Basic Chromosome Number Research Articles

Nuclear Phenotype and Karyotype Analysis in two Varieties of Lathyrus Sativus L.

Lathyrus sativus known as grass pea belongs to the family of Fabaceae commonly grown for human consumption and livestock feed throughout the world. This study based on the morphological features of the basic chromosome numbers and numerical characterization of the karyotypes using total chromosome length (TCL), arm ratio and total fraction frequency. Outcome of BARI Khesari-2 is more effective than BARI Khesari-3 on the basis of mitotic index, nuclear volume and interphase chromosome volume. Whereas, mitotic index directly relevant to cell division; when MI high than cell division rate will be high. The two varieties (BARI Khesari-2 and BARI Khesari-3) were found to possess 2n = 14 chromosomes. Karyotype analysis is an essential tool for studying the genetic constitution of any organism. In this investigation, we found the karyotype formula of BARI Khesari-2 is 7L 4m + 2sm + 1st and BARI Khesari-3 is 7L 2m +3sm + 2st. Chromosome morphology showed a variation in the chromosome length, chromosome structure and centromere position of the accessions. Presence of sub-terminal chromosome in both varieties shows asymmetric karyotype which indicates advanceness. The variation in L. sativus may be regarded as having evolution and adaptive significance. J. Bio-Sci. 30(2): 59-65, 2022

Genomic data resolve phylogenetic relationships of Australian mat-rushes, Lomandra (Asparagaceae: Lomandroideae)

Abstract Lomandra is the largest genus in Asparagaceae subfamily Lomandroideae and possesses economic, ecological, and ethnobotanical significance in Australia. Lomandra comprises four sections, L. section Capitatae, L. section Macrostachya, L. section Typhopsis and L. section Lomandra, the latter comprising series Lomandra and series Sparsiflorae, all recognized based solely on morphology. In this study, phylogenetic relationships were estimated for 79 Lomandroideae individuals, including 45 Lomandra species and subspecies (c. 63% of species and subspecies diversity). We generated genome-scale plastome sequence data and used maximum likelihood and Bayesian inference criteria for phylogenetic estimation. Lomandra was non-monophyletic, with Xerolirion divaricata nested within it. Two major clades were recovered: Capitatae–Macrostachya (CM) and Lomandra–Typhopsis (LT). The CM clade included a monophyletic Lomandra section Capitatae with a base chromosome number x = 7, and L. section Macrostachya (x = 8); the LT clade included L. sections Typhopsis and Lomandra, both x = 8. Section Lomandra series Lomandra and series Sparsiflorae were both recovered as non-monophyletic. Morphological characters were assessed to identify combinations of characters that characterize clades. A base chromosome number of x = 8 was plesiomorphic for Lomandra. The largest number of Lomandra species occupy the Mediterranean ecoregion and occupancy of sclerophyll vegetation was reconstructed as ancestral for the genus.

Cytogenetic studies in the Andropogon gayanus-Andropogon tectorum Complex in Southwestern Nigeria

The studies were carried on accessions of the Andropogon gayanus-Andropogon tectorum complex (Poaceae) in southwestern Nigeria to determine the chromosome numbers and meiotic dynamics in the species. This involves meiotic chromosome and pollen studies using standard procedures. Studies on the morphology and meiotic behaviour of collections of A. gayanus (2n = 40) and A. tectorum (2n = 20, 40) have been made. The cytogenetic studies show that the chromosome configuration of A. gayanus is a tetraploid (2n = 40) on a basic chromosome number of 10. A. tectorum occurs as a regular diploid on a chromosome number of 2n = 20 and it is the only species found in Ekiti State. Accession “Kiwani” was found to be a polyploid. A. tectorum with a chromosome number of 2n = 40. This study has also established the stability of the genome of the Andropogon complex. In spite of the occurrence of univalent and multiple associations, meiosis ensures a high percentage of pollen grains. The pollens of accession “Kiwani” (> 35 µm) were generally larger than those of other accessions while the other accessions of both A. gayanus and A. tectorum have modal pollen sizes less than 35 µm, although the A. tectorum accessions were generally smaller. The study concluded that the occurrence of the tetraploid (2n = 40 in accession AT10, “Kiwani” can be attributed to apomixis occurring in a lonely plant.

