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The flower structures of Harpachne harpachnoides (left) and Eragrostis tenella (right). (A) Inflorescence structure; (B) Spikelets structure; (C) Floret structure.
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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...
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... genomic comparative analysis was performed in combination with chloroplast genomes of four other Eragrostis species, one Uniola species, and two other Enneapogon species available in GenBank. In addition, we carried out anatomy investigations of the spikelets of H. harpachnoides and E. tenella, and compared their morphological difference (Figure 1). The main purpose of this study was to: (1) compare and analyze the chloroplast genome structure of the 20 Eragrostideae species; (2) identify highly divergent regions of all 20 Eragrostideae chloroplast genomes; (3) explore the phylogenetic position of Harpachne relative to Eragrostis, and resolve the interspecies relationships within Eragrostis. ...
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... harpachnoides was embedded in Eragrostis with high bootstrap values in all ML analyses (BS > 95%; Figure 8 and Figure S2-S7). In addition, we anatomized the morphology of H. harpachnoides and compared it with its sister group E. tenella in the phylogenetic tree we generated (Figure 1). In the early taxonomic period, Harpachne was recognized as a separate genus due to its racemes being completely different from the panicles of Eragrostis ( Figure 1A). ...
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... addition, we anatomized the morphology of H. harpachnoides and compared it with its sister group E. tenella in the phylogenetic tree we generated (Figure 1). In the early taxonomic period, Harpachne was recognized as a separate genus due to its racemes being completely different from the panicles of Eragrostis ( Figure 1A). However, for E. japonica, E. tenellula, and E. tenella, florets disarticulated from above, moved downward, and fell together with the rachilla joints, and an analogous character-that spikelets fall entire together with pedicel-is found in H. harpachnoides ( Figure 1B). ...
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... the early taxonomic period, Harpachne was recognized as a separate genus due to its racemes being completely different from the panicles of Eragrostis ( Figure 1A). However, for E. japonica, E. tenellula, and E. tenella, florets disarticulated from above, moved downward, and fell together with the rachilla joints, and an analogous character-that spikelets fall entire together with pedicel-is found in H. harpachnoides ( Figure 1B). Furthermore, Harpachne has characteristics including a ciliated ligule and three-veined lemmas ( Figure 1C), which are very similar to other Eragrostis species. ...
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... for E. japonica, E. tenellula, and E. tenella, florets disarticulated from above, moved downward, and fell together with the rachilla joints, and an analogous character-that spikelets fall entire together with pedicel-is found in H. harpachnoides ( Figure 1B). Furthermore, Harpachne has characteristics including a ciliated ligule and three-veined lemmas ( Figure 1C), which are very similar to other Eragrostis species. ...
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... this study, chloroplast genomes were conservative in genome size, gene number, and GC content among 20 Eragrostideae species (Table 2), which was consistent with previous Eragrostideae plastome studies [3]. The chloroplast genomes of these species are approximately 134 kb in genome size ( Figure S1). The GC content in each species was ca. ...
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Main conclusion
The chloroplast genomes of Mediterranean Bupleurum species are reported for the first time. Phylogenetic analysis supports the species as a basal clade of Bupleurum with divergence time at 35.40 Ma.
AbstractBupleurum is one of the most species-rich genus with high medicinal value in Apiaceae. Although infrageneric classifications of...
Crassulaceae are the largest family in the angiosperm order Saxifragales. Species of this family are characterized by succulent leaves and a unique photosynthetic pathway known as Crassulacean acid metabolism (CAM). Although the inter- and intrageneric relationships have been extensively studied over the last few decades, the infrafamilial relation...
Citations
... An increasing numbers of plastid genomes from nonmodel organisms are being sequenced and effectively used to tackle phylogenetic and taxonomic challenges across various ranks in flowering plants [29][30][31][32]. In Poaceae, the phylogenetic classifications at the subfamily, tribe, genus, and species level have been relatively well studied [33][34][35][36][37]. However, to date, there are only a few published chloroplast genomes for Arundinelleae [27,35,38]. ...
... The lengths of the 11 plastomes varied from 139,629 bp to 140,943 bp, mainly due to large indels (insertions/deletions) in non-coding regions. Despite this variation, all 11 plastomes exhibited a high degree of conservation in genome structure, gene order, and content, consistent with findings in other groups of Poaceae [31,36,37,40]. For example, each plastome encodes 110 unique genes arranged in the same order and features the typical quadripartite structure, including a pair of inverted repeats (IR) regions flanked by the large single copy (LSC) and small single copy (SSC) regions (Fig. 1). ...
