Progress, challenge and prospect of plant plastome annotation.

The plastome (plastid genome) represents an indispensable molecular data source for studying phylogeny and evolution in plants. Although the plastome size is much smaller than that of nuclear genome, and multiple plastome annotation tools have been specifically developed, accurate annotation of plastomes is still a challenging task. Different plastome annotation tools apply different principles and workflows, and annotation errors frequently occur in published plastomes and those issued in GenBank.

Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Polygonaceae).

Southwestern China, adjacent to the Qinghai-Tibetan Plateau (QTP), is known as a hotspot for plant diversity and endemism, and it is the origin and diversification center of Persicarieae. As one of the major lineages in Polygonaceae, Persicarieae represents a diverse adaptation to various habitats. As a result of morphological plasticity and poorly resolving molecular markers, phylogenetic relationships and infrageneric classification within Persicarieae have long been controversial.

Plastid phylogenomics and morphological character evolution of Chloridoideae (Poaceae).

Chloridoideae is one of the largest subfamilies of Poaceae, containing many species of great economic and ecological value; however, phylogenetic relationships among the subtribes and genera of Cynodonteae are controversial. In the present study, we combined 111 plastomes representing all five tribes, including 25 newly sequenced plastomes that are mostly from Cynodonteae. Phylogenetic analyses supported the five monophyletic tribes of Chloridoideae, including Centropodieae, Triraphideae, Eragrostideae, Zoysieae and Cynodonteae.

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica.

Background: Viola philippica Cav. is the only source plant of "Zi Hua Di Ding", which is a Traditional Chinese Medicine (TCM) that is utilized as an antifebrile and detoxicant agent for the treatment of acute pyogenic infections. Historically, many Viola species with violet flowers have been misused in "Zi Hua Di Ding".

Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes.

Koenigia, a genus proposed by Linnaeus, has a contentious taxonomic history. In particular, relationships among species and the circumscription of the genus relative to Aconogonon remain uncertain. To explore phylogenetic relationships of Koenigia with other members of tribe Persicarieae and to establish the timing of major evolutionary diversification events, genome skimming of organellar sequences was used to assemble plastomes and mitochondrial genes from 15 individuals representing 13 species.

Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae.

Background And Aims: The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear.

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae).

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, , , and In this study, the plastomes of and were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types.

Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture.

Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g.

Comparative Plastomes and Phylogenetic Analysis of and Closely Related Genera (Poaceae).

(Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of and phylogenetic relationships among taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of , the plastomes of 12 taxa (including 8 species and 4 varieties), one species, 15 species, two species, and two species were included in the present study.

The complete chloroplast genome of Willd. (Amaranthaceae).

The complete chloroplast genome (plastome) of the was assembled and annotated in this study. The complete plastome was composed of circular DNA molecules with a total length of 152,200 bp, comprising a large single-copy region (83,683 bp), a small single-copy region (18,131 bp), and two inverted repeat regions (25,193 bp). GC content of this complete plastome was 37.

Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae).

Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed.

Characterization and phylogenetic analysis of the complete plastome of (Gramineae), an annual weed.

is a weed in summer crop field, which is harmful to wheat crops. The complete plastome of was reported in this study. The genome was 136,408 bp in length, consisting of an 80,512 bp large single-copy region, a 12,836 bp small single-copy region, and two 21,530 bp inverted repeat regions.

The complete chloroplast genome sequence of a rambler rose, (Rosaceae).

The rambler Crép. is an important founder species during modern rose domestication. However, the chloroplast genome (plastome) of this wild species remains unavailable.

Characterization of the complete plastome of (Poaceae), a widespread weed.

is a predominant weed species that distributes widely in North temperate regions. The complete plastome of is reported here. It is a circular molecular of 136,382 bp in length and consists of a large single-copy region (LSC: 80,455 bp), a small single-copy region (SSC: 12,849 bp), and two inverted repeats regions (IRs: 21,539 bp).

Characterization of the complete chloroplast genome of an annual halophyte, (Amaranthaceae).

The complete chloroplast genome (plastome) of , an annual halophytic herb, was determined. The plastome was 152,191 bp in size, containing a large single-copy region (83,675 bp), a small single-copy region (18,130 bp), and two inverted repeats regions (25,193 bp). The overall GC content of this plastome was 37.

First report of the parasitic invasive weed field dodder () parasitizing the confamilial invasive weed common morning-glory () in Shandong, China.

Common morning-glory ( (L.) Roth, Convolvulaceae), an annual herbaceous vine native to South America, was first recorded to be cultivated in China in 1890, and since then it has invaded all provinces of China. It was one of the 18 alien invasive species in China (MEE.

Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat.

Plastid genomes (plastomes) of parasitic plants undergo dramatic reductions as the need for photosynthesis relaxes. Here, we report the plastome of the only known heterotrophic gymnosperm Parasitaxus usta (Podocarpaceae). With 68 unique genes, of which 33 encode proteins, 31 tRNAs, and four rRNAs in a plastome of 85.

The complete chloroplast genome of an annual halophyte herb, (Amaranthaceae).

The complete chloroplast genome (plastome) of , an annual halophytic herb, was determined in this study. The plastome was 149,807 bp in size, containing a large single-copy region (82,162 bp), a small single-copy region (18,191 bp), and two inverted repeats regions (24,727 bp). The overall GC content of this plastome was 36.

Characterization of the complete plastome of (Chenopodiaceae), an annual halophytic herb.

, an annual halophytic herb, is one of the most important Chinese herbal medicines, forages and indicator plants for saline-alkali soil. In this study, we report the complete plastome of . The plastome was 152,237 bp in length and comprises a large single-copy region (83,721 bp), a small single-copy region (18,096 bp), and a pair of inverted repeats (25,210 bp).

Characterization of the complete chloroplast genome of (Amaranthaceae/Chenopodiaceae), an annual succulent halophyte.

, an annual succulent halophytic herb, is one of the major halophyte widely distributed in both saline inland and the intertidal zone. In this study, we report the complete chloroplast genome (plastome) of . The plastome was 151,642 bp in length and comprises a large single-copy region (83,502 bp), a small single-copy region (17,780 bp), and a pair of inverted repeats (25,180 bp).

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes.

Background: Plastome (plastid genome) sequences provide valuable information for understanding the phylogenetic relationships and evolutionary history of plants. Although the rapid development of high-throughput sequencing technology has led to an explosion of plastome sequences, annotation remains a significant bottleneck for plastomes. User-friendly batch annotation of multiple plastomes is an urgent need.

Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae).

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

Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae).

Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The phylogenetic relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer stem branches than those of HCX, so their sister relationships may be attributed to LBA.