Reconstruction of gross avian genome structure,organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

Background

The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.

Results

Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species’ genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.

Conclusions

Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1060) contains supplementary material, which is available to authorized users.     

Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges,a group with holocentric chromosomes

Chromosome rearrangements may affect the rate and patterns of gene flow within species, through reduced fitness of structural heterozygotes or by reducing recombination rates in rearranged areas of the genome. While the effects of chromosome rearrangements on gene flow have been studied in a wide range of organisms with monocentric chromosomes, the effects of rearrangements in holocentric chromosomes—chromosomes in which centromeric activity is distributed along the length of the chromosome—have not. We collected chromosome number and molecular genetic data in Carex scoparia, an eastern North American plant species with holocentric chromosomes and highly variable karyotype (2n = 56–70). There are no deep genetic breaks within C. scoparia that would suggest cryptic species differentiation. However, genetic distance between individuals is positively correlated with chromosome number difference and geographic distance. A positive correlation is also found between chromosome number and genetic distance in the western North American C. pachystachya (2n = 74–81). These findings suggest that geographic distance and the number of karyotype rearrangements separating populations affect the rate of gene flow between those populations. This is the first study to quantify the effects of holocentric chromosome rearrangements on the partitioning of intraspecific genetic variance.     

青藏高原不同海拔梯度2种莎草科牧草模拟体外消化率研究

利用大板山北坡 32 0 0 m～ 380 0 m的海拔梯度 ,分别在 32 0 0 m、340 0 m、360 0 m和380 0 m处选取矮嵩草 ( Kobresia humilis)、黑褐苔草 ( Carex alrofusca) 2种青藏高原重要莎草科牧草 ,并用二级离体培养法模拟测定其体外消化率 ,1 999和 2 0 0 0年的测定结果发现 ,随着海拔升高牧草体外消化率呈增加的趋势 ,海拔高度从 32 0 0 m升高到 380 0 m,矮嵩草叶、矮嵩草茎、黑褐苔草叶、黑褐苔草茎的体外消化率分别增加了 8.30和 4.48、8.45和 5 .0 3、1 0 .94和 9.5 8、7.85和 8.0 9个百分点。显著性分析结果表明 ,牧草体外消化率与牧草所生长的海拔     

高寒矮嵩草草甸群落植物多样性和初级生产力对模拟降水的响应

通过野外控制实验,研究了高寒矮嵩草草甸群落植物多样性、初级生产力对模拟降雨条件的响应.结果表明: 1 在植物生长期 6月 ,增加降雨20%、增加降雨40%,植物群落物种多样性指数 H 和均匀度指数 J 分别比对照提高了0.188和0.011、0.735和0.076,生长期 7月 增加降雨20%物种H和J提高了0.409和0.07; 2 禾草类:增加降雨20%处理的地上生物量与对照相比没有明显的显著性差异 P>0.05 ,增加降雨40%处理的地上生物量与对照相比差异显著 P<0.05 ,说明过多增加降雨会抑制禾草的生长发育.杂类草:减少降雨50%处理的地上生物量与对照相比差异显著 P<0.05 ,其地上生物量对减少降雨的反映比较敏感.莎草类:其地上生物量对增加和减少降雨都没有显著变化; 3 0～10cm和0～30cm土层地下生物量均在增加降雨20%时最高,地下生物量的总量也在增加降雨20%时最高; 4 矮嵩草草甸地下生物量与地上生物量、总生物量的比值接近于生长季末时最大,且在模拟增加降雨20%的水平时,7、8、9月份地下和地上生物量较其它处理组高.     

亚比棉基因组原位杂交及核型分析

亚比棉异源四倍体是山西农业大学棉花育种组于上个世纪80年代用A染色体组亚洲棉(Gossypium.arboreum)(迁西小黑籽)与G染色体组野生棉比克氏棉(G.bickii)杂交成异源二倍体后,又经过加倍而获得的.亚比棉异源四倍体不仅育性得到恢复、结铃正常,而且成功地将比克氏棉的优异性状--种子腺体延缓形成转育到亚比棉中.这为实现棉花综合利用和提高抗虫性创育了新的育种材料.在随后的多年中,山西农业大学棉花育种组对亚比棉异源四倍体进行了广泛的细胞形态学研究,对其核型做了分析.然而,仅依据形态学和普通的核型图像,还不能确定该异源四倍体棉种中比克氏棉G染色体(亚)组在核型中的表现.该文以比克氏棉gDNA为探针,亚比棉异源四倍体根尖体细胞染色体为靶细胞染色体,封阻材料为亚洲棉(迁西小黑籽),进行亚比棉基因组原位杂交(Genome in situ hybridization,GISH)及核型分析.从获得的图像中可以清晰地发现有52条染色体,其中有/无杂交信号的各一半,这直观地证实了人工复合亚比棉杂交种确为异源四倍体,而且是双二倍体.A亚组与G亚组染色体长度存在交替排列.亚比棉异源四倍体基于GISH图像的核型公式为2n=4x=52=46m(4sat)+6sm(4sat).A亚组和G亚组染色体上各有2对随体.G亚组染色体中至少有5对双重显色明显的染色体,意味着可能有A亚组染色体的交换,而A亚组染色体中只观察到或多或少的探针红色荧光信号,由于分辨率不够而难于定量分析.进一步以45SrDNA为探针,以鲑鱼精DNA作为封阻DNA,对亚比棉异源四倍体进行45SrDNA-FISH,实验表明,亚比棉异源四倍体有14个NOR(核仁组织区)信号,说明亚比棉异源四倍体有14个随体,即7对随体.比克氏棉对亚洲棉的GISH结果显示,在有亚洲棉DNA封阻的条件下,亚洲棉靶细胞染色体无任何杂交信号,说明比克氏棉与亚洲棉染色体之间不存在较大的同源或相似序列.     

