A genome assembly of decaploid Houttuynia cordata provides insights into the evolution of Houttuynia and the biosynthesis of alkaloids

Houttuynia cordata Thunb., commonly known as yuxingcao in China, is known for its characteristic fishy smell and is widely recognized as an important herb and vegetable in many parts of Asia. However, the lack of genomic information on H. cordata limits the understanding of its population structure, genetic diversity, and biosynthesis of medicinal compounds. Here we used single-molecule sequencing, Illumina paired-end sequencing, and chromosome conformation capture technology to construct the first chromosome-scale decaploid H. cordata reference genome. The genome assembly was 2.63 Gb in size, with 1348 contigs and a contig N50 of 21.94 Mb further clustered and ordered into 88 pseudochromosomes based on Hi-C analysis. The results of genome evolution analysis showed that H. cordata underwent a whole-genome duplication (WGD) event ~17 million years ago, and an additional WGD event occurred 3.3 million years ago, which may be the main factor leading to the high abundance of multiple copies of orthologous genes. Here, transcriptome sequencing across five different tissues revealed significant expansion and distinct expression patterns of key gene families, such as l-amino acid/l-tryptophan decarboxylase and strictosidine synthase, which are essential for the biosynthesis of isoquinoline and indole alkaloids, along with the identification of genes such as TTM3, which is critical for root development. This study constructed the first decaploid medicinal plant genome and revealed the genome evolution and polyploidization events of H. cordata .

Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae)

Houttuynia cordata (Saururaceae), an ancient and relic species, has been used as an important medicinal and edible plant in most parts of Asia. However, because of the lack of genome information and reliable molecular markers, studies on its population structure, or phylogenetic relationships with other related species are still rare. Here, we de novo assembled the complete chloroplast (cp) genome of H. cordata using the integration of the long PacBio and short Illumina reads. The cp genome of H. cordata showed a typical quadripartite cycle of 160,226 bp. This included a pair of inverted repeats (IRa and IRb) of 26,853 bp, separated by a large single-copy (LSC) region of 88,180 bp and a small single-copy (SSC) region of 18,340 bp. A total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes, were identified in this cp genome. Eighty-one genes were located on the LSC region, 13 genes were located on the SSC region, and 17 two-copy genes were located on the IR region. Additionally, 48 repeat sequences and 86 SSR loci, which can be used as genomic markers for population structure analysis, were also detected. Phylogenetic analysis using 21 cp genomes of the Piperales family demonstrated that H. cordata had a close relationship with the species within the Aristolochia genus. Moreover, the results of mVISTA analysis and comparisons of IR regions demonstrated that the cp genome of H. cordata was conserved with that of the Aristolochia species. Our results provide valuable information for analyzing the genetic diversity and population structure of H. cordata, which can contribute to further its genetic improvement and breeding.

Meiotic abnormalities affect genetic constitution and pollen viability in dicots from Indian cold deserts

BACKGROUND

Meiotic abnormalities lead to morphological and genetic variations which caused not only to evolution but also intraspecific reproductive barriers. During present study of detailed meiotic course in dicotyledonous plants sampled from Indian cold deserts, various meiotic abnormalities have been detected. For this, the plant materials fixed in Carnoy's fixative and studied detailed meiotic course by standard squash method in 1% acetocarmine.

RESULTS

Meiotic abnormalities have been presently detected in 71 species which include multiple associations in diploids (Achillea millefolium L.), multivalents and univalents in polyploids (4 species), cytomixis (40 species), chromosome stickiness (20 species), nonsynchronous disjunction of bivalents (32 species), interbivalent connections (15 species), synaptic mutants (2 species), syncyte meiocytes (2 species), abnormal spindles (7 species), and fusion of pollen grains (1 species), laggards and chromatin bridges, hypo-, hyperploid PMCs, monads, dyads, triads, tetrads with micronuclei and polyads.

CONCLUSIONS

Consequently, variable sized apparently fertile pollen grains and considerable amount of sterile pollen grains are resulted as end products which lead to different genetic constitution (aneuploids and polyploids) and curtailed sexual reproductive success in these species.

Cytomixis in plants: facts and doubts

The migration of nuclei between plant cells (cytomixis) is a mysterious cellular phenomenon frequently observable in the male meiosis of higher plants. Cytomixis attracts attention because of unknown cellular mechanisms underlying migration of nuclei and its potential evolutionary significance, since the genetic material is transferred between the cells that form pollen. Although cytomixis was discovered over a century ago, the advance in our understanding of this process has been rather insignificant because of methodological difficulties. The data that allowed for a new insight into this phenomenon were obtained by examining the migrating nuclei with electron and confocal laser microscopy, immunostaining, and fluorescence in situ hybridization. As has been shown, the chromatin migrating between cells is surrounded by an undamaged nuclear membrane. Such chromatin does not undergo heterochromatization and contains normal euchromatin markers. The condensation degree of the migrating chromatin corresponds to the current meiotic stage, and normal structures of synaptonemal complex are present in the migrating part of the nucleus. The cells involved in cytomixis lack any detectable morphological and molecular markers of programmed cell death. It has been shown that individual chromosomes and genomes (in the case of allopolyploids) have no predisposition to the migration between cells, i.e., parts of the nucleus are involved in cytomixis in a random manner. However, the fate of migrating chromatin after it has entered the recipient cell is still vague. A huge amount of indirect data suggests that migrating chromatin is incorporated into the nucleus of the recipient cell; nonetheless, the corresponding direct evidences are still absent. No specific markers of cytomictic chromatin have been yet discovered. Thus, the causes and consequences of cytomixis are still disputable. This review briefs the recent data on the relevant issues, describes the classical and modern methodological approaches to analysis of the intercellular migration of nuclei, and discusses the problems in cytomixis research and its prospects.

