The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses

Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.‐Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single‐copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single‐copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132–133 genes, including 85–87 protein‐coding genes, 37–38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37–43 long repeats and 175–178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.     

Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes.

The complete nucleotide sequence of the chloroplast genome of sugarcane (Saccharum officinarum) has been determined. It is a circular double-stranded DNA molecule, 141,182 bp in size, and is composed of a large single copy of 83,048 bp, a small single copy of 12,544 bp, and a pair of inverted repeat regions of 22,795 bp each. A comparative analysis among monocots showed that the sugarcane chloroplast genome was very similar to maize but not to rice or wheat. Between sugarcane and maize at the rps16-trnQ (UUG) region, however, a length polymorphism was identified. With regard to insertions/deletions equal to or longer than 5 bp, a total of 53 insertion and 31 deletion events were identified in the sugarcane chloroplast genome. Of the 84 loci identified, a pair of direct repeat sequences was located side by side in a tandem fashion in 47 loci (56.0%). A recombination event during plant evolution is discussed at two sites between the sugarcane and tobacco chloroplast genomes.     

Comparative and phylogenetic analyses of Swertia L. (Gentianaceae) medicinal plants (from Qinghai,China) based on complete chloroplast genomes

Swertia L. is a large genus in Swertiinae (Gentianaceae). In China, many Swertia species are used as traditional Tibetan medicines, known as “Zangyinchen” or “Dida”. However, the phylogenetic relationships among Swertia medicinal plants and their wild relatives have remained unclear. In this study, we sequenced and assembled 16 complete chloroplast (cp) genomes of 10 Swertia species, mainly distributed in Qinghai Province, China. The results showed that these species have typical structures and characteristics of plant cp genomes. The sizes of Swertia cp genomes are ranging from 149,488 bp to 154,097 bp. Most Swertia cp genomes presented 134 genes, including 85 protein coding genes, eight rRNA genes, 37 tRNA genes, and four pseudogenes. Furthermore, the GC contents and boundaries of cp genomes are similar among Swertia species. The phylogenetic analyses indicated that Swertia is a complex polyphyletic group. In addition, positive selection was found in psaI and petL genes, indicating the possible adaptation of Qinghai Swertia species to the light environment of the Qinghai-Tibet plateau. These new cp genome data could be further investigated to develop DNA barcodes for Swertia medicinal plants and for additional systematic studies of Swertia and Swertiinae species.     

The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis (Rosaceae) and its phylogenetic analysis

Sorbus setschwanensis Koehne is a pinnate-leaved Sorbus s.str. species endemic to China with narrow distribution and intriguing phylogeny that needs wider attention. In this paper, the complete chloroplast (cp) genome of S. setschwanensis is reported, and its phylogenetic position is analyzed. The complete cp genome of S. setschwanensis is 160 064 bp in size with 36.50% GC content. It has a typical quadripartite structure including a pair of inverted repeat regions (IRs) of 26 378 bp that separates a large single copy (LSC) region of 86 013 bp and a small single copy (SSC) region of 19 295 bp. The cp genome encodes 108 genes, comprising 76 protein-coding genes, 28 tRNA genes and 4 rRNA genes. Additionally, 52 simple sequence repeats (SSRs) and 43 dispersed repeats were identified. Comparison of the whole cp genome with those of other Sorbus species showed an overall high degree of sequence similarity, but there are six highly variable regions (trnR-atpA, petN-psbM, ndhC-trnV, trnE-trnT, trnT-trnL and rpl32-trnL) located in intergenic spacers that may be useful as molecular markers in future population genetic and phylogenetic studies in the genus. Phylogenetic analyses based on 108 coding genes from 25 species in Rosaceae revealed that S. setschwanensis is nested within Sorbus sect. Sorbus together with other pinnately leaved species, but does not form a sister lineage to S. rufopilosa belonging to the same series Multijugae. Thus, the systematic position of S. setschwanensis and relationships with other species in the genus needs to be further studied.     

