The Evolutionary History of Wild,Domesticated, and Feral Brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.     

Ecological and Evolutionary Interactions between Wild Crucifers and Their Herbivorous Insects

Abstract Insects feeding on ten species of wild crucifer were investigated. Differences in host plant range and insect community structure were examined with regard to anti-herbivore defense mechanisms. Most of the crucifer species deterred insect herbivory by disappearing in the summer or by lowering their intrinsic quality as food for insects. Species with these defense mechanisms were exploited by only a few specialized herbivorous insects that seemed to have counter defenses. The plants without these defense mechanisms were used by many herbivorous insect species. Rorippa indica lacked direct defenses, but supported a low total density of herbivore individuals. This crucifer has an indirect defense mechanism: ants attracted to floral nectar defended the plant from deleterious herbivores. Crucifers that disappeared seasonally lacked other anti-herbivore defense mechanisms. This suggests that the phonological response is an alternative other responses to herbivore attack.     

First Insight into Exploration and Cognition in Wild Caught and Domesticated Sea Bass (Dicentrarchus labrax) in a Maze

European sea bass aquaculture is so recent that very little is known on the effects of the early steps of its domestication. Behavioural parameters are sensitive indicators of the domestication process since they are generally impacted as soon as the first generation. The present work compared wild-caught and domesticated sea bass juvenile swimming activity, exploration and ability to learn to discriminate between two 2-D objects associated to a simple spatial task that enabled the tested individual to visually interact with an unfamiliar congener (the reward) located behind a transparent wall at the end of one of the two arms of a maze. Ten fish from each origin were individually tested 3 times in a row during 3 days (9 trials in total). Fish were placed in a start box closed by a transparent wall located in front of two 2-D objects. Fish were filmed during 10 min after the removal of the start box wall. Different swimming variables including angular velocity, total distance travelled and velocity mean, were analyzed from videos as well as the time spent in each of 6 virtual zones including the reward zone near the congener (Cong) and the zone opposite to the reward zone (OpCong). Two learning criteria were chosen: the number of successful turns and time to reach Cong. Behavioural differences were found between domesticated and wild fish. Angular velocity was higher in wild fish while the distance travelled and the velocity mean were higher in domesticated ones. Wild and domesticated fish spent most of the time in Cong and in OpCong. No differences were seen in learning ability between wild and domesticated fish. However, our findings for learning require confirmation by further studies with larger numbers of learning sessions and experiments designed to minimise stress. This study therefore demonstrated an impact of domestication on swimming behaviour but not on spatial learning.     

一株家养野猪源猪圆环病毒2型的分离与鉴定

应用PCR方法从临诊疑似断奶仔猪多系统衰竭综合征(PMWS)家养野猪病例的淋巴结和脾脏中扩增出预期长度的猪圆环病毒2型(PCV2)的DNA片段,在Dulac细胞中进行分离和培养,扩增全基因组序列后进行同源性分析.结果显示,扩增产物与家猪源参考毒株的序列同源性均在98%以上,该病毒与家猪源病毒差异不大.     

Ecological Genetic Divergence of the Fungal Pathogen Didymella rabiei on Sympatric Wild and Domesticated Cicer spp. (Chickpea)

