Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae)

We investigated the evolutionary dynamics of duplicated copies of the granule-bound starch synthase I gene (GBSSI or Waxy) within polyploid Spartina species. Molecular cloning, sequencing, and phylogenetic analyses revealed incongruences between the expected species phylogeny and the inferred gene trees. Some genes within species were more divergent than expected from ploidy level alone, suggesting the existence of paralogous sets of Waxy loci in Spartina. Phylogenetic analyses indicate that this paralogy originated from a duplication that occurred prior to the divergence of Spartina from other Chloridoideae. Gene tree topologies revealed three divergent homoeologous sequences in the hexaploid S. alterniflora that are consistent with the proposal of an allopolyploid origin of the hexaploid clade. Waxy sequences differ in insertion–deletion events in introns, which may be used to diagnose gene copies. Both paralogous and homoeologous coding regions appear to evolving under selective constraints.     

玉米种子发育过程中直链淀粉积累规律的分析

淀粉是玉米种子的主要组成成分,它包括直链淀粉和支链淀粉。支链淀粉的合成需要淀粉合成酶、分支酶和脱支酶的共同作用,而直链淀粉的合成则是在颗粒结合型淀粉合成酶的作用下进行的。颗粒结合型淀粉合成酶基因的突变造成玉米种子的腊质（糯性）表型。与支链淀粉合成的分子机制的研究相比,目前对玉米种子中直链淀粉合成的分子机制了解相对较少。以野生型黄早4玉米自交系和突变体糯玉米为实验材料,研究了种子不同发育时期直链淀粉的积累规律。通过碘染色的方法,观察了玉米种子发育过程中淀粉积累的形态变化。定量分析表明,从授粉后10d至25d,黄早4种子中直链淀粉的含量逐渐增加,同时颗粒结合型淀粉合成酶（GBSS）的活性逐渐提高;而在糯玉米中,直链淀粉和GBSS活性均未检测到。进而,通过RT-PCR方法,从黄早4种子中分离出编码GBSSI的cDNA片段。在授粉后10d至25d的玉米胚乳中均可检测到GBSSI的表达,而在胚中直到授粉后25d才检测到该基因表达的微弱信号。在糯玉米种子中没有检测到该基因的表达。研究结果表明,在玉米种子发育过程中,GBSSI基因的表达通过控制GBSS的合成,最终控制直链淀粉的合成。研究工作为理解玉米种子中直链淀粉合成的分子机制提供了重要信息。     

枸杞属(茄科)新类群杂交起源初探

为探讨枸杞属新类群的起源及国产枸杞属植物的亲缘关系,该文使用核基因颗粒性结合淀粉合成酶基因(GBSSI)片段,对国产7个类群的枸杞属植物进行了分子系统学研究.结果表明:中国分布的枸杞属植物属于旧世界类群并分为4个强烈支持的分支,而新类群的形成与杂交密切相关.此外,初步分析还显示宁夏枸杞有较高的遗传分化.     

Identification and characterization of granule bound starch synthase I (GBSSI) gene of tartary buckwheat (Fagopyrum tataricum Gaertn.)

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is increasingly considered as an important functional food material because of its rich nutraceutical compounds. Reserve starch is the major component of tartary buckwheat seed. However, the gene sequences and the molecular mechanism of tartary buckwheat starch synthesis are unknown so far. In this study, the complete genomic sequence and full-size cDNA coding tartary buckwheat granule-bound starch synthase I (FtGBSSI), which is responsible for amylose synthesis, were isolated and analyzed. The genomic sequence of the FtGBSSI contained 3947 nucleotides and was composed of 14 exons and 13 introns. The cDNA coding sequence of FtGBSSI shared 63.3%–75.1% identities with those of dicots and 56.6%–57.5% identities with monocots (Poaceae). In deduced amino acid sequence of FtGBSSI, eight motifs conserved among plant starch synthases were identified. A cleavage at the site IVC↓G of FtGBSSI protein produces the chloroplast transit sequence of 78 amino acids and the mature protein of 527 amino acids. The FtGBSSI mature protein showed an identity of 73.4%–77.8% with dicot plants, and 67.6%–70.4% with monocot plants (Poaceae). The mature protein was composed of 20 α-helixes and 16 β-strands, and folds into two main domains, N- and C-terminal domains. The critical residues which are involved in ADP and sugar binding were predicted. These results will be useful to modulate starch composition of buckwheat kernels with the aim to produce novel improved varieties in future breeding programs.     

Phylogeny of subtribe Pyrinae (formerly the Maloideae, Rosaceae): Limited resolution of a complex evolutionary history

Generic relationships in the Pyrinae (equivalent to subfamily Maloideae) were assessed with six chloroplast regions and five nuclear regions. We also plotted 12 non-molecular characters onto molecular phylogenies. Chloroplast DNA trees are incongruent with those from nuclear regions, as are most nuclear regions with one another. Some of this conflict may be the result of hybridization, which occurs between many genera of Pyrinae in the present and may have occurred in the past, and duplication of nuclear loci. Sequence divergence between genera of Pyrinae, which is significantly less than that between genera of another large clade in Rosaceae, the Rosoideae, is concentrated in terminal branches, with short internal branches. This pattern is consistent with an ancient, rapid radiation, which has also been hypothesized from the fossil record. Even with about 500,000 bp of sequence, our results resolve only several small groups of genera and leave much uncertainty about phylogenetic relationships within Pyrinae.     