Chromosome number of three Bambusa species (Poaceae) in northeastern communities of Thailand

Abstract. Saensouk P, Saensouk S, Sudchaleaw S, Sungkaew S. 2023. Chromosome number of three Bambusa species (Poaceae) in northeastern communities of Thailand. Biodiversitas 24: 4544-4547. Bambusa is a genus within subfamily Bambusoideae, family Poaceae. This study aimed to conduct the chromosome numbers of three Bambusa species in the northeastern Communities of Thailand. All three Bambusa species were studied with somatic chromosome numbers from root tips by squash methods. The somatic chromosome numbers, ploidy, and chromosome size in length from the root tips of three Bambusa species are provided. The somatic chromosome numbers range from 2n = 56 to 2n = 72. Bambusa bambos (L.) Voss was reported as 2n = 56 with high ploidy (heptaploid or 7x), B. burmanica Gamble was reported to be 2n = 72 with high ploidy (nonaploid or 9x), and B. tuldoides Munro was investigated to be 2n = 64 with high ploidy (octaploid or 8x). The basic chromosome number of three Bambusa species studied was x=8. The chromosome numbers of B. burmanica was studied for the first time. The chromosome length of all species was very short between 0.80 µm in B. burmanica and 1.30 µm in B. bambos.

The taxonomic status, synonymy and nomenclature of Buglossoides rochelii comb. nov. (Boraginaceae), a neglected plant of south‐eastern Europe

The identity of Lithospermum rochelii, so far known only from its type locality (Bulgaria, hills in Plovdiv town), remained hitherto uncertain. Our examination of its original material and re‐collection of the species from its locus classicus in Plovdiv town revealed its identity with Lithospermum glandulosum (syn. Buglossoides glandulosa) described later from an adjacent area, in the towns of Sadovo and Asenovgrad (Plovdiv Region), and Lithospermum czernjajevii (syn. Buglossoides czernjajevii), described from north‐eastern Ukraine in the 20th century. The diagnostic characters of L. rochelii and related taxa are clarified, and the distribution area of this species is verified and mapped. A lectotype is designated for L. rochelii and a new combination is provided, Buglossoides rochelii. The chromosome number 2n = 2x = 16, the first ever record for the species, confirms its sharp separation from all other members of Buglossoides s.str., for which only the base chromosome number x = 7 has been known.

Near-complete de novo assembly of Tricholoma bakamatsutake chromosomes revealed the structural divergence and differentiation of Tricholoma genomes†.

Tricholoma bakamatsutake, which is an edible ectomycorrhizal fungus associated with Fagaceae trees, may have diverged before the other species in Tricholoma section Caligata. We generated a highly contiguous whole-genome sequence for T. bakamatsutake SF-Tf05 isolated in an Oak (Quercus salicina) forest in Japan. The assembly of high-fidelity long reads, with a median read length of 12.3 kb, resulted in 13 chromosome-sized contigs comprising 142,068,211 bases with an average GC content of 43.94%. The 13 chromosomes were predicted to encode 11,060 genes. A contig (122,566 bases) presumably containing the whole circular mitochondrial genome was also recovered. The chromosome-wide comparison of T. bakamatsutake and T. matsutake (TMA_r1.0) indicated that the basic number of chromosomes (13) was conserved, but the structures of the corresponding chromosomes diverged, with multiple inversions and translocations. Gene conservation and cluster analyses revealed at least three phylogenetic clades in Tricholoma section Caligata. Specifically, all T. bakamatsutake strains belonged to the "bakamatsutake" clade, which is most proximal to the "caligatum" clade consisting of T. caligatum and T. fulvocastaneum. The constructed highly contiguous nearly telomere-to-telomere genome sequence of a T. bakamatsutake isolate will serve as a fundamental resource for future research on the evolution and differentiation of Tricholoma species.

