Palindromic Structure Research Articles

A universal and wide-range cytosine base editor via domain-inlaid and fidelity-optimized CRISPR-FrCas9.

CRISPR-based base editor (BE) offer diverse editing options for genetic engineering of microorganisms, but its application is limited by protospacer adjacent motif (PAM) sequences, context preference, editing window, and off-target effects. Here, a series of iteratively improved cytosine base editors (CBEs) are constructed using the FrCas9 nickase (FrCas9n) with the unique PAM palindromic structure (NNTA) to alleviate these challenges. The deaminase domain-inlaid FrCas9n exhibits an editing range covering 38 nucleotides upstream and downstream of the palindromic PAM, without context preference, which is 6.3 times larger than that of traditional CBEs. Additionally, lower off-target editing is achieved when incorporating high-fidelity mutations at R61A and Q964A in FrCas9n, while maintaining high editing efficiency. The final CBE, HF-ID824-evoCDA-FrCas9n demonstrates broad applicability across different microbes such as Escherichia coli MG1655, Shewanella oneidensis MR-1, and Pseudomonas aeruginosa PAO1. Collectively, this tool offers robust gene editing for facilitating mechanistic studies, functional exploration, and protein evolution in microbes.

Widespread HCD-tRNA derived SINEs in bivalves rely on multiple LINE partners and accumulate in genic regions

BackgroundShort interspersed nuclear elements (SINEs) are non-autonomous non-LTR retrotransposons widespread across eukaryotes. They exist both as lineage-specific, fast-evolving elements and as ubiquitous superfamilies characterized by highly conserved domains (HCD). Several of these superfamilies have been described in bivalves, however their overall distribution and impact on host genome evolution are still unknown due to the extreme scarcity of transposon libraries for the clade. In this study, we examined more than 40 bivalve genomes to uncover the distribution of HCD-tRNA-related SINEs, discover novel SINE-LINE partnerships, and understand their possible role in shaping bivalve genome evolution.ResultsWe found that bivalve HCD SINEs have an ancient origin, and they can rely on at least four different LINE clades. According to a “mosaic” evolutionary scenario, multiple LINE partner can promote the amplification of the same HCD SINE superfamilies while homologues LINE-derived tails are present between different superfamilies. Multiple SINEs were found to be highly similar between phylogenetically related species but separated by extremely long evolutionary timescales, up to ~ 400 million years. Studying their genomic distribution in a subset of five species, we observed different patterns of SINE enrichment in various genomic compartments as well as differences in the tendency of SINEs to form tandem-like and palindromic structures also within intronic sequences. Despite these differences, we observed that SINEs, especially older ones, tend to accumulate preferentially within genes, or in their close proximity, consistently with a model of survival bias for less harmful, short non-coding transposons in euchromatic genomic regions.ConclusionHere we conducted a wide characterization of tRNA-related SINEs in bivalves revealing their taxonomic distribution and LINE partnerships across the clade. Moreover, through the study of their genomic distribution in five species, we highlighted commonalities and differences with other previously studied eukaryotes, thus extending our understanding of SINE evolution across the tree of life.

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial TFs-DNA interactions remains an intricate challenge. A deeper understanding of DNA secondary structures could greatly enhance our knowledge of how TFs recognize and interact with DNA, thereby elucidating their biological function. In this study, we employed machine learning algorithms to predict transcription factor binding sites (TFBS) and classify them as directed-repeat (DR) or inverted-repeat (IR). To accomplish this, we divided the set of TFBS nucleotide sequences by size, ranging from 8 to 20 base pairs, and converted them into thermodynamic data known as DNA duplex stability (DDS). Our results demonstrate that the Random Forest algorithm accurately predicts TFBS with an average accuracy of over 82% and effectively distinguishes between IR and DR with an accuracy of 89%. Interestingly, upon converting the base pairs of several TFBS-IR into DDS values, we observed a symmetric profile typical of the palindromic structure associated with these architectures. This study presents a novel TFBS prediction model based on a DDS characteristic that may indicate how respective proteins interact with base pairs, thus providing insights into molecular mechanisms underlying bacterial TFs-DNA interaction.

Approximating the closest structured singular matrix polynomial

Consider a matrix polynomial P ( λ ) = A 0 + λ A 1 + ⋯ + λ d A d , with A 0 , … , A d complex (or real) matrices with a certain structure. In this paper we discuss an iterative method to numerically approximate the closest structured singular matrix polynomial P ~ ( λ ) , using the distance induced by the Frobenius norm. An important peculiarity of the approach we propose is the possibility to include different types of structural constraints. The method also allows us to limit the perturbations to just a few matrices and also to include additional structures, such as the preservation of the sparsity pattern of one or more matrices A i , and also collective-like properties, like a palindromic structure. The iterative method is based on the numerical integration of the gradient system associated with a suitable functional which quantifies the distance to singularity of a matrix polynomial.