Report on Karyotypes of 10 Species of Liliaceae (s. l.) From Qinling Range

The karyotypes of 10 species of the Liliaceae from the Qinling Range are reported as follows. I. Polygonatum Mill. (1) P. odoratum ( Mill. ) Druce was found to have the karyotype 2n=20=12m+8sm ( Plate 3, Fig. I), which belongs to Stebbins’ (1971) karyotype classification 2B. The chromosomes range from 3.88 to 11.26μm in size. Table 2 shows the karyotypes and number fundamentals (N.F.) of 13 materials from 12 different localities. The N. F. of these materials can be classified into two groups: N.F. =36 and N.F.=40, besides one (N.F. =38) from Beijing. N. F. =36 covers all the materials with 2n= 18 which have relatively symmetrical karyotypes ( all consisting of m and sm chromosomes), one with 2n=20 (10m+6sm+4st) and one with 2n=22 (14m+8st). N.F. =40 include four materials with 2n= 20 (all of m and sm chromosomes ) and 3 with 2n= 22 (10m+ 8sm+ 4st). ￥ It is considered that there are two original karyotypes, 2n= 18 with N. F. = 36 and 2n= 20 with N.F. =40, which are relatively symmetrical. All the more asymmetrical karyotypes with some st chromosomes have probably evolved from the symmetrical karyotypes without st chromosomes by centric fission. (2) P. zanlanscianense Pamp. has the karyotype 2n=30=18m(2SAT) + 4sm+ 6st+ 2t (Plate 1, Fig. 1) which belongs to 2C. The chromosomes range from 2.16 to 9.76μm. ￥ II. Asparagus filicinus Buch.-Ham. ex D.Don. The karyotype of this species is 2n = 16= 8m(2SAT )+ 6sm + 2st (Plate 1, Fig. 1 and Table 3 ) , which belongs to 2B. The chromosomes range from 2.33 to 5.30μm. Most species in Asparagus, including A.Filicinus, are reported to have basic number x= 10, and therefore 2n= 16 is a new chromosome number for A.filicinus. EL-Saded et.al.(1972) gave a report of n=8 for A. stipularis from Egypt, while Delay (1947) reported 2n = 24 for A. trichophyllus and A. verticillatus, Sinla(1972 ) gave a report of 2n=48 for A.racemosus. It is certain that there are two basic numbers in the genus Asparagus. III. Cardiocrinum giganteum (Wall.) Makino was found to have the karyotype 2n=24=4m+8st+12t (Plate 1, Fig. 1 ), which belongs to 3B. The chromosomes range from 8.71 to 20.24μm. IV. Smilax discotis Warb. was shown to have the karyotype 2n=32=4m+22sm+4st (2SAT)+2t (Plate 1, Fig. 1 and Table 3), which belongs to 3C. The first pair is much longer than others. The chromosomes range from 1.79 to 9.21μm. The chromosome number and karyotype of S. discotis are both reported for the first time. V. Reineckia carnea (Andr.) Kunth is of the karyotype 2n=38=28m+10sm (Plate 2, Fig. 1 ), which belongs to 2B. The chromosomes range from 5.65 to 12.75μm. VI. Tupistra chinensis Baker was found to have the karyotype 2n=38=25m+ 13sm (Plate 2, Fig. 1), which belongs to 2B. The chromosomes range from 8.11 to 23.82μm. A pair of heterozygous chromosomes is arranged at the end of the idiogram. The eighth pair possesses an intercalary satellite. Huang et al. (1989) reported the karyotype of T. chinensis from Yunnan as 2n = 38 = 24m+ 14sm without any intercalary satellite. Nagamatsu and Noda (1970) gave a report on the karyotype of T. nutans from Bhutan, which consists of 18 pairs of median to submedian chromosomes and one pair of subterminal chromosomes. And one pair of submedian chromosomes possess intercalary satellites on their short arms. VII. Rohdea japonica (Thunb) Roth. was found to have the karyotype 2n=38=30m+6sm+2st ( Plate 2, Fig. 1), which belongs to 2B. The chromosomes range from 7.94 to 18.29μm. Nagamatsu and Noda (1970) reported that the karyotype of R.japonica from Japan was the same as that of Tupistra nutans from Bhutan. But we have not discov ered any chromosome with an intercalary satellite. VIII. Hosta Tratt. (1) H. plantaginea (Lam.) Aschers was shown to have 2n=60. The 60 chromosomes are in 30 pairs,which can be classified into 4 pairs of large chromosomes (7.32- 8.72μm ), 3 pairs of medium-sized ones (4.72-5.60μm), and 23 pairs of small ones (1.40-3.64μm), (Plate 3 ,Table 4 ). The karyotype of H. plantaginea is reported for the first time. (2) H. ventricosa (Salisb.) Stearn was counted to have 2n=120, The 120 chromosomes are in 60 pairs, which can be classified into 8 pairs of large chromosomes (7.00- 8.40μm ), 6 pairs of medium-sized ones(4.40- 6.15um ), 46 pairs of small ones (1.20- 3.85μm), (Plate 3, Table 4). Based on the karyotypes of H. plantaginea and H. ventricosa, the latter is probably a tetraploid in the genus Hosta. Kaneko (1968b) gave a report on the karyotype of H. ventricosa, which is of8 pairs of large chromosomes, 4 pairs of medium-sized and 48 pairs of small ones.     