For millennia, chickpea (Cicer arietinum) has been grown in the Levant sympatrically with wild Cicer species. Chickpea is traditionally spring-sown, while its wild relatives germinate in the autumn and develop in the winter. It has been hypothesized that the human-directed shift of domesticated chickpea to summer production was an attempt to escape the devastating Ascochyta disease caused by Didymella rabiei. We estimated genetic divergence between D. rabiei isolates sampled from wild Cicer judaicum and domesticated C. arietinum and the potential role of temperature adaptation in this divergence. Neutral genetic markers showed strong differentiation between pathogen samples from the two hosts. Isolates from domesticated chickpea demonstrated increased adaptation to higher temperatures when grown in vitro compared with isolates from the wild host. The distribution of temperature responses among progeny from crosses of isolates from C. judaicum with isolates from C. arietinum was continuous, suggesting polygenic control of this trait. In vivo inoculations of host plants indicated that pathogenic fitness of the native isolates was higher than that of their hybrid progeny. The results indicate that there is a potential for adaptation to higher temperatures; however, the chances for formation of hybrids which are capable of parasitizing both hosts over a broad temperature range are low. We hypothesize that this pathogenic fitness cost is due to breakdown of coadapted gene complexes controlling pathogenic fitness on each host and may be responsible for maintenance of genetic differentiation between the pathogen demes.Environmental heterogeneity and genetic variability in host populations are major factors distinguishing natural from agricultural habitats. These differences exert powerful selective forces on plants and their pathogens, shaping the biology of pathosystems, epidemiological patterns, and pathogenic fitness (11, 21). Plant pathogens are dependent upon the abiotic environment as well as on their host plants and are subjected to strong selective forces exerted by their hosts. This process is shaped especially (but not exclusively) by genetic variation at loci controlling differential host specificity, which may ultimately be an important driver in speciation (37, 48, 49).The Neolithic revolution and the adoption of farming have had a large impact on plant communities as well as their related pathogens (11, 34, 57). The long-term interplay between plant pathogens and their hosts and the resulting evolutionary trajectories may have different patterns in natural plant communities as compared to agro-ecosystems (12). One striking observation is that pathogens of natural plant populations, although prevalent, rarely cause the destruction of their hosts (21). Therefore, investigations of the epidemiological and biological differences between pathogen populations from wild and domesticated origins are of fundamental interest and are highly relevant to understanding disease patterns, parasite evolution, and host resistance in agricultural systems. Such studies are expected to be especially fruitful in the centers of origin of crop species, because these regions are generally considered to be pathogen centers of origin as well (40, 57).Throughout West Asia, wild cereals and legumes and their domesticated derivatives have been growing sympatrically since the beginning of Near Eastern farming systems (41, 61). Domesticated chickpea, Cicer arietinum L, is grown sympatrically with a number of annual and perennial Cicer relatives, including the immediate wild progenitor of domesticated chickpea, C. reticulatum Ladiz (39, 58). Following the Neolithic agricultural revolution in southeastern Turkey (41), the Near Eastern crop package spread in all directions throughout the east Mediterranean and reached the southern Levant within 1 millennium (2, 3). This “passage” of the cultigens, from their core region in southeast Turkey into the southern Levant, traversed populations of many of their wild progenitors and more distantly related wild relatives (e.g., wild barley, wild emmer wheat, wild bitter vetch, wild lentils, and wild peas), (2, 3). Presumably, these natural populations were infested by pathogens capable of infecting the domesticated forms (2, 20, 24).Domesticated chickpea differs from the Near Eastern founder crops in its seasonal growth pattern. While most