Background
Arundinelleae is a small tribe within the Poaceae (grass family) possessing a widespread distribution that includes Asia, the Americas, and Africa. Several species of Arundinelleae are used as natural forage, feed, and raw materials for paper. The tribe is taxonomically cumbersome due to a paucity of clear diagnostic morphological characters. There has been scant genetic and genomic research conducted for this group, and as a result the phylogenetic relationships and species boundaries within Arundinelleae are poorly understood.
Results
We compared and analyzed 11 plastomes of Arundinelleae, of which seven plastomes were newly sequenced. The plastomes range from 139,629 base pairs (bp) (Garnotia tenella) to 140,943 bp (Arundinella barbinodis), with a standard four-part structure. The average GC content was 38.39%, but varied in different regions of the plastome. In all, 110 genes were annotated, comprising 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Furthermore, 539 simple sequence repeats, 519 long repeats, and 10 hyper-variable regions were identified from the 11 plastomes of Arundinelleae. A phylogenetic reconstruction of Panicoideae based on 98 plastomes demonstrated the monophyly of Arundinella and Garnotia, but the circumscription of Arundinelleae remains unresolved.
Conclusion
Complete chloroplast genome sequences can improve phylogenetic resolution relative to single marker approaches, particularly within taxonomically challenging groups. All phylogenetic analyses strongly support the monophyly of Arundinella and Garnotia, respectively, but the monophylly of Arundinelleae was not well supported. The intergeneric phylogenetic relationships within Arundinelleae require clarification, indicating that more data is necessary to resolve generic boundaries and evaluate the monophyly of Arundinelleae. A comprehensive taxonomic revision for the tribe is necessary. In addition, the identified hyper-variable regions could function as molecular markers for clarifying phylogenetic relationships and potentially as barcoding markers for species identification in the future.
... The chloroplast genomes of this genus were similar to those of other species of the subfamily Bambusoideae and family Poaceae, with complete chloroplast genomes ranging from 134,494-140,384 bp, large single-copy (LSC) regions ranging from 80,348-83,470 bp, small single-copy (SSC) regions ranging from 12,346-12,912 bp, and inverted repeat (IR) regions ranging from 20,703-22,748 bp (Table 2). Highly conserved chloroplast genomes commonly exist in angiosperms and have been reported in several other plant lineages, including Poaceae, Malvaceae, Araceae, and Asteraceae (Abdullah et al. 2020b;Henriquez et al. 2020;Liu et al. 2021;Mehmood et al. 2020). The conservation of the genome is attributed to its slow evolutionary rate, which is linked to several molecular mechanisms, such as the organization of plastid genes into operons, uniparental inheritance (maternal or paternal), an active repair system, and the rarity of plastid fusion (Wicke et al. 2011). ...
... These genes are reported to function in other angiosperms, such as those in the families Malvaceae, Araceae, Asteraceae, and Solanaceae (Abdullah et al. 2020b;Mehmood et al. 2020;Shahzadi et al. 2020), and are considered essential in some studies (Kikuchi et al. 2013;Kode et al. 2005). However, they are commonly found missing in Poaceae, or only some degraded fragments have been detected (Guisinger et al. 2010;Liu et al. 2021). The guanine-cytosine (GC) content was highly similar among all the species (Table 2). ...
... This high GC content of the IR regions is associated with the presence of ribosomal RNA, which has a GC content of up to 44%. The same phenomenon was previously reported in other angiosperms, including Poaceae (Abdullah et al. 2020a(Abdullah et al. , 2021Ben Romdhane et al. 2024;Liu et al. 2021). ...
... Previous reports on Poaceae chloroplast genomes also noted the loss of ycf1 and ycf2 genes [14,15]. Additionally, we identified the trans-spliced gene rps12, which, like in most species, comprises three exons [16]. ...
Giant reed (Arundo donax) is widely distributed across the globe and is considered an important energy crop. This study presents the first comprehensive analysis of the chloroplast genome of giant reed, revealing detailed characteristics of this species’ chloroplast genome. The chloroplast genome has a total length of 137,153 bp, containing 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes, with a GC content of 39%. Functional analysis indicates that a total of 45 photosynthesis-related genes and 78 self-replication-related genes were identified, which may be closely associated with its adaptability and growth characteristics. Phylogenetic analysis confirmed that Arundo donax cv. Lvzhou No.1 belongs to the Arundionideae clade and occupies a distinct evolutionary position compared to other Arundo species. The findings of this study not only enhance our understanding of the giant reed genome but also provide valuable genetic resources for its application in biotechnology, bioenergy crop development, and ecological restoration.