A Comprehensive Study of the Effects by Sequence Truncation within Inverted Terminal Repeats (ITRs) on the Productivity, Genome Packaging, and Potency of AAV Vectors.

One of the primary challenges in working with adeno-associated virus (AAV) lies in the inherent instability of its inverted terminal repeats (ITRs), which play vital roles in AAV replication, encapsidation, and genome integration. ITRs contain a high GC content and palindromic structure, which occasionally results in truncations and mutations during plasmid amplification in bacterial cells. However, there is no thorough study on how these alterations in ITRs impact the ultimate AAV vector characteristics. To close this gap, we designed ITRs with common variations, including a single B, C, or D region deletion at one end, and dual deletions at both ends of the vector genome. These engineered ITR-carrying plasmids were utilized to generate AAV vectors in HEK293 cells. The crude and purified AAV samples were collected and analyzed for yield, capsid DNA-filled percentage, potency, and ITR integrity. The results show that a single deletion had minor impact on AAV productivity, packaging efficiency, and in vivo potency. However, deletions on both ends, except A, showed significant negative effects on the above characteristics. Our work revealed the role of ITR regions, A, B, C, and D for AAV production and DNA replication, and proposes a new strategy for the quality control of ITR-bearing plasmids and final AAV products.

The role of synthetic peptides derived from bovine lactoferricin against breast cancer cell lines: a mini-review

Abstract Breast cancer represents the most commonly diagnosed cancer worldwide, accounting for approximately one in eight cancers diagnosed. Despite significant advances in the diagnosis and detection of this disease, there is still a great need for more effective therapies to combat the invasive forms, especially those with a high incidence of metastasis. For that reason, bioactive molecules as peptides, including bovine lactoferricin (LfcinB), have been investigated. In this sense, there are reports that 20RRWQWR25 motif derivate from the LfcinB has shown activity against different cancer cell lines. Thus, current studies are being carried out with synthetic derivatives (linear, palindromic, dimer and tetrameric structures) that contain the 20RRWQWR25 motif in order to increase its activity against cancer cell lines by altering its hydrophobicity and net positive charge. In this regard, studies have focused on the use of LfcinB derivatives to combat breast cancer cell lines, with encouraging results. Therefore, in this mini-review, we present the state of the art regarding the activity of LfcinB and its analogs against breast cancer cell lines.

Finding top-k longest palindromes in substrings

Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with the motivation of their application to biology. The longest palindrome problem is one of the most important and classical problems regarding palindromic structures, that is, to compute the longest palindrome appearing in a string T of length n. The problem can be solved in O(n) time by the famous algorithm of Manacher (1975) [27]. This paper generalizes the longest palindrome problem to the problem of finding the top-k longest palindromes in an arbitrary substring, including the input string T itself. The internal top-k longest palindrome query is, given a substring T[i..j] of T and a positive integer k as a query, to compute the top-k longest palindromes appearing in T[i..j]. This paper proposes a linear-size data structure that can answer internal top-k longest palindromes query in optimal O(k) time. Also, given the input string T, our data structure can be constructed in O(nlog⁡n) time. For k=1, the construction time is reduced to O(n).

Characterization of transcriptional regulator PicR of picolinic acid-degrading bacterium Bordetella petrii strain MY10

Picolinic acid (PA) is a natural carboxylated pyridine derivative with multiple biological sources and applications, which is toxic to both human and animals. PA degradation processes was negatively controlled by MarR-family regulator PicR. However, the regulatory mechanisms have not been fully investigated and the orphan picR-encoding gene has been rarely reported. In this study, the degradation and regulatory characterizations of PA by a soil bacterium Bordetella petrii strain MY10, were investigated. The pic cluster of strain MY10 consisted of four individual transcriptional units (picR, picCGEDF, picB1B2B3B4 and picA1A2A3) and the picRMY10 gene was separated from the other three transcriptional units. The lag phase of PA degradation was shortened by deleting picRMY10 gene. Electrophoretic Mobility Shift Assay (EMSA) results illustrated that PicRMY10 bound to the promoter regions of transcriptional units of picA, picB, picC and picRMY10. Four DNA-binding regions shared a common palindromic structure: TCAG-N4-CTNN. Three key amino acid residues R19, Q22, V73 of PicRMY10 were studied by site-directed mutagenesis and played crucial roles in PicRMY10 regulation. Bioinformatics analysis of the pic cluster of strain MY10 and 19 related bacteria showed that the PicR proteins were taxon-related and co-evolved with its host. This study provides new insights on understandings of the biodiversity of regulatory mechanisms of PA biodegradation by bacteria in nature.

