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Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis‐related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species. [ABSTRACT FROM AUTHOR]

Abstract Background Trapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time. Results The Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA—atpF and rps2—rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds. Conclusion In summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future.

Abstract Background Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species. Results The results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9–37.0%. Gene annotation revealed 106–109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust. Conclusions Our study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae.

Common millet (Panicum miliaceum) is the most valuable and ancient domesticated important crops in the world. We compared five common millet complete chloroplast genomes. A complete map of the variability across the genomes of the five common millet was produced that included single nucleotide variants, InDels, and structural variants, as well as differences in simple sequence repeats and repeat sequences. Molecular phylogeny strongly supported division of the five walnut species into single monophyly with a 100% bootstrap value. The availability of these genomes will provide genetic information for identifying species and hybrids, taxonomy, phylogeny, and evolution in common millet.

Background: Trapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time. Results: The Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA—atpF and rps2—rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds. Conclusion: In summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future. [ABSTRACT FROM AUTHOR]

Zanthoxylum bungeanum var. pubescensis is a variety species of Z. bungeanum Maxim. that is characterized with small leaf plants and possess high resistant to cold stress among the genus Zanthoxylum. In the current study, the complete chloroplast genome sequences of two different leaf shapes were assembled. One type of leaflets is thin paper, and the color on both sides is obviously different after drying, and the fruit stalk is slender and elongated; the other type of leaflets are the thick paper, the leaf surface and fruit stalk are glabrous, the fruit stalk is thicker, and the lateral veins are recessed on the leaf surface and appear to be cracked. Their circular DNA lengths were all 158,565 bp. Both genomes were made up of a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IRs) regions. Each genome encoded 132 genes, including 87 protein-coding, 37 tRNA, and 8 rRNA genes. Phylogenetic analysis indicated that both species were closely related to the congeneric Z. bungeanum.

Zanthoxylum piasezkii Maxim. is a widely distributed species of edible medicinal plant in China. It has been used for traditional spicy condiment and medicinal ingredients for quite a long time. In this study, the complete chloroplast genome sequence of Z. piasezkii was first reported and characterized from sequencing data. The complete chloroplast genome was determined to be 158,728 bp in length, consisting of a large single-copy (LSC) region (85,918 bp) and a small single copy (SSC) region (17,612 bp), which were separated by a pair of 27,599 bp inverted repeat (IR) regions. The chloroplast genome is predicted to contain 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of cpDNA is 38.4%. The phylogenetic analysis of 12 complete chloroplast genomes reveals that Z. piasezkii is mostly related to the congeneric Z. bungeanum.

Zanthoxylum bungeanum var. pubescensis is a variety species of Z. bungeanum Maxim. that is characterized with small leaf plants and possess high resistant to cold stress among the genus Zanthoxylum. In the current study, the complete chloroplast genome sequences of two different leaf shapes were assembled. One type of leaflets is thin paper, and the color on both sides is obviously different after drying, and the fruit stalk is slender and elongated; the other type of leaflets are the thick paper, the leaf surface and fruit stalk are glabrous, the fruit stalk is thicker, and the lateral veins are recessed on the leaf surface and appear to be cracked. Their circular DNA lengths were all 158,565 bp. Both genomes were made up of a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IRs) regions. Each genome encoded 132 genes, including 87 protein-coding, 37 tRNA, and 8 rRNA genes. Phylogenetic analysis indicated that both species were closely related to the congeneric Z. bungeanum. [ABSTRACT FROM AUTHOR]