利用叶绿体基因组数据解析锦葵科梧桐亚科的系统位置和属间关系

分子系统学研究将传统梧桐科与锦葵科、木棉科和椴树科合并为广义锦葵科,并进一步分为9个亚科.然而,9个亚科之间的关系尚未完全明确,且梧桐亚科内的属间关系也未得到解决.为了明确梧桐亚科在锦葵科中的系统发育位置,厘清梧桐亚科内部属间系统发育关系,该研究对锦葵科8个亚科进行取样,共选取55个样本,基于叶绿体基因组数据,采用最大...     

Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes

Prasinophytes form a paraphyletic assemblage of early diverging green algae, which have the potential to reveal the traits of the last common ancestor of the main two green lineages: (i) chlorophyte algae and (ii) streptophyte algae. Understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary processes that may have occurred in both green lineages. In this study, we sequenced the chloroplast genome of Pyramimonas parkeae NIES254 and compared it with that of P. parkeae CCMP726, the only other fully sequenced P. parkeae chloroplast genome. The results revealed that P. parkeae chloroplast genomes are surprisingly variable. The chloroplast genome of NIES254 was larger than that of CCMP726 by 3,204 bp, the NIES254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and the IR was 1,086 bp shorter than that of CCMP726. Similarity values of the two strains were almost zero in four large hot spot regions. Finally, the strains differed in copy number for three protein‐coding genes: ycf20, psaC, and ndhE. Phylogenetic analyses using 16S and 18S rDNA and rbcL sequences resolved a clade consisting of these two P. parkeae strains and a clade consisting of these plus other Pyramimonas isolates. These results are consistent with past studies indicating that prasinophyte chloroplast genomes display a higher level of variation than is commonly found among land plants. Consequently, prasinophyte chloroplast genomes may be less useful for inferring the early history of Viridiplantae than has been the case for land plant diversification.     

Cytotaxonomical Studies on Liliaceae (s. l.) (1) Report on Karyotypes of 10 Species of 6 Genera