Holocentromeres can consist of merely a few megabase-sized satellite arrays

The centromere is the chromosome region where microtubules attach during cell division. In contrast to monocentric chromosomes with one centromere, holocentric species usually distribute hundreds of centromere units along the entire chromatid. We assembled the chromosome-scale reference genome and analyzed the holocentromere and (epi)genome organization of the lilioid Chionographis japonica. Remarkably, each of its holocentric chromatids consists of only 7 to 11 evenly spaced megabase-sized centromere-specific histone H3-positive units. These units contain satellite arrays of 23 and 28 bp-long monomers capable of forming palindromic structures. Like monocentric species, C. japonica forms clustered centromeres in chromocenters at interphase. In addition, the large-scale eu- and heterochromatin arrangement differs between C. japonica and other known holocentric species. Finally, using polymer simulations, we model the formation of prometaphase line-like holocentromeres from interphase centromere clusters. Our findings broaden the knowledge about centromere diversity, showing that holocentricity is not restricted to species with numerous and small centromere units.

DNA:RNA Hybrids Are Major Dinoflagellate Minicircle Molecular Types.

Peridinin-containing dinoflagellate plastomes are predominantly encoded in nuclear genomes, with less than 20 essential chloroplast proteins carried on "minicircles". Each minicircle generally carries one gene and a short non-coding region (NCR) with a median length of approximately 400-1000 bp. We report here differential nuclease sensitivity and two-dimensional southern blot patterns, suggesting that dsDNA minicircles are in fact the minor forms, with substantial DNA:RNA hybrids (DRHs). Additionally, we observed large molecular weight intermediates, cell-lysate-dependent NCR secondary structures, multiple bidirectional predicted ssDNA structures, and different southern blot patterns when probed with different NCR fragments. In silico analysis suggested the existence of substantial secondary structures with inverted repeats (IR) and palindrome structures within the initial ~650 bp of the NCR sequences, in accordance with conversion event(s) outcomes with PCR. Based on these findings, we propose a new transcription-templating-translation model, which is associated with cross-hopping shift intermediates. Since dinoflagellate chloroplasts are cytosolic and lack nuclear envelope breakdown, the dynamic DRH minicircle transport could have contributed to the spatial-temporal dynamics required for photosystem repair. This represents a paradigm shift from the previous understanding of "minicircle DNAs" to a "working plastome", which will have significant implications for its molecular functionality and evolution.

Target-responsive DNA translator for amplified and sensitive sensing of Myc-Max transcription factor dimer

Myc-Max is a central eukaryotic transcription factor dimer that plays key roles in regulating cellular activities such as cell growth, proliferation, and differentiation. Selective and sensitive quantification of Myc-Max thus has valuable significances for biological studies and disease diagnosis. On the basis of a new DNA translator probe, we construct an amplified FRET sensing strategy for sensitively detecting Myc-Max in human serums via DNAzyme and clamped hybridization chain reaction (cHCR)-integrated signal amplifications. Myc-Max binds the DNA translator and switches its conformation to activate the DNAzyme and trigger cHCR for the assembly generation of DNA networks from two respective dye-labeled dual stem-loop and palindromic sequence-containing hairpin structures. Such DNA networks pull the two dyes into proximity position to exhibit highly magnified FRET responses for sensitively detecting Myc-Max with a 1.2 pM low detection limit in the dynamic range between 10 pM and 1 nM. Besides, sensitive discrimination of low levels of Myc-Max in diluted human serums has been verified by the developed method. Moreover, the sequence of the DNA translator can be tuned to accommodate different biomolecules, making the developed sensing strategy a versatile tool for detecting various trace biomarkers for diagnosing diseases at their early stages.

Evolution of transcriptional regulation of histidine metabolism in Gram-positive bacteria

BackgroundThe histidine metabolism and transport (his) genes are controlled by a variety of RNA-dependent regulatory systems among diverse taxonomic groups of bacteria including T-box riboswitches in Firmicutes and Actinobacteria and RNA attenuators in Proteobacteria. Using a comparative genomic approach, we previously identified a novel DNA-binding transcription factor (named HisR) that controls the histidine metabolism genes in diverse Gram-positive bacteria from the Firmicutes phylum.ResultsHere we report the identification of HisR-binding sites within the regulatory regions of the histidine metabolism and transport genes in 395 genomes representing the Bacilli, Clostridia, Negativicutes, and Tissierellia classes of Firmicutes, as well as in 97 other HisR-encoding genomes from the Actinobacteria, Proteobacteria, and Synergistetes phyla. HisR belongs to the TrpR family of transcription factors, and their predicted DNA binding motifs have a similar 20-bp palindromic structure but distinct lineage-specific consensus sequences. The predicted HisR-binding motif was validated in vitro using DNA binding assays with purified protein from the human gut bacterium Ruminococcus gnavus. To fill a knowledge gap in the regulation of histidine metabolism genes in Firmicutes genomes that lack a hisR repressor gene, we systematically searched their upstream regions for potential RNA regulatory elements. As result, we identified 158 T-box riboswitches preceding the histidine biosynthesis and/or transport genes in 129 Firmicutes genomes. Finally, novel candidate RNA attenuators were identified upstream of the histidine biosynthesis operons in six species from the Bacillus cereus group, as well as in five Eubacteriales and six Erysipelotrichales species.ConclusionsThe obtained distribution of the HisR transcription factor and two RNA-mediated regulatory mechanisms for histidine metabolism genes across over 600 species of Firmicutes is discussed from functional and evolutionary points of view.