Cytological Pattern Reveals Genome Downsizing in Cynodon dactylon (L.) Pers along the Longitudinal Gradient

Understanding the cytological pattern of genome size and ploidy level of the bermudagrass (Cynodon dactylon) is vital to explore the evolution pattern and breeding of the species. To study the diversification of the cytological pattern of bermudagrass along the longitudinal gradient, the genome size and ploidy level were measured and explored with the relationship to climate factors. The corresponding ploidy level was verified through the mitotic chromosome counts method. Bermudagrass accessions ploidy level included diploids, triploid, tetraploid, pentaploid and hexaploid with a basic chromosome number of x = 9. The major ploidy level was tetraploid (45%) and aneuploidy was commonly discovered in collected regions. Mean genome size of bermudagrasswas was estimated to be 1.31 pg/1Cx along longitudinal gradient. The 1Cx values of diploid were higher than that of triploid and tetraploid, while the tetraploid had minimum basic genome size. In the current study, we observed that genome downsizing exists in tetraploids of Cynodon dactylon. Tetraploids have a wider distribution than other ploidy levels, especially in arid areas, occupying a relatively high proportion. In addition, at the same ploidy level, genome size was remarkably variable in the current study. The coefficient of determination analysis showed that longitude and mean annual rainfall were significantly correlated to genome size rather than ploidy level. This cytological study will be helpful for further genetic mechanisms and molecular characteristics to landscape adaptation of bermudagrass.

Chromosomal observations on Eliea (Hypericaceae), a monospecific Madagascar endemic

A meiotic chromosome number of n=9 is reported for Eliea articulata, a monospecific genus of Hypericaceae endemic to Madagascar. This first report for the genus is a new number for the small tribe Cratoxlyeae which includes only one other genus, Cratoxylum. A hypothetical scenario for the origin of n=9 is provided in the context of known chromosome numbers for Cratoxylum and the two other tribes in the Hypericaceae. Given that x=12 has been proposed as the basic chromosome number for the family with numbers of n=11 and n=10 also reported for related species and genera, n=9 appears to have arisen as a descending dysploid from these higher numbers. Field photos of Eliea articulata are provided along with a distribution map and camera lucida drawings of meiotic chromosome figures.

Molecular phylogeny of Onobrychis sect. Onobrychis (Fabaceae-Hedysareae) with insights into its taxonomy and character evolution

Onobrychis sect. Onobrychis, as the most species-rich section of the genus Onobrychis, ranges from Central Asia to Europe with a south extension into North Africa. In this study, we concentrated on the systematics of previously poorly represented O.sect. Onobrychis using a substantial taxon sampling. To test the monophyly of the section as well as to clarify interspecific relationships, the nuclear ribosomal DNA internal transcribed spacer(nrDNA ITS) and three chloroplast sequences (ndhF-rlp32, rpl32-trnL(UAG), and trnG(UCC)-trnS(GCU)) were employed. Phylogenetic analyses were performed by maximum likelihood and Bayesian inferences. The results showed that O.sect. Onobrychis is monophyletic and composed of two main well-supported clades which are redefined as two subsections (O.subsect. Onobrychis, O. subsect. Macropterae).Ancestral character reconstruction of morphological traits: life form, wing to standard ratio, chromosome number, and ploidy level, indicated that short-winged petal is a synapomorphy for a group of species in the section while other traits have undergone parallel evolution. Possessing the basic chromosome number x= 7 has arisen twice, independently. It seems that perenniality and polyploidy are probably the key innovations in the diversification of O. sect. Onobrychis.