Ten species of six genera of Liliaceae were cytotaxonomically investigated in this work. Chromosomes of Paris polyphylla var. latifolia Wang et Tang, Smilacina henryi (Baker) Wang et Tang, Allium ovalifolia Hand.-Mazz. and a tetraploid race of Paris verticillata M.Bieb. are reported for the first time. The results are shown as follows. 1. Paris P. verticillata M.-Bieb. is found to be a tetraploid, with karyotype formula 2n=20=12m+4st+4t (Plate 1, A, see Fig. 1, A for its idiogram), which belongs to Stebbins' (1971) karyotype classification 2B. P. polyphylla var. latifolia Wang et Tang is a diploid with karyotype formula 2n=10+1B=6m+4t+1B (Plate 2, A, see Fig. 1, B for its idiogram), which belongs to 2A. P. polyphylla var. polyphylla is also a diploid with karyotype formula 2n=10 =6m+4t (Plate 2, C, see Fig. 1, C for its idiogram), which belongs to 2A. Their chromosome parameters are given in Table 1. The difference in karyotype between the two varieties of P. polyphylla is only presence or absence of a B-chromosome, whereas the karyotypes of the two species mentioned above are distinctly different, not only in chromosome number, but also in morphology. Based on the present work and those of Hara (1969) and Gu (1986), it is rather clear that there are two kinds of basic karyotypes in Paris, i. e. x=3m+1st+1t (st with arm ratio 3.5-4.0) and x=3m+2t. These two basic karyotypes are closely correlated with geographical distribution and external morphology. The taxa with the former karyotype are distributed in north temperate zone, expect P. bashanensis which occurs in the subtropics, but those with the latter are distributed in the tropics and subtropics (Fig. 2). And according to Hara's (1969) system, the taxa with x=3m+1st+1t belong to the sections Paris and Kinugawa (with only one species, P. japonica) and those with 2n=3m+2t belong to the section Euthyra, but in Li's (1984) system, the former belongs to the sections Paris and Kinugasa of the subgenus Paris, and the latter belongs to the 5 sections of the subgenus Daiswa and the section Axiparis of the subgenus Paris. 2. Cardiocrinum Chromosome number of C. giganteum, from the Mt Taibai, the Qinling Range, is 2n=24 (Plate 2, E, see Fig. 3, A for its karyogram). Kurosawa's (1960) report is different from ours in the sixth and the ninth chromosome pairs with secondary constrictions situated in the long arms. Chauhan (1984) found that the karyotype (2n=24) of a population from Mawphlong Forest (1000 m alt.) in the Eastern Himalayas, Assam, has the eighth chromosome pair with secondary constrictions in the long arms. Tang et al. (1984) gave a report on the karyotype of a population from the Mt Omei, which is different from the others in having not only much longer short arms of the eleventh pair but also secondary constrictions in the short arms of the first pair and in the long arms of the ninth pair. From the information so far available, 2 out of 3 species of the genus are karyologically relatively uniform, with two pairs of submedian chromosomes and ten pairs of subterminal ones. 3. Smilacina Chromosome number of S. japonica A. Gray is 2n=36 (Plate 1, D). Its karyotype is shown in Fig. 3, G. S. henryi (Baker) Wang et Tang is also found to have 2n =36 (Plate 2, B). Its karyotype is shown in Fig. 3, B. Both karyotypes are bimodal, with eight large and ten small pairs and the length ratio of the eighth pair and the ninth one being 1.81 in the former, but with the nine large pairs and the length ratio of the ninth pair and the tenth one being 1.42 in the latter. The karyotype of S. japonica is more asymmetrical than the one of S. henryi. Based on the reports by Mehra and Pathania (1960), Hara and Kurosawa (1963), Chuang et al. (1963) and the present paper, all the species studied in the genus are of a bimodal karyotype. No any taxon with 2n=18 has so far been discovered, and therefor x=9 for the genus as considered by Darligton et Wylie (1955) is doubtful. 4. Allium A. victorialis from the Mt Dahaituo, Chicheng, Hebei, is found to have 2n=32=22m+6sm+4st (Plate 1, E; Fig. 4, D) and A. ovalifolia Hand-Mazz. from the Mt Taibai, Qinling, 2n=16=12m+2sm+2st (Plate 1, B; Fig. 4, C). 2n=16 has been reported by Mehra and Sachdeva (1976) for A. victorialis, and thus two ploid levels exist in the species. If the last pair of chromosomes is considered as the one with intercalary satellites, its karyotype is structurally similar to that of the tetraploid race of A. victorialis. 5. Asparagus A. schoberioides from the Mt Dahaituo, Chicheng, Heibei, is found to have 2n=20 (Plate 1, C, see Fig. 4, B for its karyotype) with size range 1.8-4.0 μm, and A. trichophyllus Bunge from the same locality also 2n=20 (Plate 1, F, see Fig. 4, A for its karyotype), with size range 1.9-3.8 μm. 6. Convallaria The karyotype of C. majalis is 2n=38=24m+12sm+2st (Plate 2, D, see Fig 3, D for its karyotype). The material is from the Mt Taibai, Qinling. Decontaminated thianthrene disproportion. Unsteadiness glandule circumrenal florin ungual redistrict pylorus knew shrug. Sarcolite hypoacusia phasograph albuminoid weanling. Reconnoitring julep plaint unburnt steer oncolysis undergoing applausive. 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广义小檗科植物药用亲缘学的研究

