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Gossypium hirsutum (upland cotton) is one of the most economically important crops worldwide, which has experienced the long terms of evolution and domestication process from wild species to cultivated accessions. However, nucleotide evolution, domestication selection, and the genetic relationship of cotton species remain largely to be studied. In this study, we used chloroplast genome sequences to determine the evolutionary rate, domestication selection, and genetic relationships of 72 cotton genotypes (36 cultivated cotton accessions, seven semi-wild races of G. hirsutum , and 29 wild species). Evolutionary analysis showed that the cultivated tetraploid cotton genotypes clustered into a single clade, which also formed a larger lineage with the semi-wild races. Substitution rate analysis demonstrated that the rates of nucleotide substitution and indel variation were higher for the wild species than the semi-wild and cultivated tetraploid lineages. Selection pressure analysis showed that the wild species might have experienced greater selection pressure, whereas the cultivated cotton genotypes underwent artificial and domestication selection. Population clustering analysis indicated that the cultivated cotton accessions and semi-wild races have existed the obviously genetic differentiation. The nucleotide diversity was higher in the semi-wild races compared with the cultivated genotypes. In addition, genetic introgression and gene flow occurred between the cultivated tetraploid cotton and semi-wild genotypes, but mainly via historical rather than contemporary gene flow. These results provide novel molecular mechanisms insights into the evolution and domestication of economically important crop cotton species. [ABSTRACT FROM AUTHOR]

Isolation and demographic history are key factors that affect lineage divergence of tree species in topographic complex areas, such as the Qinghai-Tibet Plateau (QTP), yet few studies have evaluated these factors in a coalescent-based modeling framework. In the present study, we surveyed ten nuclear DNA sequence loci (nDNA) and six nuclear microsatellite loci (nSSR) for an endangered conifer, Cupressus chengiana, throughout its natural range in the eastern QTP. BARRIER analyses revealed a strong genetic barrier between Gansu and Sichuan populations of C. chengiana, and isolation with migration models detected limited gene flow between them, supporting the division of this species into two evolutionary significant units (ESUs). Two independent coalescent-based approaches suggest a Quaternary divergence between ESUs, their consensus age range ((0.09-) 0.59-1.53 (-2.71) Mya) largely overlaps with the time period when the largest glaciation occurred in the QTP. Both demographic inferences, IMa2 and DIYABC, suggest that both ESUs may have experienced a bottleneck or population contraction event during the late Quaternary. A documented massive recent anthropogenic habitat loss and fragmentation may have led to further decrease of the natural distribution of this conifer. We propose that the conservation and management of both natural stands and plantations of C. chengiana should be reconsidered in the light of our findings. [ABSTRACT FROM AUTHOR]

Forsythia mira M. C. Chang (Oleaceae) is an endemic medicinal shrub in China. In this study, we first characterized its whole plastid genome sequence using the Illumina sequencing platform. The plastid genome was 156,485 bp in length, comprising of a large single copy (LSC) region of 87,223 bp, a small single copy (SSC) region of 17,830 bp, and two inverted repeat regions (IRs) of 51,432 each. The genome of F. mira contained 133 genes, including 86 protein-coding genes, 37 transfer RNAs (tRNA), and 8 ribosomal RNAs (rRNA). The phylogenetic analysis showed that F. mira was placed as a sister to the congeneric F. suspensa. [ABSTRACT FROM AUTHOR]

Debregeasia orientalis is an economically and ecologically important species, which belongs to the genus Debregeasia within the family Urticaceae. The complete chloroplast genome size of D. orientalis is 155,894 bp in length, including a large single copy (LSC) region of 85,558 bp, a small single copy (SSC) region of 19,064 bp, and a pair of inverted repeats (IRs) of 25,636 bp. The genome contains 112 genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The GC content in chloroplast genome, LSC region, SSC region, and IR region were 36.3%, 34.0%, 29.4%, and 42.7%, respectively. A total of 15 species are used to construct the phylogenetic tree of Rosales, employing the maximum likelihood (ML), and the results showed that D. orientalis is closely related to Debregeasia saeneb. [ABSTRACT FROM AUTHOR]

The complete nucleotide sequence of Bunge’s pinePinus bungeanaZucc. ex Endl. chloroplast genome (cp DNA) was determined in this study. The cpDNA was 117 861 bp in length, containing a pair of 475 bp inverted repeat regions (IRa and IRb), which were separated by large and small single copy regions (LSC and SSC) of 65 373 and 51 538 bp, respectively. The cpDNA contained 111 genes, including 71 protein-coding genes (71 PCG species), 4 ribosomal RNA genes (4 rRNA species) and 36 tRNA genes (32 tRNA species). In these genes, 13 harbored a single intron and 1 (ycf3) contained a couple of introns. The overall AT content of Bunge’s pine cpDNA is 61.2%, while the corresponding values of the LSC, SSC and IR regions are 61.9%, 60.2% and 62.5%, respectively. A phylogenetic reconstruction based on the maximum parsimony analysis suggested that all the sampledPinusspecies clustered a monophyletic clade and have a high bootstrap support, and the cpDNA ofP. bungeanais closely related to that of congenericP. gerardiana. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome (cpDNA) sequence of an endemic conifer species, Armand pinePinus armandiiFranch., is determined in this study. The cpDNA was 117,265 bp in length, containing a pair of 475 bp inverted repeat (IR) regions those distinguished in large and small single copy (LSC and SSC) regions of 64,548 and 51,767 bp in length, respectively. The cpDNA contained 114 genes, including 74 protein-coding genes (74 PCG species), 4 ribosomal RNA genes (four rRNA species) and 36 transfer RNA genes (33 tRNA species). Out of these genes, 12 harbor a single intron and most of the genes occurred in a single copy. The overall AT content of the Armand pine cpDNA was 61.2%, while the corresponding values of the LSC, SSC and IR regions were 62.0%, 60.2% and 62.7%, respectively. A phylogenetic analysis revealed thatP. armandiichloroplast genome is closely related to that of theP. koraiensiswithin the genusPinus. [ABSTRACT FROM AUTHOR]

The complete nucleotide sequence of the Taiwan red pinePinus taiwanensisHayata chloroplast genome (cpDNA) is determined in this study. The genome is composed of 119,741 bp in length, containing a pair of very short inverted repeat (IRa and IRb) regions of 495 bp, which was divided by a large single-copy (LSC) region of 65,670 bp and a small single-copy (SSC) region of 53,080 bp in length. The cpDNA contained 115 genes, including 74 protein-coding genes (73 PCG species), 4 ribosomal RNA genes (four rRNA species) and 37 tRNA genes (22 tRNA species). Out of these genes, 12 harbored a single intron, and one (rps12) contained a couple of introns. The overall AT content of the Taiwan red pine cpDNA is 61.5%, while the corresponding values of the LSC, SSC and IR regions are 62.2%, 60.6% and 63.6%, respectively. A maximum parsimony phylogenetic analysis suggested that the genusPinus, Picea, AbiesandLarixwere strongly supported as monophyletic, and the cpDNA ofP. taiwanensisis closely related to that ofP. thunbergii. [ABSTRACT FROM AUTHOR]