Karyology of eight bamboo species endemic to Southern India

Species belonging to the genus Ochlandra Thwaites, the reed bamboos, play a significant role in sustaining the ecology of forests and the livelihood of rural communities in the Western Ghats. Karyology of this predominantly endemic genus of the region is poorly understood. Of the ten species belonging to the genus, chromosomal information is known for only two species. We studied mitotic and/or meiotic chromosomes of eight species, using squash and smear techniques. We report chromosome number (2n) of six species for the first time and two additional 2n reports of a previously studied species, O. travancorica (Bedd.) Gamble. The species and their chromosome numbers are: O. keralensis M. Kumar, Remesh & Sequiera and O. spirostylis M. Kumar, K. K. Seethal. & Sequiera (2n = 48), O. ebracteata Raizada & Chatterji (2n = 64), O. beddomei Gamble and O. setigera Gamble (n = 36, 2n = 72), O. scriptoria (Dennst.) C. E. C. Fisch. (2n = 72), O. wightii (Munro) C. E. C. Fisch. (n = 36, 2n = 60, 72) and O. travancorica (n = 24, 2n = 48, 72, 96). The basic chromosome number of the genus is x = 12. The somatic chromosomes of all studied Ochlandra species are small in size, with a length ranging from 0.45 to 2.50 µm. The present study has provided new perceptions on speciation, evolution and taxonomy of the genus and indicates that the taxonomic muddle in O. travancorica is due to intraspecific genetic variability as evident by chromosomal numerical variation and polyploidy.

Karyological studies of Iranian Allium (Amaryllidaceae) species with a focus on sect. Acanthoprason. 2. Meiotic chromosomes

Meiosis in pollen mother cells (PMCs) was studied of 23 Iranian Allium species (33 accessions, 105 individuals) that belong to two subgenera and six sections. Materials of 13 species were sampled from (near) type locations. Gametic chromosome numbers, chromosome configurations at metaphase I, chiasma frequency, as well as type and percentages of abnormalities were recognized. The basic chromosome number for all taxa investigated was x = 8. Most taxa were diploid and showed eight bivalents or in rare cases two or four pairs of univalents, but in A. subakaka, A. ubipetrense and A. zagricum tetravalents also occurred. Meiosis in less than 10% of PMCs of diploid accessions was disturbed displaying lagging chromosomes, chromatid bridges, micronuclei, or unbalanced chromosome segregations, but very rarely more than one kind of irregularities were found within one dividing cell. One to three B chromosomes were found in 11 accessions, and were recognized for the first time in A. alamutense, A. elburzense and A. iranshahrii. Our data showed no correlation between the occurrence of B chromosomes and the chiasma frequency, and also no noticeable effect of habitat factors on meiotic chromosome behavior. The studied accessions of A. atroviolaceum and A. sabalense were tetraploid (n = 16) showing irregular meiosis in 20–69% of the PMCs which is regarded as sign of autopolyploidy. Since only two out of 31 investigated accessions belonging to subg. Melanocrommyum were tetraploid, we may suggest a trivial role of polyploidy in the evolution of this subgenus.

Cytogenetic Characteristics of Four Gymnocalycium (Cactaceae) Species along Altitudinal Gradients

Species can have broad altitudinal distributions and their characteristics may vary throughout distribution ranges. Ploidy level can vary along environmental gradients, such as altitudinal ones. However, the relationships between ploidy level and altitude may be diverse. The karyotype allows us to know the structural and quantitative characteristics of the chromosomal pairs and to relate these characteristics to the environment where the species occur. Species of the Cactaceae family can be found from sea level to 4500 m above sea level (asl). The greatest species richness is found in mountain areas, where species occupy wide altitudinal ranges. Gymnocalycium belongs to the subfamily Cactoideae; it is a genus endemic to southern South America and its main center of diversity is found in the mountain ranges of central and northern Argentina. The basic chromosome number for Cactaceae is x = 11, with polyploidy being the main existing variation. The aim of this work was to analyze cytogenetic variables in populations of four species of the genus Gymnocalycium (G. andreae, G. erinaceum, G. monvillei, and G. mostii) along their altitudinal distribution. Idiograms were constructed using HCl/Giemsa, CMA/DAPI fluorescent chromosomal banding and fluorescent in situ hybridization (FISH). The karyotypes of the analyzed populations of each species were symmetric and showed little variation in size and symmetry. All the populations of G. andreae, G. erinaceum and G. mostii were found to be diploid and had the greatest distribution; G. monvillei was found to be tetraploid in all the populations analyzed. CMA+/DAPIbands associated with secondary constrictions (NORs) were detected in all the populations of all the species. The cytogenetic characteristics of the studied species were constant along the altitudinal gradients, showing that they can occur at different altitudes without major cytogenetic modifications.