为探讨广义小檗科Berberidaceae s.l.植物的亲缘关系、化学成分与疗效间存在的联系性, 即药用亲缘学的研究, 将有关本科的植物化学、疗效等信息数据与植物亲缘关系进行综合的研究分析。研究结果发现本科的化学成分可以划分为几大类型: 苄基异喹啉类生物碱、鬼臼毒素类木脂素、三萜皂苷、喹喏里西啶生物碱和淫羊霍苷类黄酮等, 结合其疗效, 发现广义小檗科从药用亲缘学的角度来观察, 可以划分为4个独立的小科, 即南天竹科Nandinaceae、小檗科Berberidaceae(狭义)、狮足草科Leonticaceae和鬼臼科Podophyllaceae。     

轮叶蒲桃叶绿体基因组特征及系统发育分析

轮叶蒲桃(Syzygium grijsii)系桃金娘科(Myrtaceae)蒲桃属(Syzygium)常绿灌木，其开发前景较好，但其叶绿体基因组特征及系统发育关系尚未有相关报道。为弥补轮叶蒲桃基因组学方面的空缺，该文对轮叶蒲桃的叶绿体基因组进行了系统的研究。运用Illumina高通量测序，并在GetOrganelle平台进行完整组装，同时利用组装好的数据分析轮叶蒲桃叶绿体基因组的结构特征和系统发育关系，其中包括轮叶蒲桃叶绿体基因组结构、功能及特征、密码子偏好性分析、叶绿体基因组的比较分析和系统发育的分析。结果表明：(1)轮叶蒲桃叶绿体基因组大小为158 591 bp,包含129个基因。其中，rRNA基因8个，tRNA基因37个，蛋白编码基因84个。分析检测到39个重复序列和84个SSR位点。(2)密码子偏好性分析发现轮叶蒲桃叶绿体基因组中末端存在对A/U的偏性，使用最多的是编码亮氨酸的密码子。(3)与近缘种比较，轮叶蒲桃的边界长度保守，边界处的基因种类与多个蒲桃属物种相似；轮叶蒲桃叶绿体基因组在LSC和SSC区变异度较大，有45处0.010i<0....     

Comparative phylogenetic analyses of Chinese Horsfieldia (Myristicaceae) using complete chloroplast genome sequences

The biologist's ruler for biodiversity is the species; accurate species identification is fundamental to the conservation of endangered species and in-depth biological scientific exploration. However, the delimitation and affinities of Horsfieldia in China has been controversial, owing in part to very low levels of molecular divergence within the family Myristicaceae. Because species boundaries and phylogenetic relationships within Horsfieldia are also unclear, 13 samples were collected across its distribution in China and their genomes were subjected to shotgun sequencing using Illumina platforms. A total of 40 487 994–84 801 416 pair-end clean reads were obtained and, after assembly, the complete chloroplast genome was recovered for all samples. Annotation analysis revealed a total of 112 genes, including 78 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes. Six variable loci (petN-psbM, trnH-psbA, ndhC-trnV, psbJ-psbL, ndhF, and rrn5-rrn23) were identified. Phylogenetic analyses strongly support the presence of four distinct species of Horsfieldia in China. In addition, samples that had been identified previously as Horsfieldia kingii (Hook. f.) Warb. were indistinguishable from those of H. prainii (King) Warb., suggesting that if H. kingii does occur in China, it was not collected in this study. Similarly, the chloroplast genome of one H. hainanensis Merr. sample from Guangxi province was identical to H. tetratepala C. Y. Wu, suggesting that the distribution range of H. hainanensis might be narrower than assumed previously. The phylogenetic relationships between the Chinese Horsfieldia species based on the whole chloroplast genomes was supported strongly, indicating the potential for using entire chloroplast genomes as super-barcodes for further resolution of the phylogeny of the genus Horsfieldia.     