founder crops have retained the autumnal germination/spring maturation cycle like their wild relatives, domesticated chickpea is a spring-sown crop, germinating and developing up to 4 months later than its wild relatives (1, 3). This shift of life cycle is puzzling since water availability in the Levant is a major yield-limiting factor and autumn-sown crops enjoy a substantial yield benefit. It has been recently hypothesized that this shift was driven by the extreme vulnerability of chickpea to Ascochyta blight during the rainy season and was the only means to secure stable yields in ancient times (3). Didymella rabiei (Kovachevski) var. Arx. (Anamorph: Ascochyta rabiei (Pass) Labr.) is one of the most destructive diseases of domesticated chickpea, affecting all above-ground parts of the plant. Secondary spread of D. rabiei conidia occurs through rain splash, and epidemic intensity is governed by rain frequency and quantity. As Ascochyta blight epidemics proceed, foci of diseased plants become visible. Unlike other Ascochyta diseases of legumes and Septoria diseases of cereals, Ascochyta blight of chickpea may cause total yield loss under the appropriate environmental conditions (43). Autumn-sown chickpea is severely affected by Ascochyta blight because the crop growth period coincides with the rainy season and optimum environmental conditions for pathogen development and spread (3, 56).Unlike the often massive stands of wild cereals, C. reticulatum has a very narrow and fragmented distribution (2, 8, 38). However, other wild annual Cicer taxa are more common across the region and can be found in close proximity to the domesticated crop (1, 8). In the southern Levant, domesticated chickpea is grown sympatrically, often just few meters apart from C. judaicum (27). C. judaicum grows in patchy distributions in stony/rocky habitats in Israel and neighboring territories, mostly in sites with annual precipitation of >480 mm and altitude of <900 m (6). Unlike C. judaicum, modern chickpea cropping in Israel spans large tracts of land employing a 5-year rotation in individual fields. Recently, D. rabiei isolates sampled from C. judaicum and isolates sampled from C. arietinum were studied and found to be better adapted to their respective original host than to the other Cicer species (26, 27). In addition, in vitro hyphal growth rate experiments exposed an adaptation to higher temperatures among isolates originating from C. arietinum compared to isolates from C. judaicum (26). Given that the natural growing season of C. judaicum occurs during the Levantine winter and that chickpea is a traditional spring-sown crop in the region, it is likely that the apparent adaptation to higher temperatures of D. rabiei isolates from domesticated chickpea may represent an ecological shift following the introduction of summer cropping practices in the Near East (3). These sympatric wild and domesticated pathosystems of Cicer/Ascochyta represent a unique opportunity for studying the genetic basis of the pathogen''s ecological adaptation and its association with pathogenic fitness. Such a system may also help to determine the role of ecological factors and pathogenic fitness in pathogenic divergence and the evolutionary relationships among pathogen populations in natural and human-directed agro-ecosystems (57).In this context, our underlying hypotheses were as follows: (i) isolates sampled from C. arietinum and C. judaicum are conspecific but represent genetically distinct populations; (ii) the temperature growth response of D. rabiei isolates from C. judaicum and C. arietinum has a heritable genetic basis; (iii) the temperature growth response plays an important role in the ongoing pathogen divergence process and, therefore, it is expected to have high heritability values; and (iv) the existence of two sympatric D. rabiei populations (demes) requires the action of one or more genetic isolation mechanisms. In accord with the above hypotheses, the aims of this study were (i) to assess the genetic differentiation between D. rabiei isolates originating from C. judaicum versus C. arietinum, (ii) to determine the genetic basis of temperature response and estimate its heritability, and (iii) to assess the relationship between temperature adaptation and pathogenic fitness among progeny from crosses between D. rabiei isolates from C. judaicum and C. arietinum on the two original hosts.     