Analysis of cytomixis in tobacco microsporocytes with confocal laser scanning microscopy

Confocal laser scanning microscopy for the first time is used to examine the structure of the tobacco microsporocytes involved in the intercellular migration of nuclei (cytomixis). As is observed, the cytomictic channels are distributed over the surface of tobacco microsporocytes in a non-random manner and their number depends on the meiotic stage. Analysis of non-squash cells demonstrates the differences in cytological patterns of cytomixis in a normal meiosis of control tobacco plants (SR1 line) and the abnormal meiosis of polyploids. As a rule, two to three adjacent cells are involved in cytomixis during meiosis of control tobacco plants; after cytomixis, several micronuclei are formed in recipient cells; cytoplasts (enucleated cells) are rare; and polyads are undetectable. In the meiosis of polyploids, cytomixis is massive, with a larger number of cells (sometimes, over ten) involved in nuclear migration simultaneously; recipient cells on completion of cytomixis develop tens of micronuclei; cytoplasts and polyads are frequently detectable.

A rise of ploidy level influences the rate of cytomixis in tobacco male meiosis

The effect of plant ploidy level on the rate of cytomixis in microsporogenesis has been analyzed with the help of a unique model, the collection of tobacco plants of different ploidies (2n = 2x = 24, 4x = 48, 6x = 72, and 8x = 96). As has been shown, the rate of cytomixis proportionally increases in 6x and 8x cytotypes, being rather similar in 2x and 4x plants. The rate of cytomixis is highly variable, differing even in the genetically identical plants grown under the same conditions. The cytological pattern of cytomixis in the microsporogenesis of control 4x plants has been compared with the corresponding patterns of 2x, 6x, and 8x plants. Involvement of cytomixis in production of unreduced gametes and stabilization of the newly formed hybrid and polyploidy genomes is discussed.

Cytomixis in the cereal (Gramineae) microsporogenesis

The specific features in behavior of the nuclei and chromatin migrating through cytomictic channels as well as in formation of micronuclei in the cereal microsporogenesis have been studied. Immunofluorescence microscopy has allowed for demonstration that the tubulin cytoskeleton does not play a significant role in the intercellular migration of nuclei. Potential involvement of the actin cytoskeleton and SUN-KASH linker complexes in cytomixis is discussed. Comparative analysis of the published and own data suggests that the cytological patterns of cytomixis in monocots and dicots are conserved. As has been shown, each higher ploidy level in the polyploid series of the family Gramineae is accompanied by an increase in the rate of cytomixis independently of individual species. The results confirm the assumption on a correlation between the rate of cytomixis, ploidy level, and genome balance.

Impact of polyploidy on fertility variation of Mediterranean Arundo L. (Poaceae)

Failure of seed production in the genus Arundo L. (Poaceae) is often attributed to polyploidy. This study tested the impact of two ploidy levels (2n=12 and 18x) on the fertility of four Mediterranean Arundo. Viable pollen was screened from its production to its germination, and seed occurrence was monitored in admixture or isolated conditions. In addition, insights on restructuration of polyploid genomes were analysed using molecular cytogenetics. Our results show that high ploidy levels do not automatically induce failure of sexual reproduction. The two ploidy levels are able to produce viable pollen and seed set depending on species and cultural conditions. The sterility of A. micrantha (2n=12x) and A. donax (2n=18x) is due to the early failures of gametogenesis steps. For 18x cytotypes of A. donaciformis and A. plinii, seed absence for isolated genotype vs. seed production in admixed culture support their auto-incompatibility.

New insights into cytomixis: specific cellular features and prevalence in higher plants

The phenomenon of intercellular migration of nuclei in plant tissues (cytomixis) was discovered over a century ago, which has been followed by numerous attempts to clarify the essence of this process as well as to determine its causes and consequences. Most attention of researchers has been paid to cytomixis in microsporogenesis, since the transfer of part of genetic material between microsporocytes may influence the ploidy level of the produced pollen and, presumably, have an evolutionary significance. This review compiles the data on cytological pattern of cytomixis and proposes a scheme as to how cytomictic channels are formed and function in angiosperms. The prevalence of cytomixis in different plant taxa is analyzed using the published data. The causes, mechanisms, and consequences of the nuclear migration between cells in plant tissues are discussed.