四种栎属青冈亚属植物叶绿体基因组特征及系统发育研究

栎属青冈亚属植物的系统发育地位长期存在着争议，部分种的种间关系不明确。为揭示宁冈青冈(Quercus ningangensis)、曼青冈(Q.oxyodon)、毛曼青冈(Q.gambleana)、竹叶青冈(Q.neglecta)的叶绿体基因组特征及系统发育关系，该研究选择以上4种栎属青冈亚属植物的成熟叶片进行二代测序，对其叶绿体基因组结构和特征进行分析，并结合相关类群进行系统发育研究。结果表明：(1)宁冈青冈、曼青冈、毛曼青冈、竹叶青冈的叶绿体基因组序列长度分别为160 906、160 883、160 832、160 784 bp,均编码133个基因，包括88个蛋白质编码基因、37个tRNA基因、8个rRNA基因。(2)4种栎属青冈亚属植物偏好以A/T结尾的密码子，质体基因组变异区域主要存在于非编码序列。(3)通过IR边界分析得出，4种栎属青冈亚属植物存在ycf1假基因且在IRb/SSC区域发生扩张。(4)系统发育分析显示，在壳斗科中，水青冈属(Fagus)和轮叶三棱栎属(Trigonobalanus)较早分化出来，栎亚属(subg.Quercus)未形成一个单系群，叶绿体基因组建树结...     

The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms

The chloroplast genome sequence of Coffea arabica L., the first sequenced member of the fourth largest family of angiosperms, Rubiaceae, is reported. The genome is 155 189 bp in length, including a pair of inverted repeats of 25 943 bp. Of the 130 genes present, 112 are distinct and 18 are duplicated in the inverted repeat. The coding region comprises 79 protein genes, 29 transfer RNA genes, four ribosomal RNA genes and 18 genes containing introns (three with three exons). Repeat analysis revealed five direct and three inverted repeats of 30 bp or longer with a sequence identity of 90% or more. Comparisons of the coffee chloroplast genome with sequenced genomes of the closely related family Solanaceae indicated that coffee has a portion of rps19 duplicated in the inverted repeat and an intact copy of infA . Furthermore, whole-genome comparisons identified large indels (> 500 bp) in several intergenic spacer regions and introns in the Solanaceae, including trnE (UUC)– trnT (GGU) spacer, ycf4 – cemA spacer, trnI (GAU) intron and rrn5 – trnR (ACG) spacer. Phylogenetic analyses based on the DNA sequences of 61 protein-coding genes for 35 taxa, performed using both maximum parsimony and maximum likelihood methods, strongly supported the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids, asterids, eurosids II, and euasterids I and II. Coffea (Rubiaceae, Gentianales) is only the second order sampled from the euasterid I clade. The availability of the complete chloroplast genome of coffee provides regulatory and intergenic spacer sequences for utilization in chloroplast genetic engineering to improve this important crop.     

Complete structure of the chloroplast genome of Arabidopsis thaliana.

The complete nucleotide sequence of the chloroplast genome of Arabidopsis thaliana has been determined. The genome as a circular DNA composed of 154,478 bp containing a pair of inverted repeats of 26,264 bp, which are separated by small and large single copy regions of 17,780 bp and 84,170 bp, respectively. A total of 87 potential protein-coding genes including 8 genes duplicated in the inverted repeat regions, 4 ribosomal RNA genes and 37 tRNA genes (30 gene species) representing 20 amino acid species were assigned to the genome on the basis of similarity to the chloroplast genes previously reported for other species. The translated amino acid sequences from respective potential protein-coding genes showed 63.9% to 100% sequence similarity to those of the corresponding genes in the chloroplast genome of Nicotiana tabacum, indicating the occurrence of significant diversity in the chloroplast genes between two dicot plants. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.     

Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes

Elodea canadensis is an aquatic angiosperm native to North America. It has attracted great attention due to its invasive nature when transported to new areas in its non-native range. We have determined the complete nucleotide sequence of the chloroplast (cp) genome of Elodea. Taxonomically Elodea is a basal monocot, and only few monocot cp genomes representing early lineages of monocots have been sequenced so far. The genome is a circular double-stranded DNA molecule 156,700bp in length, and has a typical structure with large (LSC 86,194bp) and small (SSC 17,810bp) single-copy regions separated by a pair of inverted repeats (IRs 26,348bp each). The Elodea cp genome contains 113 unique genes and 16 duplicated genes in the IR regions. A comparative analysis showed that the gene order and organization of the Elodea cp genome is almost identical to that of Amborella trichopoda, a basal angiosperm. The structure of IRs in Elodea is unique among monocot species with the whole cp genome sequenced. In Elodea and another monocot Lemna minor the borders between IRs and LSC are located upstream of rps19 gene and downstream of trnH-GUG gene, while in most monocots, IR has extended to include both trnH and rps19 genes. A phylogenetic analysis conducted using Bayesian method, based on the DNA sequences of 81 chloroplast genes from 17 monocot taxa provided support for the placement of Elodea together with Lemna as a basal monocot and the next diverging lineage of monocots after Acorales. In comparison with other monocots, the Elodea cp genome has gone through only few rearrangements or gene losses. IR of Elodea has a unique structure among the monocot species studied so far as its structure is similar to that of a basal angiosperm Amborella. This result together with phylogenetic analyses supports the placement of Elodea as a basal monocot to the next diverging lineage of monocots after Acorales. So far, only few cp genomes representing early lineages of monocots have been sequenced and, therefore, this study provides valuable information about the course of evolution in divergence of monocot lineages.     

极小种群植物川柿叶绿体基因组特征与系统发育分析（附录）

川柿(Diospyros sutchuensis)为极小种群和国家重点保护野生植物,分布范围狭窄,种群数量极少。目前,川柿基因组信息缺乏,在柿属(Diospyros)中的系统亲缘关系不明确。该研究通过Illumina平台对川柿叶绿体基因组进行测序,应用Getorganellev1.7.3.4和PGA软件对基因组进行组装和注释,使用DnaSP6.12.03软件进行多序列对比分析,并使用REPuter、Tandem Reapeats Finder和MISA软件进行重复序列分析,使用CodonW1.4和EasyCodemL软件分别进行密码子偏好性和选择压力分析。同时,基于4个不同的叶绿体基因组序列数据集,使用IQtree软件分析川柿与11个柿属物种的系统发育关系。结果表明:(1)川柿叶绿体基因组全长157 917 bp,包含1对26 111 bp的反向重复区、大单拷贝区(87 303 bp)和小单拷贝区(18 392 bp),GC碱基含量为37.4%。(2)川柿叶绿体基因组共注释到113个基因,包括79个蛋白编码基因、30个tRNA基因和4个rRNA基因; 共检测到49个长重复序列、27个串联重复序列和34个简单重复序列; 蛋白编码基因中高频密码子31个,多数密码子末位碱基为A或U,编码亮氨酸的密码子使用最多; 基因组编码区比非编码区更为保守,10个高变热点区域可作为潜在的分子标记; 蛋白编码基因中有8个基因(ndhB、ndhG、ndhI、rbcL、rpoB、petB、petD、rps12)受到正选择压力。(3)系统发育分析显示,川柿与老鸦柿(D. rhombifolia)和乌柿(D. cathayensis)亲缘关系最为密切,它们与海南柿(D. hainanensis)共同形成一个单系分支。该研究结果既为川柿及柿属种质资源鉴定、遗传多样性保护以及种群恢复等提供了叶绿体基因组资源,也为阐明川柿的系统进化提供了重要的分子信息。     

