We present reference-quality genome assembly and annotation for the stout camphor tree (Cinnamomum kanehirae (Laurales, Lauraceae)), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry than monocots. Two whole-genome duplication events were inferred within the magnoliid lineage: one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small-scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history of Cinnamomum. For example, expansion of the terpenoid synthase gene subfamilies within the Laurales spawned the diversity of Cinnamomum monoterpenes and sesquiterpenes.

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Weedy rice is one of the most dominant and competitive weed species found throughout rice planting areas worldwide. In Malaysia, a combination of agricultural practices such as direct seeding and shared use of machinery has contributed to the rapid proliferation of weedy rice across paddy fields in recent decades. Here, we report on the morphological characterization of weedy rice populations and inferred origin(s) of different morphotypes present in Peninsular Malaysia. Eight weedy rice morphotypes were distinguished based on a combination of traits such as awn presence/absence and hull color, from 193 accessions collected in 17 locations. Results showed a high proportion of awnless accessions (strawhull-, intermediate strawhull-, and brownhull-colored morphotypes, together composing 65% of sampled accessions), with awned accessions represented by strawhull, brownhull, and blackhull forms. Clustering and PCA analyses revealed four major clusters: (1) O. rufipogon and the majority of awned, blackhull, and brownhull—suggestive of a type of weedy rice originating from wild Oryza populations; (2) elite indica cultivar rice and the majority of strawhull weeds—supporting a previous proposal that weedy rice from Malaysia mainly evolved from indirect selection on cultivars for easy-shattering feral forms; (3) the majority of brownhull; and (4) a mixture of other weedy morphotypes—potentially reflecting multiple origins and subsequent admixture. The combination of key morphological descriptors will be useful for advising farmers appropriately in strategies for controlling the spread of weedy rice, including periodic manual weeding to reduce buildup of the seed bank in the fields.

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Acetyl-CoA carboxylase (ACCase) is the key regulator of fatty acid biosynthesis. In most plants, ACCase exists in two locations (cytosol and plastids) and in two forms (homomeric and heteromeric). Heteromeric ACCase comprises four subunits, three of them (ACCA–C) are nuclear encoded (nr) and the fourth (ACCD) is usually plastid encoded. Homomeric ACCase is encoded by a single nr-gene ( ACC ). We investigated the ACCase gene evolution in gymnosperms by examining the transcriptomes of newly sequenced Gnetum ula , combined with 75 transcriptomes and 110 plastomes of other gymnosperms. AccD- coding sequences are elongated through the insertion of repetitive DNA in four out of five cupressophyte families (except Sciadopityaceae) and were functionally transferred to the nucleus of gnetophytes and Sciadopitys . We discovered that, among the three genera of gnetophytes, only Gnetum has two copies of nr- accD . Furthermore, using protoplast transient expression assays, we experimentally verified that the nr- accD precursor proteins in Gnetum and Sciadopitys can be delivered to the plastids. Of the two nr- accD copies of Gnetum , one dually targets plastids and mitochondria, whereas the other potentially targets plastoglobuli. The distinct transit peptides, gene architectures, and flanking sequences between the two Gnetum accD s suggest that they have independent origins. Our findings are the first account of two distinctly targeted nr- accD s of any green plants and the most comprehensive analyses of ACCase evolution in gymnosperms to date.

Phylogeny of the ten Pinaceous genera has long been contentious. Plastid genomes (plastomes) provide an opportunity to resolve this problem because they contain rich evolutionary information. To comprehend the plastid phylogenomics of all ten Pinaceous genera, we sequenced the plastomes of two previously unavailable genera, Pseudolarix amabilis (122,234 bp) and Tsuga chinensis (120,859 bp). Both plastomes share similar gene repertoire and order. Here for the first time we report a unique insertion of tandem repeats in accD of T. chinensis. From the 65 plastid protein-coding genes common to all Pinaceous genera, we re-examined the phylogenetic relationship among all Pinaceous genera. Our two phylogenetic trees are congruent in an identical tree topology, with the five genera of the Abietoideae subfamily constituting a monophyletic clade separate from the other three subfamilies: Pinoideae, Piceoideae, and Laricoideae. The five genera of Abietoideae were grouped into two sister clades consisting of (1) Cedrus alone and (2) two sister subclades of Pseudolarix—Tsuga and Abies—Keteleeria, with the former uniquely losing the gene psaM and the latter specifically excluding the 3 psbA from the residual inverted repeat.

Combination of PCR HRM with either RFLP or direct DNA sequencing was useful to detect K-RAS exon 2 and extended RAS mutations, respectively. Frequency of all RAS mutations in stage IV Indonesian (41%) was similar among Asians (41-49%), which tend to be lower than western (55%) CRC.

Bananas (Musa spp.) are some of the most important fruit crops in the world, contributing up to US$10 billion in export values annually. In this study, we use high-throughput sequencing to obtain genomic resources of high-copy DNA molecules in bananas. We sampled 13 wild species and eight cultivars that represent the three genera (Ensete, Musa, and Musella) of the banana family (Musaceae). Their plastomic, 45S rDNA, and mitochondrial scaffolds were recovered from genome skimming data. Two major clades (Clades I & II) within Musa are strongly supported by the three genomic compartment data. We document, for the first time, that the plastomes of Musaceae have expanded inverted repeats (IR) after they diverged from their two close relatives, Heliconiaceae (the lobster-claws) and Strelitziaceae (the traveler's bananas). The presence/absence of rps19 within IR regions reinforces the two intra-generic clades within Musa. Our comparisons of the bananas' plastomic and mitochondrial DNA sequence trees aid in identifying hybrid bananas' parentage. As the mitochondrial genes of Musa have elevated substitution rates, paternal inheritance likely plays an influential role on the Musa mitogenome evolution. We propose genome skimming as a useful method for reliable genealogy tracing and phylogenetics in bananas.