Karyology Study of Six Cytotypes of Vicia L. in Tehran Province, Iran

The genus Vicia L. is an important forage crop and consists of approximately 160 annual and perennial species. This genus has variety in phenotypic characters. In this study, six genotypes of this taxon was choosen to determine the chromosome numbers, ploidy levels and to compare the karyotypic trairts. Based on the results, the basic chromosome number varied from x=5, x=6 and x=7. According to Stebbins classification, species were classified as symmetric class of 3A. Based on intra chromosomal symmetry, V. villosa Roth. had the most asymmetrical and evolutionary karyotype. V. cordata (Wulf. ex Hoppe) Arcangeli, Comp. had the most symmetrical karyotype. The highest distance was observed between these two species using cluster analysis.

An Overview to the Index to Chromosome Numbers in Asteraceae Database: Revisiting Base Chromosome Numbers, Polyploidy, Descending Dysploidy, and Hybridization.

A brief overview to the Index to Chromosome Numbers in Asteraceae database is provided. The database contains karyological information on Asteraceae and has been repeatedly improved and updated and is now hosted at the National Bioscience Database center. Also, we take the opportunity to revisit the evolution of base chromosome numbers in Asteraceae, emphasizing the phenomena of polyploidy, descending dysploidy, and hybridization, common in the family. Chromosome numbers for species included in one of the most recent phylogenetic treatments of the Asteraceae were obtained from the Index to Chromosome Numbers in Asteraceae database were mapped on to the modified phylogeny diagram, and base chromosome numbers were determined for each branch of the phylogeny. Results for tribal base numbers were the same as those hypothesized in our previous work with additional base numbers added for tribes not previously recognized but supported by newer phylogenetic methods. The Asteraceae show an ancestral base chromosome number of x=9 and originated in the Antarctica (Gondowanaland) in Cretaceous (80 Mys ago). The x=9 number has been retained through successive South American lineages of the Barnadesieeae, Gochnatieae, Stiffieae, Wunderlichieae, Astereae, and Senecioneae following northward migration. Northward migration to Africa was accompanied with x=10 becoming the dominant base chromosome number as the family evolved multiple additional tribes. Northward migration to Australasia with x=9 was in Astereae and the families Goodeneaseae, Menyanthaceae, and Stylydiaceae. The evolution of the North American Heliantheae alliance began with the appearance of x2=19 which persisted in multiple additional new tribes. Frequent dysploidy decreases, polyploidy and hybridization occurred throughout the history of the family.

Heterochromatin patterns in four diploid Zephyranthes species with different basic chromosome number (Amaryllidaceae)

Diverse species-specific karyotypes have been reported within Zephyranthes Herb., as well as different basic chromosome numbers (x = 5, 6, 7, and 9), with x = 6 being the most common. The aim of this work was to analyze the constitutive heterochromatin (C-Het) pattern of karyotypes in four diploid Zephyranthes species. For this purpose, a cytomolecular analysis of the karyotypes of Z. andalgalensis (2n = 2x = 12 = 4 m + 2 sm), Z. chacoensis (2n = 2x = 12 = 3 m + 2 sm + 1 st), Z. robusta (2n = 2x = 12 = 3 m + 2 sm + 1 st), and Z. pedunculosa (2n = 2x = 14 = 1 m + 3 sm + 3 st) was performed for the first time. All the species analyzed showed CMA+ terminal bands that could be distinguished by their heterochromatin pattern. Interestingly, DAPI+ interstitial bands were also found in the karyotype of Z. robusta. The four Zephyranthes C-Het patterns analyzed show that diploid species have little GC-rich heterochromatin, which is generally associated with terminal satellites, and that AT-rich heterochromatin is rare. The dysploidy evolutionary change between two basic chromosome numbers (x = 6 and 7) is discussed in the present study.

