As the largest and basal-most family of conifers, Pinaceae provides key insights into evolutionary history conifers. We present comparative chloroplast genomics analysis concatenated 49 protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, address long-standing controversy about phylogeny. The complete cpDNAs Cathaya argyrophylla Cedrus deodara (Abitoideae) draft Larix decidua, Picea morrisonicola, Pseudotsuga wilsoniana are reported. found 21- 42-kb...

The relationships among the extant five gymnosperm groups—gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads—remain equivocal. To clarify this issue, we sequenced chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana Taiwania cryptomerioides, 53 common protein-coding genes another three Agathis dammara, Nageia nagi, Sciadopitys verticillata, a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed...

In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent conversions in inverted repeat (IR) than single copy (SC) regions result contrasting substitution rates between these two regions. However, little about effect evolution gymnosperm plastomes. Cycads (Cycadophyta) are second largest group. Evolutionary study their plastomes is limited basal cycad genus, Cycas. this study, we addressed three questions. 1)...

Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated complexities of plastid genome (plastome) or examined possibility whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced from two to three individuals for each 16 recognized (including potential cryptics) Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred yews, resulting a lower...

Phylogenetic relationships among the 5 groups of extant seed plants are presently unsettled. To reexamine this long-standing debate, we determine complete chloroplast genome (cpDNA) Cycas taitungensis and 56 protein-coding genes encoded in cpDNA Gnetum parvifolium. The is a circular molecule 163,403 bp with 2 typical large inverted repeats (IRs) 25,074 each. We inferred phylogenetic major plant lineages using concatenated 37 land plants. Phylogenies, generated by use 3 independent methods,...

Pinaceae, the largest family of conifers, has diversified organizations chloroplast genomes (cpDNAs) with two typical inverted repeats (IRs) highly reduced. To unravel mechanism this genomic diversification, we examined cpDNA from 53 species ten Pinaceous genera, including those Larix decidua (122,474 bp), Picea morrisonicola (124,168 and Pseudotsuga wilsoniana (122,513 which were firstly elucidated. The results uncovered four distinct forms (A−C P) that are due to rearrangements ∼20 ∼21 kb...

We determined the complete chloroplast genome (cpDNA) of Ginkgo biloba (common name: ginkgo), only relict ginkgophytes from Triassic Period. The cpDNA molecule ginkgo is quadripartite and circular, with a length 156,945 bp, which 6,458 bp shorter than that Cycas taitungensis. In cpDNA, rpl23 becomes pseudo, one copy ycf2 retained, there are at least five editing sites. propose retained duplicate ancestral ycf2, has been lost inverted repeat A (IRA). This loss event should have occurred led...

Summary Although conifers are of immense ecological and economic value, bioengineering their chloroplasts remains undeveloped. Understanding the chloroplast genomic organization can facilitate bioengineering. Members conifer II clade (or cupressophytes) highly diverse in both morphologic features organization. We compared six cupressophyte genomes (cpDNAs) that represent four five families, including three first reported here ( A gathis dammara , C alocedrus formosana N ageia nagi ). The...

Molecular phylogenetic studies have not yet reached a consensus on the placement of Ginkgoales, which is represented by only living species, Ginkgo biloba (common name: ginkgo). At least six discrepant placements ginkgo been proposed. This study aimed to use chloroplast phylogenomic approach examine possible factors that lead such disagreeing placements. We found sequence types used in analyses as most critical factor conflicting ginkgo. In addition, varied trees inferred from nucleotide...

The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few species have been reported to contain isomeric plastomes, but whether the existence is ubiquitous remains be investigated with broader taxon sampling. In this study, we sequenced complete ten Cupressoideae, largest subfamily. Cupressoideae showed relatively accelerated rates substitutions at both nonsynonymous and synonymous sites as...