Evolutionary and Structural Analyses of Mammalian Haloacid Dehalogenase-type Phosphatases AUM and Chronophin Provide Insight into the Basis of Their Different Substrate Specificities

Mammalian haloacid dehalogenase (HAD)-type phosphatases are an emerging family of phosphatases with important functions in physiology and disease, yet little is known about the basis of their substrate specificity. Here, we characterize a previously unexplored HAD family member (gene annotation, phosphoglycolate phosphatase), which we termed AUM, for aspartate-based, ubiquitous, Mg²⁺-dependent phosphatase. AUM is a tyrosine-specific paralog of the serine/threonine-specific protein and pyridoxal 5′-phosphate-directed HAD phosphatase chronophin. Comparative evolutionary and biochemical analyses reveal that a single, differently conserved residue in the cap domain of either AUM or chronophin is crucial for phosphatase specificity. We have solved the x-ray crystal structure of the AUM cap fused to the catalytic core of chronophin to 2.65 Å resolution and present a detailed view of the catalytic clefts of AUM and chronophin that explains their substrate preferences. Our findings identify a small number of cap domain residues that encode the different substrate specificities of AUM and chronophin.     

Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica,Arabidopsis and Other Angiosperm Species

Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules.     

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals

Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30–75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.     

野生与人工驯养长爪沙鼠群体遗传结构比较分析

目的探索野生与人工驯养的长爪沙鼠群体遗传状况。方法采用12个微卫星引物,对银川与呼和浩特地区捕获的野生长爪沙鼠群体和首都医科大学人工驯养20余年的长爪沙鼠群体的遗传结构进行比较分析。结果12个微卫星位点中有等位基因29个,3个群体的平均等位基因数分别为2.4167、2.2500、2.2500,平均有效等位基因数分别为1.7505、1.7195、1.6968;有11个微卫星位点呈现多态,多态位点百分率分别为91.67%、83.33%、83.33%,香隆指数分别为0.6239、0.5962、0.5591;平均观测杂合度分别为0.5231、0.5051、0.4825,平均期望杂合度分别为0.4008、0.3882、0.3655;银川和首医群体之间的遗传距离最大,为0.1033;呼和浩特和首医群体之间的距离最小,为0.0592。结论3个群体处于Hardy-Weinberg平衡状态,3个群体之间及与总体之间的遗传结构差异无显著性（P〉0.05）。     

Evolutionary Insight into the Functional Amyloids of the Pseudomonads

Functional bacterial amyloids (FuBA) are important components in many environmental biofilms where they provide structural integrity to the biofilm, mediate bacterial aggregation and may function as virulence factor by binding specifically to host cell molecules. A novel FuBA system, the Fap system, was previously characterized in the genus Pseudomonas, however, very little is known about the phylogenetic diversity of bacteria with the genetic capacity to apply this system. Studies of genomes and public metagenomes from a diverse range of habitats showed that the Fap system is restricted to only three classes in the phylum Proteobacteria, the Beta-, Gamma- and Deltaproteobacteria. The structural organization of the fap genes into a single fapABCDEF operon is well conserved with minor variations such as a frequent deletion of fapA. A high degree of variation was seen within the primary structure of the major Fap fibril monomers, FapC, whereas the minor monomers, FapB, showed less sequence variation. Comparison of phylogenetic trees based on Fap proteins and the 16S rRNA gene of the corresponding bacteria showed remarkably similar overall topology. This indicates, that horizontal gene transfer is an infrequent event in the evolution of the Fap system.     

Concentrated Distribution of Wild Yam Patches: Historical Ecology and the Subsistence of African Rainforest Hunter-Gatherers

Availability of annually reproducing wild yam species (Dioscorea praehensilis and Dioscorea semperflorens) is considered to be a key factor for the viability of forest hunter-gatherer subsistence in the African rainforests. I here describe the habitat and distribution of wild yam patches, and discuss possible human impacts on the formation of wild yam patches, which currently support long-term forest expeditions by Baka hunter-gatherers in southeastern Cameroon. An analysis of canopy photographs shows that annual yams favor a habitat of canopy gaps which receive sufficient sunlight. However, the fact that annual yams patches are limited to specific locations even though gaps in the canopy occur throughout the forest, combined with the mostly vegetative reproductive system of the yams, suggests annual yams do not propagate extensively in the wild. Moreover, areas with abundant annual yam patches that are presently situated far from any villages contain several abandoned village sites. Since the Baka often transplant parts of yam tubers to encourage their spread, it seems that human activities may have contributed to the formation of locally concentrated annual yam patches.     

Morphofunctional State of Epiphysis in Relatively Wild and Domesticated Silver-Black Foxes during Pregnancy

Morphological indices of changes in the epiphysis activity during pregnancy are analyzed in relatively wild and domesticated silver-black foxes. The diameter of light actively functioning nuclei of pinealocytes increased most significantly and reliably in the end of pregnancy and, at the same time, the area of their surface decreased. These signs witness an enhanced protein synthesis. Unlike other stages of ontogenesis, the degree and dynamics of epiphysis activity during the period of pregnancy were similar in animals of both groups.     

