Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses

Edger, Patrick P.; Hall, Jocelyn C.; Harkess, Alex; Tang, Michelle; Coombs, Jill; Mohammadin, Setareh; Schranz, M. Eric; Xiong, Zhiyong; Leebens‐Mack, James H.; Meyers, Blake C.; Sytsma, Kenneth J.; Koch, Marcus A.; Al‐Shehbaz, Ihsan A.; Pires, J. Chris

doi:10.1002/ajb2.1040

Cited by 70 publications

(77 citation statements)

References 64 publications

(118 reference statements)

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“…Phylogenetic analysis was performed on a data set including 82 gene sequences using RAxML version 8.2.11 with 1000 bootstrap replicates (Stamatakis 2014). Relationships among sampled families of Brassicales were fully resolved with strong supports at most nodes, which are consistent with previous studies (Edger et al 2018).…”

supporting

confidence: 80%

The plastid genome of Pentadiplandra brazzeana Baillon (Pentadiplandraceae)

2019

Mitochondrial DNA Part B

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Pentadiplandra brazzeana is the only species of Pentadiplandraceae. This species is shrubs or tuberous liana with a natural distribution in tropical West Africa. This study firstly determined its complete plastome. The plastome is totally 156,625 bp in length, which contains a pair of 26,751-bp-long inverted repeat regions (IRs), a large single copy region of 85,318 bp, and a small single copy region of 17,805 bp. A total of 112 unique genes were identified in this plastome, of which 78 are protein-coding genes, 30 are tRNA genes, and 4 are rRNA genes. Phylogenetic analysis based on 82 genes fully resolved relationships among sampled families of Brassicales, which are consistent with previous studies.

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supporting

confidence: 80%

The plastid genome of Pentadiplandra brazzeana Baillon (Pentadiplandraceae)

2019

Mitochondrial DNA Part B

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“…In fact, PP7L was also detected in Camelina sativa and Aethionema arabicum, both of which belong to the Brassicaceae, but not in Carica papaya, which belongs to the Caricaceae family. The Brassicaceae and Caricaceae diverged from a common ancestor ;72-92 million years ago (MYA; Wikström et al, 2001;Edger et al, 2018). In light of the absence of PP7L in C. papaya, and its presence in T. hassleriana, it can be concluded that PP7L evolved after the divergence of Caricaceae from the other Brassicales families, but before the separation of Cleomaceae from Brassicaceae, i.e.…”

Section: Pp7l Evolved 43-92 Million Years Ago In the Lineage Leading mentioning

confidence: 99%

Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance

Marino

Klingl

et al. 2019

Plant Physiol.

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Chloroplast biogenesis is indispensable for proper plant development and environmental acclimation. In a screen for mutants affected in photosynthesis, we identified the protein phosphatase7-like (pp7l) mutant, which displayed delayed chloroplast development in cotyledons and young leaves. PP7L, PP7, and PP7-long constitute a subfamily of phosphoprotein phosphatases. PP7 is thought to transduce a blue-light signal perceived by crys and phy a that induces expression of SIGMA FACTOR5 (SIG5). We observed that, like PP7, PP7L was predominantly localized to the nucleus in Arabidopsis (Arabidopsis thaliana), and the pp7l phenotype was similar to that of the sig6 mutant. However, SIG6 expression was unaltered in pp7l mutants. Instead, loss of PP7L compromised translation and ribosomal RNA (rRNA) maturation in chloroplasts, pointing to a distinct mechanism influencing chloroplast development. Promoters of genes deregulated in pp7l-1 were enriched in PHYTOCHROME-INTERACTING FACTOR (PIF)-binding motifs and the transcriptome of pp7l-1 resembled those of pif and CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) signalosome complex (csn) mutants. However, pif and csn mutants, as well as cop1, cryptochromes (cry)1 cry2, and phytochromes (phy)A phyB mutants, do not share the pp7l photosynthesis phenotype. PhyB protein levels were elevated in pp7l mutants, but phyB overexpression plants did not resemble pp7l. These results indicate that PP7L operates through a different pathway and that the control of greening and photosystem biogenesis can be separated. The lack of PP7L increased susceptibility to salt and high-light stress, whereas PP7L overexpression conferred resistance to highlight stress. Strikingly, PP7L was specifically recruited to Brassicales for the regulation of chloroplast development. This study adds another player involved in chloroplast biogenesis.