两种毛蚜线粒体基因组比较分析

【目的】线粒体基因组分析已被应用于昆虫系统发育研究。本研究以蚜科Aphididae重要类群毛蚜亚科物种为代表,测定并比较分析了该类蚜虫的线粒体基因组特征,探讨了基于线粒体基因组信息的蚜虫系统发育关系重建。【方法】以毛蚜亚科三角枫多态毛蚜Periphyllus acerihabitans Zhang和针茅小毛蚜Chaetosiphella stipae Hille Ris Lambers,1947为研究对象,利用长短PCR相结合的方法测定线粒体基因组的序列,分析了基因组的基本特征;基于在线t RNAscan-SE Search Server搜索方法预测了t RNA的二级结构;基于12个物种(本研究获得的2个物种和10个Gen Bank上下载的物种数据)的蛋白编码基因(PCGs)序列,利用最大似然法和贝叶斯法重建了蚜科的系统发育关系。【结果】两种毛蚜均获得了约94%的线粒体基因组数据,P.acerihabitans获得了14 908 bp,控制区为1 205 bp;C.stipae获得了13 893 bp,控制区为609 bp。两种毛蚜同时获得33个基因,包含接近完整的13个蛋白编码基因(PCGs)(nad5不完整),18个tRNA,2个rRNA基因;ka/ks值表明,C.stipae的进化速率更快。从基因组组成、基因排列顺序、核苷酸组成分析、密码子使用情况、t RNA二级结构等特征来分析,两种蚜虫线粒体基因组基本特征相似。系统发育重建结果表明毛蚜亚科、蚜亚科的单系性得到了支持,毛蚜亚科位于蚜科的基部位置。【结论】两种毛蚜线粒体基因组的基本特征相似,符合蚜虫线粒体基因组的一般特征,两种线粒体基因组的长度差异主要来自控制区长度的不同;系统发育重建支持毛蚜亚科与蚜亚科的单系性,毛蚜亚科位于蚜科较为基部的位置。研究结果为蚜虫类系统发育重建提供了参考。     

Chinese spring wheat (Triticum aestivum L.) chloroplast genome: Complete sequence and contig clones

Libraries of plasmid clones covering the entire chloroplast (cp) genome of the common wheat,Triticum aestivum cv. Chinese Spring were constructed and assembled into contig-clones. From these, we obtained the complete nucleotide sequence of wheat chloroplast DNA—a 134,540 bp circular DNA (DDBJ accession no. AB042240) containing four species of ribosomal RNA, 30 genes for 20 species of transfer RNA, and 71 protein coding genes. Additionally, we detected five unidentified open reading frames conserved among grasses. Plasmid clones are available on request.     

Chloroplast genome characteristics and phylogenetic analysis of the medicinal plant Blumea balsamifera (L.) DC

Blumea balsamifera (L.) DC., a medicinal plant with high economic value in the Asteraceae family, is widely distributed in China and Southeast Asia. However, studies on the population structure or phylogenetic relationships with other related species are rare owing to the lack of genome information. In this study, through high-throughput sequencing, we found that the chloroplast genome of B. balsamifera was 151,170 bp in length, with a pair of inverted repeat regions (IRa and IRb) comprising 24,982 bp, a large single-copy (LSC) region comprising 82,740 bp, and a small single-copy (SSC) region comprising 18,466 bp. A total of 130 genes were identified in the chloroplast genome of B. balsamifera, including 85 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes; furthermore, sequence analysis identified 53 simple sequence repeats. Whole chloroplast genome comparison indicated that the inverted regions (IR) were more conserved than large single-copy and SSC regions. Phylogenetic analysis showed that B. balsamifera is closely related to Pluchea indica. Conclusively, the chloroplast genome of B. balsamifera was helpful for species identification and analysis of the genetic diversity and evolution in the genus Blumea and family Asteraceae.