中国近缘野生大麦的RAPD分析与进化途径探讨

采用ＲＡＰＤ技术对１２份中国近缘野生大麦和栽培大麦（Ｈｏｒｄｅｕｍ ｖｕｌｇａｒｅ Ｌ．）、１份多年生短芒大麦草（Ｈ．ｂｒｅｖｉｓｕｂｕｌａｔｕｍ（Ｔｒｉｎ．）Ｌｉｎｋ）进行了分析。６３个随机引物中有３６个能产生２８５个稳定的扩增产物,其中２１９个产物具多态性。将每个扩增产物看作一个独立的性状,按其有无列出二元数据矩阵,计算单匹配系数（Ｍ）,Ｎｅｉ氏相似性系数（Ｓ）。ＰＨＹＬＩＰ ３．５ｃ软件包聚     

RAPD Analysis and the Probable Evolutionary Route of Wild Relatives of Barley from China

he genetic relationships among 12 wild relatives and cultivar of barley ( Hordeum vulgare L.) as well as 1 perennial wild barley grass (H. brevisubulatum (Trin.) Link) from China were investigated by RAPD analysis. 36 out of 63 arbitrary primers produced 285 distinctive bands in total, 219 of which were polymorphic. Clearly resolved bands were treated as independent characters and scored for their presence or absence in a binary data matrix. Simple matching coefficients and Nei's similarity coefficients were calculated respectively. Dendrograms were generated by using the PHYLIP 3.5c software. The results revealed that the cultivated barley and their wild relatives from China were clustered into one group, among which, the two-rowed wild relatives of barley ( H. vulgare L. ssp. spontaneum (Koch) Hsü) and the six-rowed wild forms (H. vulgare L. ssp. agriocrithon (Aberg) Hsü) were respectively clustered into different subgroups. It was considered that wild relatives of barley from China were subspecies of H.vulgare. And it was proposed that the cultivated barley was originally evolved from the two-rowed wild barley. The retrogressive two-rowed wild barley and the bottle-shaped wild forms (H. vulgare L. ssp. agriocrithon var. lagunculiforme Bakht Hsü) were the intermediate types in the evolutionary route from the two-rowed wild barley to the six-rowed wild forms and eventually evolved to the cultivated barley.     

Analysis of the Molecular Evolutionary History of the Ascorbate Peroxidase Gene Family: Inferences from the Rice Genome

Ascorbate peroxidase (APx) is a class I peroxidase that catalyzes the conversion of H₂O₂ to H₂O and O₂ using ascorbate as the specific electron donor. This enzyme has a key function in scavenging reactive oxygen species (ROS) and the protection against toxic effects of ROS in higher plants, algae, and Euglena. Here we report the identification of an APx multigene family in rice and propose a molecular evolutionary relationship between the diverse APx isoforms. In rice, the APx gene family has eight members, which encode two cytosolic, two putative peroxisomal, and four chloroplastic isoforms, respectively. Phylogenetic analyses were conducted using all APx protein sequences available in the NCBI databases. The results indicate that the different APx isoforms arose by a complex evolutionary process involving several gene duplications. The structural organization of APx genes also reflects this process and provides evidence for a close relationship among proteins located in the same subcellular compartment. A molecular evolutionary pathway, in which cytosolic and peroxisomal isoforms diverged early from chloroplastic ones, is proposed.Reviewing Editor: Dr. Niles Lehman     

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this “RAD-sex” method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, “male genotypes” became males and some “female genotypes” also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.     

Immature and Mature Dengue Serotype 1 Virus Structures Provide Insight into the Maturation Process

Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, respectively. The subnanometer-resolution maps allow accurate placement of all of the surface proteins. Although the immature and mature viruses showed vastly different surface protein organizations, the envelope protein transmembrane (E-TM) regions remain in similar positions. The pivotal role of the E-TM regions leads to the identification of the start and end positions of all surface proteins during maturation.