Genome architecture drives protein evolution in ciliates

Studies of microbial eukaryotes have been pivotal in the discovery of biological phenomena, including RNA editing, self-splicing RNA, and telomere addition. Here we extend this list by demonstrating that genome architecture, namely the extensive processing of somatic (macronuclear) genomes in some ciliate lineages, is associated with elevated rates of protein evolution. Using newly developed likelihood-based procedures for studying molecular evolution, we investigate 6 genes to compare 1) ciliate protein evolution to that of 3 other clades of eukaryotes (plants, animals, and fungi) and 2) protein evolution in ciliates with extensively processed macronuclear genomes to that of other ciliate lineages. In 5 of the 6 genes, ciliates are estimated to have a higher ratio of nonsynonymous/synonymous substitution rates, consistent with an increase in the rate of protein diversification in ciliates relative to other eukaryotes. Even more striking, there is a significant effect of genome architecture within ciliates as the most divergent proteins are consistently found in those lineages with the most highly processed macronuclear genomes. We propose a model whereby genome architecture-specifically chromosomal processing, amitosis within macronuclei, and epigenetics-allows ciliates to explore protein space in a novel manner. Further, we predict that examination of diverse eukaryotes will reveal additional evidence of the impact of genome architecture on molecular evolution.     

高寒草甸小嵩草种群繁殖生态学研究

研究从繁殖生态学的角度对高寒草甸小嵩草（Kobresia pygmaea)种群进行了初步研究。结果表明：小嵩草属寒冷中生密丛短根茎地下芽植物,在高寒生境中采用以营养繁殖为主、有性繁殖为辅的繁策略,具体体现在以下几个方面：虽然小嵩草种子产量达4553.8粒／m^2,但种子萌发率较低,室内和野外萌发率分别仅有4％和1％,经氢氧化钠溶液和赤霉素溶液处理后的种子萌发率分别为1％和2％,而削去种皮后种子萌发率达52．6％,种皮坚硬是造成种子萌发率低的主要原因;进入种子库、保留至返青期且具有活性的种子仅占种子总数的24．35％,其室内萌发率仅有3％,而在野外理论实生苗仅为11．09个／m^2,与此相反小嵩草营养繁殖所形成的新个体数为6256．25个／m^2,远远多于种子萌发所形成的实生苗数。此外,小嵩草营养繁殖效力也远高于有性繁殖效力,营养繁殖效力占总繁殖效力的90．92％。     

12种中国葱属植物的核型分析

采用细胞压片法,对采自中国西部的12种葱属植物的根尖有丝分裂中期进行了观察,其巾天蓝韭(A.cyaneum)、梭沙韭(Aforrestii)、昌都韭(A.changduense)、西川非(A.xichuanense)、野黄韭(A.rude)、野葱(A.chrysanthum)和真籽韭(A.eusperma)等7种植物的核型为首次报道.供试类群中,峨眉韭(A.omeiense)和多星韭(A.wallichii)的染色体基数分别为11和7,其余类群的染色体基数均为8.观察发现,随体杂合和多侪性现象在供试类群中很普遍.分析推测:(1)随体和倍性的变异在葱属某些类群的进化中可能起重要作用,随体的类型在葱属具有重要的分类意义;(2)多倍化和地下走茎的无性繁殖方式可能是天蓝韭(A.cyaneum)的进化策略;(3)西川韭(A.xichuanense)、野黄非(A.rude)和野葱(A.chrysanthum)有密切的亲缘关系;(4)真籽韭(A.eusperma)与多籽组在核型上有密切的亲缘关系.     