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“…There have been multiple whole genome duplications in the Brassicales, which has resulted in many polyploids within the Brassicaceae family (69–71). We considered the possibility of transcriptional differences between gene copies in distal, joint, and proximal regions that were undetected because we were unable to determine copy number in our transcriptome.…”

Section: Resultsmentioning

confidence: 99%

How to Build a Fruit: Transcriptomics of a Novel Fruit Type in the Brassiceae

Carey

Hall

Mendler

2018

Preprint

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20Comparative gene expression studies are invaluable for predicting how existing genetic 21 pathways may be modified or redeployed to produce novel and variable phenotypes. Fruits are 22 ecologically important organs because of their impact on plant fitness and seed dispersal, 42 siliques within the Brassicaceae, facilitating future studies on seed shattering in important 43 Brassicaceous crops and pernicious weeds.44 45 3 46 62Arabidopsis, especially amongst close relatives e.g., the loss of dehiscence in many species 63 across the Brassicaceae (1). 65Brassicaceae fruits vary markedly in shape, structure, and size (1,8). Their variation in 66 dehiscence is a focal point for research because it fundamentally changes fruit structure, 67 subsequently affecting dispersal and diversification (9). A prerequisite for exploring how 68 differences in fruit morphology are achieved across the Brassicaceae is familiarity with both the 69 fruit structure and underlying genetic pathways in Arabidopsis (10,11). Arabidopsis fruits, 102 results in indehiscent fruits in Arabidopsis: SHP1/2, SPT,. Overexpression 103 of FUL or NO TRANSMITTING TRACT (NTT) also results in indehiscent fruits (28,29); FUL 104 overexpression completely suppresses SHP1/2, resulting in reduced lignification in the enb layer 105 and reduced valve margin formation; overexpression of NTT phenocopies the ful mutation 106 resulting in valve margin specific genes being expressed throughout valve. In summary, a 107 modification of many components in this pathway results in a loss of dehiscence. Because 108 indehiscence is observed in at least 20 different lineages across the family, it is likely that this 109 phenotype evolved via multiple modifications to this pathway (30). As such, there is no singular 110 alteration to the fruit patterning pathway implicated in this shift for all tribes. 111 112 To date, little is known about the genetic basis of indehiscence in the Brassicaceae, although it is 113 currently being bridged by studies in taxa with varying indehiscent morphologies. Recently, a114 study demonstrated a deviation in expression of eight key genes between pod shatter sensitive 115 species and shatter resistant species of Brassica and Sinapis (2). In Lepidium, there has been an 116 evolutionary shift from dehiscence to indehiscence, e.g., valve margin genes that are conserved 6 117 between the dehiscent L. campestre and Arabidopsis have been lost in the indehiscent L.118 apellianum (31,32). Upregulation in upstream regulator AP2 has been suggested as a factor in 119 this indehiscence (32).120 121 A notable morphological adaptation is the evolution of a complex fruit type known as 122 heteroarthrocarpy, which is only found in some members of the tribe Brassiceae (30,33,34). This 123 modified silique is defined by the presence of a variably abscising central joint, an indehiscent 124 distal region, and a variably dehiscent proximal region (Fig 2). As such, this novel morphology 125 offers an opportunity to investigate fruit variation beyond shifts from ...

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Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses

Abstract: We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.

Cited by 70 publications

References 64 publications

The plastid genome of Pentadiplandra brazzeana Baillon (Pentadiplandraceae)

The plastid genome of Pentadiplandra brazzeana Baillon (Pentadiplandraceae)

Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance

How to Build a Fruit: Transcriptomics of a Novel Fruit Type in the Brassiceae

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