The complete plastid genome and characteristics analysis of Achillea millefolium.

Achillea is a crop with Chinese herbal characteristics and horticultural values. Its leaves and flowers contain aromatic oil, and the ripe herb can also be used as medicine to induce sweat and relieve rheumatic pains. It is seen cultivated in gardens all over China. Currently, the most comprehensive chloroplast genome sample involved in the study refers to New World clades of Achillea, which are used for marker selection and phylogenetic research. We completely sequenced the chloroplast genomes of Achillea millefolium. These sequencing results showed that the plastid genome is 149,078 bp in size and possesses a typical quadripartite structure containing one large single copy (LSC) with 82,352 bp, one small single copy (SSC) with 18,426 bp, and a pair of inverted repeat (IR) regions with 24,150 bp in Achillea millefolium. The chloroplast genome encodes a common number of genes, of which 88 are protein-coding genes, 37 transfer ribonucleic acid genes, and 8 ribosomal ribonucleic acid genes, which are highly similar in overall size, genome structure, gene content, and sequence. The exact similarity was observed when compared to other Asteraceae species. However, there were structural differences due to the restriction or extension of the inverted repeat (IR) regions-the palindromic repeats being the most prevalent form. Based on 12 whole-plastomes, 3 hypervariable regions (rpoB, rbcL, and petL-trnP-UGG) were discovered, which could be used as potential molecular markers.

The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold.

BACKGROUND: An ornamental plant often seen in gardens and farmhouses, Musa basjoo Siebold can also be used as Chinese herbal medicine. Its pseudostem and leaves are diuretic; its root can be decocted together with ginger and licorice to cure gonorrhea and diabetes; the decoct soup of its pseudostem can help relieve heat, and the decoct soup of its dried flower can treat cerebral hemorrhage. There have not been many chloroplast genome studies on M. basjoo Siebold. METHODS AND RESULTS: We characterized its complete chloroplast genome using Novaseq 6000 sequencing. This paper shows that the length of the chloroplast genome M. basjoo Siebold is 172,322 bp, with 36.45% GC content. M. basjoo Siebold includes a large single-copy region of 90,160 bp, a small single-copy region of 11,668 bp, and a pair of inverted repeats of 35,247 bp. Comparing the genomic structure and sequence data of closely related species, we have revealed the conserved gene order of the IR and LSC/SSC regions, which has provided a very inspiring discovery for future phylogenetic research. CONCLUSIONS: Overall, this study has constructed an evolutionary tree of the genus Musa species with the complete chloroplast genome sequence for the first time. As can be seen, there is no obvious multi-branching in the genus, and M. basjoo Siebold and Musa itinerans are the closest relatives.

The complete chloroplast genome and characteristics analysis of Callistemon rigidus R.Br.

Callistemon rigidus R.Br. one of the traditional Chinese medicinal plants, is acrid-flavored and mild-natured, with the prominent effects reducing swelling, resolving phlegm, and dispelling rheumatism. Clinically, it has been commonly used to treat cold, cough and asthma, pain and swelling from impact injuries, eczema, rheumatic arthralgia. The chloroplast genome study on Callistemon rigidus R.Br. is a few seen. This study demonstrates the data collected from the assembly and annotation of the chloroplast (cp) genome of Callistemon rigidus R.Br., followed by furthers comparative analysis with the cp genomes of closely related species. C. rigidus R.Br. showed a cp genome in the size of 158, 961 bp long with 36.78% GC content, among which a pair of inverted repeats (IRs) of 26, 671 bp separated a large single-copy (LSC) region of 87, 162 bp and a small single-copy (SSC) region of 18, 457 bp. Altogether 131 genes were hosted, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. 284 simple sequence repeats (SSRs) were also marked out. A comparative analysis of the genome structure and the sequence data of closely related species unveiled the conserved gene order in the IR and LSC/SSC regions, a quite constructive finding for future phylogenetic research. Overall, this study providing C. rigidus R.Br. genomic resources could positively contribute to the evolutionary study and the phylogenetic reconstruction of Myrtaceae.

MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species.

BACKGROUND: With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F1 population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional statistical methods or tools because the linkage phase and segregation pattern of molecular markers are not always fixed as in inbred lines. RESULTS: We implemented the traditional composite interval mapping (CIM) method to multivariate trait data in forest trees and developed the corresponding software, mvqtlcim. Our method not only incorporated the various segregations and linkage phases of molecular markers, but also applied Takeuchi's information criterion (TIC) to discriminate the QTL segregation type among several possible alternatives. QTL mapping was performed in a hybrid F1 population of Populus deltoides and P. simonii, and 12 QTLs were detected for tree height over 6 time points. The software package allowed many options for parameters as well as parallel computing for permutation tests. The features of the software were demonstrated with the real data analysis and a large number of Monte Carlo simulations. CONCLUSIONS: We provided a powerful tool for QTL mapping of multiple or longitudinal traits in an outbred F1 population, in which the traditional software for QTL mapping cannot be used. This tool will facilitate studying of QTL mapping and thus will accelerate molecular breeding programs especially in forest trees. The tool package is freely available from https://github.com/tongchf /mvqtlcim.

De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies.

BACKGROUND: Restriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species. RAD-seq is capable of discovering thousands of genetic markers for linkage mapping across many individuals, and can be applied in species with or without a reference genome. Although several analytical tools are available for RAD-seq data, alternative strategies are necessary for improving the marker quality and hence the genetic mapping accuracy. RESULTS: We demonstrate a strategy for constructing dense genetic linkage maps in hybrid forest trees by combining RAD-seq and whole-genome sequencing technologies. We performed RAD-seq of 150 progeny and whole-genome sequencing of the two parents in an F1 hybrid population of Populus deltoides × P. simonii. Two rough references were assembled from the whole-genome sequencing reads of the two parents separately. Based on the parental reference sequences, 3442 high-quality single nucleotide polymorphisms (SNPs) were identified that segregate in the ratio of 1:1. The maternal linkage map of P. deltoides was constructed with 2012 SNPs, containing 19 linkage groups and spanning 4067.16 cM of the genome with an average distance of 2.04 cM between adjacent markers, while the male map of P. simonii consisted of 1430 SNPs and the same number of linkage groups with a total length of 4356.04 cM and an average interval distance of 3.09 cM. Collinearity between the parental linkage maps and the reference genome of P. trichocarpa was also investigated. Compared with the result on the basis of the existing reference genome, our strategy identified more high-quality SNPs and generated parental linkage groups that nicely match the karyotype of Populus. CONCLUSIONS: The strategy of simultaneously using RAD and whole-genome sequencing technologies can be applied to constructing high-density genetic maps in forest trees regardless of whether a reference genome exists. The two parental linkage maps constructed here provide more accurate genetic resources for unraveling quantitative trait loci and accelerating molecular breeding programs, as well as for comparative genomics in Populus.