Botanica Pacifica plant chromosome data 3

The chromosome numbers (CNs, 2n) and ploidy level (nx) according to the inferred basic chromosome number (x) are presented for 27 vascular plant species from 16 genera and 11 families: Amaryllidaceae: Allium; Asteraceae: Galinsoga; Caryophyllaceae: Dianthus; Geraniaceae: Erodium; Iridaceae: Crocus; Liliaceae: Fritillaria, Lilium, and Tulipa; Malvaceae: Malva; Onagraceae: Oenothera; Plantaginaceae: Chaenorhinum and Digitalis; Poaceae: Lolium, Panicum, and Setaria; Violaceae: Viola. The studied specimens originated from Europe (Bulgaria), Caucasus (Russia), West Asia (Turkey), Central Asia (Tajikistan), Siberia (Altai Republic, Novosibirsk Region, Republic of Buryatia, and Republic of Khakassia), and Russian Far East (Amur Region and Kamchatka Territory). The CN was for the first time established in Lolium × hybridum (2n = 28). For the other species, previously known CNs have been confirmed.

Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes.

Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae. The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes. The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.

Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.

Here, we report the genome sequence of a popular Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'. We used long-read sequencing and optical mapping, together with the genetic mapping technique, to obtain the chromosome-scale genome assembly of 'Takanotsume'. The assembly consists of 12 pseudomolecules, which corresponds to the basic chromosome number of C. annuum, and is 3,058.5 Mb in size, spanning 97.0% of the estimated genome size. A total of 34,324 high-confidence genes were predicted in the genome, and 83.4% of the genome assembly was occupied by repetitive sequences. Comparative genomics of linked-read sequencing-derived de novo genome assemblies of two Capsicum chinense lines and whole-genome resequencing analysis of Capsicum species revealed not only nucleotide sequence variations but also genome structure variations (i.e. chromosomal rearrangements and transposon-insertion polymorphisms) between 'Takanotsume' and its relatives. Overall, the genome sequence data generated in this study will accelerate the pan-genomics and breeding of Capsicum, and facilitate the dissection of genetic mechanisms underlying the agronomically important traits of 'Takanotsume'.

Identification of Sugarcane S. spontaneum (Poaceae) Germplasm: Evidence from rDNA-ITS and rDNA Locus Analyses

Sugarcane is a major crop for sugar production around the world. The complexity of the sugarcane genome creates challenges for the use of both conventional and molecular breeding methods to improve sugarcane at a genetic level. DNA sequencing is an important tool to assess how the genus Saccharum and the genera of the Saccharum complex are interrelated. Here, we identify the kinship of Nepal2013-6 (Saccharum spontaneum, x = 10) using a tetra-primer amplification refractory mutation system (ARMS) PCR. Based on rDNA-ITS sequence analysis, the accession Nepal2013-6 falls within a single cluster with S. spontaneum (Yunnan82-114 and SES208), which is consistent with the previous results. Moreover, fluorescence in situ hybridization (FISH) results indicate that the 5S rDNA spots are consistent with the chromosomal ploidy in the analytical Saccharum materials, whereas 35S rDNA has similar or fewer sites than the ploidy. Therefore, 5S rDNA FISH patterns would be more suitable than 35S rDNA for chromosomal ploidy analysis in S. spontaneum with varied basic chromosome number x = 8, 9, 10. Altogether, these results indicate that the rDNA sequences will be a useful marker for further rapidly identifying the relationship and ploidy of S. spontaneum in sugarcane breeding.

ROWANS, WHITEBEAMS AND SERVICE TREES

ROWANS, WHITEBEAMS AND SERVICE TREES