Polyploidy on islands – concerted evolution and gene loss amid chromosomal stasis

Background and AimsPolyploidy is an important process that often generates genomic diversity within lineages, but it can also cause changes that result in loss of genomic material. Island lineages, while often polyploid, typically show chromosomal stasis but have not been investigated in detail regarding smaller-scale gene loss. Our aim was to investigate post-polyploidization genome dynamics in a chromosomally stable lineage of Malvaceae endemic to New Zealand.MethodsWe determined chromosome numbers and used fluorescence in situ hybridization to localize 18S and 5S rDNA. Gene sequencing of 18S rDNA, the internal transcribed spacers (ITS) with intervening 5.8S rDNA, and a low-copy nuclear gene, GBSSI-1, was undertaken to determine if gene loss occurred in the New Zealand lineage following polyploidy.Key ResultsThe chromosome number for all species investigated was 2n = 42, with the first published report for the monotypic Australian genus Asterotrichion. The five species investigated all had two 5S rDNA signals localized interstitially on the long arm of one of the largest chromosome pairs. All species, except Plagianthus regius, had two 18S rDNA signals localized proximally on the short arm of one of the smallest chromosome pairs. Plagianthus regius had two additional 18S rDNA signals on a separate chromosome, giving a total of four. Sequencing of nuclear ribosomal 18S rDNA and the ITS cistron indicated loss of historical ribosomal repeats. Phylogenetic analysis of a low-copy nuclear gene, GBSSI-1, indicated that some lineages maintained three copies of the locus, while others have lost one or two copies.ConclusionsAlthough island endemic lineages show chromosomal stasis, with no additional changes in chromosome number, they may undergo smaller-scale processes of gene loss and concerted evolution ultimately leading to further genome restructuring and downsizing.     

Development of waxy cassava with different Biological and physico-chemical characteristics of starches for industrial applications

The quality of cassava starch, an important trait in cassava breeding programs, determines its applications in various industries. For example, development of waxy (having a low level of amylose) cassava is in demand. Amylose is synthesized by granule-bound starch synthase I (GBSSI) in plants, and therefore, down-regulation of GBSSI expression in cassava might lead to reduced amylose content. We produced 63 transgenic cassava plant lines that express hair-pin dsRNAs homologous to the cassava GBSSI conserved region under the control of the vascular-specific promoter p54/1.0 from cassava (p54/1.0::GBSSI-RNAi) or cauliflower mosaic virus (CaMV) 35S (35S::GBSSI-RNAi). After the screening storage roots and starch granules from field-grown plants with iodine staining, the waxy phenotype was discovered: p54/1.0::GBSSI-RNAi line A8 and 35S::GBSSI-RNAi lines B9, B10, and B23. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that there was no detectable GBSSI protein in the starch granules of plants with the waxy phenotype. Further, the amylose content of transgenic starches was significantly reduced (<5%) compared with the level in starch granules from the wild-type (about 25%). The inner structure of the waxy starch granules differed from that of the untransformed ones, as revealed by transmission electron microscopy analysis as well as morphological changes in the iodine-starch complex. Endothermic enthalpy was reduced in waxy cassava starches, according to differential scanning calorimeter analysis. Except B9, all waxy starches displayed the A-type X-ray diffraction pattern. Amylogram patterns of the waxy cassava starches were analyzed using a rapid viscosity analyzer and found to have increased values for clarity, peak viscosity, gel breakdown, and swelling index. Setback, consistency, and solubility were notably reduced. Therefore, waxy cassava with novel starch in its storage roots was produced using the biotechnological approach, promoting its industrial utilization.     

Phylogenetic utility of nuclear nitrate reductase: A multi-locus comparison of nuclear and chloroplast sequence data for inference of relationships among American Lycieae (Solanaceae)

There has been considerable interest and research into the benefits of multiple low-copy nuclear regions for phylogenetic studies at low taxonomic levels. In this study, the phylogenetic utility of DNA sequence data from two low-copy nuclear genes, nitrate reductase (NIA) and granule-bound starch synthase I (GBSSI), was compared with data from nuclear ribosomal ITS and the cpDNA spacers trnT–trnF and trnD–trnT across 33 closely related taxa in tribe Lycieae (Solanaceae). The NIA data (introns 1–2) had the most parsimony-informative characters, with over twice the number provided by GBSSI, but NIA also had greater homoplasy. Although gene trees were generally concordant across the four regions, there were some notable areas of incongruence, suggesting both incomplete lineage sorting as well as possible reticulate origins.