... As observed in Ctenium species, the position of ndhH gene in relation to the SSC/IRA boundary can vary among species of the same genus in this family. Variation in the position of the ndhH gene has also been observed within other genera of the PACMAD clade of the Poaceae family, e.g., in Eragrostis (Liu & al., 2021) and Eriachne (Davis & Soreng, 2010). However, the position of the ndhH gene in relation to the SSC/IRA boundary does not affect phylogenetic relationships. ...
Ctenium has about 20 species distributed in Africa, Arabia, and the Neotropics, with no species occurring on more than one continent. Its relationship with the morphologically similar Kampochloa is still unclear and has not been investigated. In this study, we performed phylogenomic analyses using 71 protein‐coding genes of 24 newly sequenced plastomes, of 13 species of Ctenium and 1 species of Kampochloa to understand their biogeography and the phylogenetic and evolutionary relationships between these two genera and within Ctenium . Our results support two major clades of Ctenium : the Neotropics and Old‐World clades. Kampochloa is shown to be a close relative of the genus Ctenium , and their morphological similarities support this. Divergence time estimation analyses show that Kampochloa and Ctenium diverged around 7.99 Ma, and might have originated in the late Miocene during the rapid expansion of C 4 grasslands. With this evidence from morphology and phylogenomic data, we propose the inclusion of the previously unplaced Kampochloa into the subtribe Cteniinae.
... The plastomes of E. strigosa, H. arbainense, and H. longiflorum were structurally similar to the plastomes of other Boraginales species [48][49][50]. The plastome sizes were 155,174 bp in E. strigosa, 154,709 bp in H. arbainense, and 154,496 bp in H. longiflorum (Fig. 2) (Table S1), which was greater than that of the SSC and LSC regions, possibly as a result of the presence of all rRNAs in these regions of the plastome [51]. Considering that they possess greater GC than the LSC and SSC regions, the IR regions might be more stable [52]. ...
Background
Heliotropiaceae is a family of the order Boraginales and has over 450 species. The members of the family Heliotropiaceae have been widely reported to be used in traditional medicine Over time, the classification of Heliotropiaceae has remained uncertain and has moved from family to subfamily, or conversely.
Results
In the present study, we sequenced, analyzed, and compared the complete plastomes of Euploca strigosa, Heliotropium arbainense, and Heliotropium longiflorum with the genomes of related taxa. The lengths of the plastomes of E. strigosa, H. arbainense, and H. longiflorum were 155,174 bp, 154,709 bp, and 154,496 bp, respectively. Each plastome consisted of 114 genes: 80 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The long repeats analysis indicated that reverse, palindromic, complement and forward repeats were all found in the three plastomes. The simple repeats analysis showed that the plastomes of E. strigosa, H. arbainense, and H. longiflorum contained 158, 165, and 151 microsatellites, respectively. The phylogenetic analysis confirmed two major clades in the Boraginales: clade I comprised Boraginaceae, while clade II included Heliotropiaceae, Ehretiaceae, Lennoaceae, and Cordiaceae. Inside the family Heliotropiaceae, E. strigosa is nested within the Heliotropium genus.
Conclusions
This study expands our knowledge of the evolutionary relationships within Heliotropiaceae and offers useful genetic resources.
... The fact that different taxa possess different codon usage biases might be responsible for the variation in GC content across different species within the same genus. The highest GC contents were found within IR regions, with 43.41% in C. monoica and 43.48% in C. sinensis, possibly because all rRNA genes are located within these regions [57]. Since the IR regions have more GC than the LSC and SSC regions, they are highly stable [58]. ...
Cordiaceae is a family comprising more than 400 species in the order Boraginales. The classification of this family has undergone changes over time, transitioning between family and subfamily status. In the present study, the complete chloroplast (cp) genomes of Cordia monoica and Cordia sinensis were sequenced, and their cp genomes were then characterized, analyzed, and compared to those of closely related taxa. The lengths of the cp genomes of C. monoica and C. sinensis were 151,813 bp and 152,050 bp, respectively. Both genomes consisted of 114 genes, divided into 4 ribosomal RNA genes, 30 transfer RNA genes, and 80 protein-coding genes. We observed a unique gene inversion in the trnM-rbcL region of both Cordia species. The long repeats analysis revealed that both species’ chloroplast genomes contained forward and palindromic repeats. The simple sequence repeats (SSRs) analysis detected 155 microsatellites in each genome, with the majority being mononucleotide repeats (A/T). Phylogenetic analysis based on maximum likelihood and Bayesian analyses confirmed two major clades in the order Boraginales: clade I comprised Boraginaceae, while clade II included Cordiaceae, Ehretiaceae, and Heliotropiaceae. This study expands our knowledge of the evolutionary relationships across the order Boraginales and offers useful genetic resources.
