Background: Cymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Results: The complete nucleotide sequences of eight individuals from a total of five Cymbidium species’ chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155 kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae. Conclusions: Phylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification—organelle-scale “barcodes”, and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium.

The world’s herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today’s next-generation sequencing world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. As a practical test of routine recovery of rDNA and plastid genome sequences from herbarium specimens, we sequenced 25 herbarium specimens up to 80 years old from 16 different Angiosperm families. Paired-end reads were generated, yielding successful plastid genome assemblies for 23 species and nuclear rDNAs for 24 species, respectively. These data showed that genome skimming can be used to generate genomic information from herbarium specimens as old as 80 years and using as little as 500 pg of degraded starting DNA. The routine plastome sequencing from herbarium specimens is feasible and cost-effective (compare with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.

GetOrganelle is a state-of-the-art toolkit to assemble accurate organelle genomes from NGS data. This toolkit recruit organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published samples, we reassembled the circular plastome in 47 samples using GetOrganelle, but only in 12 samples using NOVOPlasty. In comparison with published/NOVOPlasty plastomes, we demonstrated that GetOrganelle assemblies are more accurate. Moreover, we assembled complete mitogenomes of fungi and animals using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).

Background: The castor bean (Ricinus communis L.), a monotypic species in the spurge family (Euphorbiaceae, 2n = 20), is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85%) in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs) provide valuable resources to develop gene-associated SSR markers. Results: In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A) with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (H _e) with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Conclusion: Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly useful for both genetic mapping and population structure analysis, facilitating breeding and crop improvement of castor bean.

Available plastomes of the Lauraceae show similar structure and varied size, but there has been no systematic comparison across the family. In order to understand the variation in plastome size and structure in the Lauraceae and related families of magnoliids, we here compare 47 plastomes, 15 newly sequenced, from 27 representative genera. We reveal that the two shortest plastomes are in the parasitic Lauraceae genus Cassytha, with lengths of 114,623 (C. filiformis) and 114,963 bp (C. capillaris), and that they have lost NADH dehydrogenase (ndh) genes in the large single-copy region and one entire copy of the inverted repeat (IR) region. The plastomes of the core Lauraceae group, with lengths from 150,749 bp (Nectandra angustifolia) to 152,739 bp (Actinodaphne trichocarpa), have lost trnI-CAU, rpl23, rpl2, a fragment of ycf2, and their intergenic regions in IRb region, whereas the plastomes of the basal Lauraceae group, with lengths from 157,577 bp (Eusideroxylon zwageri) to 158,530 bp (Beilschmiedia tungfangensis), have lost rpl2 in IRa region. The plastomes of Calycanthus (Calycanthaceae, Laurales) have lost rpl2 in IRb region, but the plastome of Caryodaphnopsis henryi (Lauraceae) remain intact, as do those of the nonLaurales magnoliid genera Piper, Liriodendron, and Magnolia. On the basis of our phylogenetic analysis and structural comparisons, different loss events occurred in different lineages of the Laurales, and fragment loss events in the IR regions have largely driven the contraction of the plastome in the Lauraceae. These results provide new insights into the evolution of the Lauraceae as well as the magnoliids as a whole.