞科和早熟禾亞科（Pooideae）的姐妹群關(guān)系得到了強(qiáng)烈的支持,，首次從系統(tǒng)發(fā)育基因組學(xué)的角度證實(shí)了近期的分子系統(tǒng)學(xué)研究結(jié)果,，在竹亞科分支中熱帶分支和溫帶分支也分別為兩個(gè)很好的單系,。此外，與以前的研究結(jié)果相比,，溫帶分支內(nèi)部的系統(tǒng)學(xué)關(guān)系也得到了較好的解決,。
為探討序列數(shù)據(jù)量的大小對系統(tǒng)關(guān)系的影響，研究組分別利用了四組數(shù)據(jù)分別構(gòu)建系統(tǒng)樹,，分析表明,，基于葉綠體基因組全序列的系統(tǒng)發(fā)育分析結(jié)果較為理想。對基因中插入或缺失的研究,，發(fā)現(xiàn)45個(gè)插入或缺失中有25個(gè)可能為共近裔性狀,，20個(gè)可能為平行演化或回復(fù)突變的結(jié)果，且不同性質(zhì)的插入或缺失在各個(gè)基因中的分布并不均勻,，對其在系統(tǒng)發(fā)育學(xué)研究中的應(yīng)用提供了參考,。目前，采用葉綠體系統(tǒng)發(fā)育基因組學(xué)手段對溫帶竹子進(jìn)行系統(tǒng)發(fā)育重建是比較行之有效的方法，這對于其它困難類群的系統(tǒng)學(xué)研究也有一定的啟示意義,。（生物谷Bioon.com）
生物谷推薦原文出處：
PLoS ONE DOI：10.1371/journal.pone.0020596
High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)
Yun-Jie Zhang,Peng-Fei Ma,De-Zhu Li
Background Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. Methodology/Principal Findings Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with 鈮?.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. Conclusions/Significance The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly.