... The difference in GC content among separate species from the same genus may be due to the fact that various species have different codon use biases. The GC content in the IR regions was 43.17% in E. cymosa and 43.18% in E. obtusifolia, which was higher than the content in the regions of the SSC and LSC, possibly due to the fact that all the rRNAs are present in IR regions [52]. The IR regions may be more stable because of their high GC content in comparison to the LSC and SSC regions [53]. ...
Ehretiaceae is a family in the order Boraginales. It contains more than 150 species. The Ehretiaceae classification has remained elusive and changed over time from subfamily to family, or vice versa. In this paper, we sequenced, characterized, and analyzed the complete chloroplast (cp) genomes of Ehretia cymosa and Ehretia obtusifolia, and their cp genomes were compared to those of related species. The length of the chloroplast genomes of E. cymosa was 156,328 bp, whereas that of E. obtusifolia was 155,961 bp. Each genome contained 114 genes, including 80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Repeat analysis revealed that complement, forward, palindromic, and reverse repeats were present in the chloroplast genomes of both species. Simple sequence repeat analysis showed that the chloroplast genomes of E. cymosa and E. obtusifolia comprise 141 and 139 microsatellites, respectively. Phylogenetic analysis based on Bayesian and maximum likelihood analyses divided the order Boraginales into two well-supported clades. The first clade includes a single family (Boraginaceae), and the second clade includes three families (Ehretiaceae, Cordiaceae, and Heliotropiaceae). This study provides valuable genomic resources and insights into the evolutionary relationships within Boraginales.
... The chloroplast genome is AT-rich, with GC content typically ranging from 35% to 40%. The GC content of Poaceae chloroplast genomes is mostly concentrated between 37% and 40%, with the highest GC content in the IR region and the lowest in the SSC region [113][114][115][116]. The Poaceae chloroplast genomes usually contain 110-130 genes [105,117]. ...
The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.
... P. hainanensis had the least number of repeats, and the number of long repeats of P. longicarpa and P. tiantangensis were exactly the same. SSRs are repeating sequences of typically 1-6 bp 29 , which are widely distributed in eukaryotic genomes 32 . SSRs of cp genome are usually used for population genetics and phylogenetic analysis 27,30 . ...
... Codon usage bias is a common phenomenon in plants. It is generally considered to be an intricate combined outcome of natural selection, mutation, and genetic drift during the long-term evolution of species and genes 45 , which reflects the different pressures of different genes or genomes in the course of evolution 32 . The total number of codons in six Polyspora were different, which were 22,993 in P. axillaris and P. hainanensis, 23,003 in P. speciosa, 22,999 in P. chrysandra, 22,997 in P. longicarpa and 22,989 in P. tiantangensis (Table S9). ...
Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.
... The trnK-UUU/ rps16 has been successfully used to confirm the evolutionary relationship and complete Latin name changes of the Sium alliance within the Apiaceae tribe Oenantheae (Spalik et al., 2009). The phylogenetic analysis based on sequencing data from different molecular markers ndhF/rpl32 and rpl32/trnL-UAG is also separate in the families Aristidoideae and Eragrostideae, and in the genuses Fagopyrum and Dolomiaea, respectively (Shen et al., 2020;Fan et al., 2021;Kuan Liu et al., 2021;Guo et al., 2022). The ycf1 has been employed to assist in inferring the evolution of Pinus, Hoya, and Curcuma (Liang et al., 2020;Odago et al., 2021;Zeb et al., 2022). ...
Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species’ ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constitutes the complete chloroplast genome of A. ukurunduense into a 156,645-bp circular DNA, which displayed a typical quadripartite structure. In addition, 133 genes were identified, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In total, 107 simple sequence repeats and 49 repetitive sequences were observed. Thirty-two codons indicated that biased usages were estimated across 20 protein-coding genes (CDS) in A. ukurunduense. Four hotspot regions (trnK-UUU/rps16, ndhF/rpl32, rpl32/trnL-UAG, and ycf1) were detected among the five analyzed Acer species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that A. ukurunduense is most closely associated with the species of Sect. Palmata. A. ukurunduense and A. pubipetiolatum var. pingpienense diverged in 22.11 Mya. We selected one of the hypervariable regions (trnK-UUU/rps16) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five Acer species through Sanger sequencing. By sequencing the cp genome of A. ukurunduense and comparing it with the relative species of Acer, we can effectively address the phylogenetic problems of Acer at the species level and provide insights into future research on population genetics and genetic diversity.