Conifers II (cupressophytes), comprising about 400 tree species in five families, are the most diverse group of living gymnosperms. Their plastid genomes (plastomes) highly variable size and organization, but such variation has never been systematically studied. In this study, we assessed potential mechanisms underlying evolution cupressophyte plastomes. We analyzed plastomes 24 representative genera all focusing on their size, noncoding DNA content, nucleotide substitution rates. Using a...

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], two types wild boar (Hainan Dongbei boar) based on 34 microsatellite loci was carried out to clarify the phylogeny Chinese indigenous breeds. The allele frequencies, effective numbers alleles, average heterozygosity within populations were calculated. results showed that variability Lingao largest, while Jiaxing lowest. greatest distance between domestic pigs found Shanggao DU shortest...

To date, little is known about the evolution of plastid genomes (plastomes) in Lauraceae. As one top five largest families tropical forests, Lauraceae contain many species that are important ecologically and economically. Lauraceous also provide wonderful materials to study evolutionary trajectory response parasitism because they both nonparasitic parasitic species. This compared plastomes nine species, including sole hemiparasitic herbaceous genus Cassytha (laurel dodder; here represented...

The living gymnosperms include about 1,100 species in five major groups: cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cuppressophytes II). Molecular phylogenetic studies have yet to reach a unanimously agreed relationship among them. Moreover, cytonuclear incongruence has been repeatedly observed gymnosperms. We collated comprehensive data set from available genomes added our own high-quality assembly of Podocarpaceae (the 2nd largest conifer family) increase sampling width. used...

The living gymnosperms include about 1200 species in five major groups: cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cupressophytes II). Molecular phylogenetic studies have yet to reach a unanimously agreed-upon relationship among them. Moreover, cytonuclear incongruence has been repeatedly observed gymnosperms. We collated comprehensive dataset from available genomes of 17 across the groups added our own high-quality assembly Podocarpaceae (the second largest conifer family)...

Many genes in the plastid genomes (plastomes) of plants are organized as gene clusters, which co-transcribed, resembling bacterial operons. These operons highly conserved, even among conifers, whose plastomes rearranged relative to other seed plants. We have determined complete plastome sequence Sciadopitys verticillata (Japanese umbrella pine), sole member Sciadopityaceae. The is characterized by extensive inversions, pseudogenization four tRNA after tandem duplications, and a unique pair...

SUMMARY To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized genomes (mitogenomes), plastid genomes, sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four five extant gymnosperm clades. The assembled mitogenomes vary gene content due to massive losses Gnetum Conifer II Mitochondrial expression levels also according protein function, with most highly expressed genes involved respiratory complex. We identified 9132 C‐to‐U as well...

Abstract Background Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms West African, South American, and Southeast Asian rainforests. Only single acquisition of an angiosperm mitochondrial intron has documented to date mitogenomes. We wanted develop more comprehensive understanding frequency fragment length distribution such as well their evolutionary history this genus. Results...

Abstract Background Triploid bananas are almost sterile. However, we succeeded in harvesting seeds from two edible triploid banana individuals (Genotype: ABB) our conservation repository where various wild diploid were also grown. The resulting rare offspring survived to seedling stages. DNA content analyses reveal that they tetraploid. Since contain maternally inherited plastids and paternally mitochondria, sequenced assembled plastomes mitogenomes of these seedlings trace their...

The Lanyu pig is an indigenous breed from the Islet, which southeast of Taiwan. Two herds pigs were introduced Islet into Taiwan in 1975 and 1980. current population conserved consists only 44 animals with unknown genetic lineage. possesses a distinct maternal lineage remote Asian European pigs. present study aimed to understand phylogenetic relationship among Lanyu, Asian, type based on cytochrome b coding gene, ascertain diversity within pigs, address whether introgression exotic or...

The environmental stresses caused by climate change have become more severe in recent decades, affecting tree growth and physiology. Tropical forests great potential for global carbon sequestration. However, they suffer from heavy rainfall prolonged dry periods due to change. Swietenia macrophylla King Melia azedarach L. are economically valuable trees that widely planted southern Taiwan. Plantations exposed either or within the seasons of tropical monsoon areas. Photo-physiological...