鹅观草属五个类群的核型与进化

报道了鹅观草属５个类群的核型,即长芒鹅观草,核型２ｎ＝４ｘ＝２８＝２２ｍ＋６ｓｍ（２ＳＡＴ）;短颖鹅观草,核型２ｎ＝４ｘ＝２８＝２０ｍ（２ＳＡＴ）＋８ｓｍ（２ＳＡＴ）;短柄鹅观草,核型２ｎ＝４ｘ＝２８＝２２ｍ（２ＳＡＴ）＋６ｓｍ;纤毛鹅观草,核型２ｎ＝４ｘ＝２８＝２０ｍ＋８ｓｍ（４ＳＡＴ）;毛盘鹅观草,核型２ｎ＝４ｘ＝２８＝１８ｍ＋６ｓｍ（４ＳＡＴ）＋４ｓｔ。同时,通过核型重要性状的递变分析,揭示了鹅观草属５个类群的相对进化程度以及宏观分类中４个组的系统发育关系,表明鹅观草属的半颖组在系统发育中可能既派生了颖体短小的小颖组,又派生了颖体长大的大颖组和长颖组。     

赖草属5个种的核型与进化

报道了国产赖草属５个种的核型,即大赖草,２ｎ＝４ｘ＝２８＝２４ｍ（２ＳＡＴ）＋４ｓｍ（２ＳＡＴ）;粗穗赖草２ｎ＝４ｘ＝２８＝２２ｍ（２ＳＡＴ）＋４ｓｍ＋２ｓｔ（２ＳＡＴ）;若羌赖草,２ｎ＝４ｘ＝２８＝２０ｍ（４ＳＡＴ）＋６ｓｍ＋２ｓｔ（２ＳＡＴ）;羊草,２ｎ＝４ｘ＝２８＝２２ｍ（４ＳＡＴ）＋２ｓｍ＋４ｓｔ（４ＳＡＴ）;窄颖赖草,２ｎ＝４ｘ＝２８＝２２ｍ（２ＳＡＴ）＋４ｓｍ（２ＳＡＴ）＋２ｓｔ（２Ｓ     

高寒草甸矮蒿草种群繁殖对策的研究

繁殖对策是指生物对环境的生殖适应趋势 ,是资源或能量向生存、生长和生殖等活动中最适分配的结果 ,在不同的环境中具有其独特的表现形式。研究植物在不同环境中的繁殖对策可以反映出植物对环境的适应能力和在该生境中的生殖潜能。国内外学者对植物繁殖对策的研究已有不少报道[2 ,4 ,5,6] 。但对高寒草甸矮嵩草 (Ｋｏｂｒｅｓｉａｈｕｍｉｌｉｓ)种群繁殖对策的研究报道甚少。矮嵩草是青藏高原矮嵩草草甸的建群种 ,它具有草质柔软、营养丰富、热值含量较高等特点 ,是青藏高原重要的可更新草地资源。本研究对矮嵩草的繁殖对策进行了较全面、…     

高寒草甸麻花艽和美丽风毛菊的光合速率午间降低现象

在中国科学院海北高寒草甸生态系统定位研究站地区,用便携式光合蒸腾测定仪(CI-301PS)和液相极谱氧电极(SP-2)观测到,全晴天2种高山植物麻花艽和美丽风毛菊叶片的净光合速率(Pn)、光合放氧速率和表观量子效率(AQY)有明显的午间降低现象.遮光实验表明,这种现象是由高原地区当地太阳正午时前后较强的太阳辐射造成的.     

A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago

Previous research on barcoding sedges (Carex) suggested that basic searches within a global barcoding database would probably not resolve more than 60% of the world’s some 2000 species. In this study, we take an alternative approach and explore the performance of plant DNA barcoding in the Carex lineage from an explicitly regional perspective. We characterize the utility of a subset of the proposed protein-coding and noncoding plastid barcoding regions (matK, rpoB, rpoC1, rbcL, atpF-atpH, psbK-psbI) for distinguishing species of Carex and Kobresia in the Canadian Arctic Archipelago, a clearly defined eco-geographical region representing 1% of the Earth’s landmass. Our results show that matK resolves the greatest number of species of any single-locus (95%), and when combined in a two-locus barcode, it provides 100% species resolution in all but one combination (matK + atpFH) during unweighted pair-group method with arithmetic mean averages (UPGMA) analyses. Noncoding regions were equally or more variable than matK, but as single markers they resolve substantially fewer taxa than matK alone. When difficulties with sequencing and alignment due to microstructural variation in noncoding regions are also considered, our results support other studies in suggesting that protein-coding regions are more practical as barcoding markers. Plastid DNA barcodes are an effective identification tool for species of Carex and Kobresia in the Canadian Arctic Archipelago, a region where the number of co-existing closely related species is limited. We suggest that if a regional approach to plant DNA barcoding was applied on a global scale, it could provide a solution to the generally poor species resolution seen in previous barcoding studies.