The beauty of language structure: A single-case fMRI study of palindrome creation

Humans seem to be inherently driven to engage in wordplay. An example is the creation of palindromes – sentences that read the same backward and forward. This activity can be framed as a curiosity-driven behaviour, in which individuals seek for information that serves no direct purpose and in the absence of external rewards. In this fMRI case study, an experienced palindrome creator was scanned while he generated palindromes with different levels of difficulty. Palindrome creation was alternated with resting periods and with a working memory task, both serving as control conditions. Relative to resting, palindrome creation recruited frontal domain-specific language networks and fronto-parietal domain-general networks. The comparison with the working memory task evidenced partial overlap with the multiple-demand cortex, which participates in solving a variety of cognitively challenging tasks. Intriguingly, greater difficulty during palindrome creation differentially activated the right frontopolar cortex (BA 10), a region that was also linked to palindrome resolution. The latter is consistent with exploratory behaviour – in this case, with seeking new but interdependent linguistic segments within a complex internal model (i.e., a palindromic structure)– and bears resemblance with brain substrates sustaining hard logical reasoning, altogether pointing to a commonplace for curiosity in discovering new and complex relations.

Repetitive DNA Sequences in the Human Y Chromosome and Male Infertility.

The male-specific Y chromosome, which is well known for its diverse and complex repetitive sequences, has different sizes, genome structures, contents and evolutionary trajectories from other chromosomes and is of great significance for testis development and function. The large number of repetitive sequences and palindrome structure of the Y chromosome play an important role in maintaining the stability of male sex determining genes, although they can also cause non-allelic homologous recombination within the chromosome. Deletion of certain Y chromosome sequences will lead to spermatogenesis disorders and male infertility. And Y chromosome genes are also involved in the occurrence of reproductive system cancers and can increase the susceptibility of other tumors. In addition, the Y chromosome has very special value in the personal identification and parentage testing of male-related cases in forensic medicine because of its unique paternal genetic characteristics. In view of the extremely high frequency and complexity of gene rearrangements and the limitations of sequencing technology, the analysis of Y chromosome sequences and the study of Y-gene function still have many unsolved problems. This article will introduce the structure and repetitive sequence of the Y chromosome, summarize the correlation between Y chromosome various sequence deletions and male infertility for understanding the repetitive sequence of Y chromosome more systematically, in order to provide research motivation for further explore of the molecules mechanism of Y-deletion and male infertility and theoretical foundations for the transformation of basic research into applications in clinical medicine and forensic medicine.

Bartók's Most Daring Concept of a Palindromic Structure: The Sonata-Form Opening Movement of the Fifth Quartet

Abstract In movement I of String Quartet no. 5 inversion shapes of the themes are recapitulated in reverse order – probably the most daring concept of a palindromic structure of a sonata-form movement in Bartók's realm. After all, for him a strict hin und zurück form with strong thematic characters was unthinkable. Already the strategy of this opening movement involved danger. If Theme I after a transition leads to Theme II, which leads to Theme III, as a dramatic series of actions, how could the reverse order of these themes be “natural”? To minimize the danger, in this movement Bartók reconsidered the usual dramaturgy of the exposition. Instead of a continuous growth of the musical “scenes” welded together, he presented three thematic blocks very much different in character, heavily punctuated by fragments of the first theme. Therefore, dramatic contrast rather than organic development is the key term, and so the reverse order of the thematic blocks in the recapitulation is less artificial.

NMR solution structures of d(GGCCTG)n repeats associated with spinocerebellar ataxia type 36

Expansion of d(GGCCTG)n hexanucleotide repeats in the NOP56 gene is the genetic cause of spinocerebellar ataxia type 36 (SCA36) which is an inheritable neurodegenerative disease. Non-B DNA is known to be the structural intermediate causing repeat expansions. Yet, the structure and mechanism of genetic instability of d(GGCCTG)n repeats remain elusive. In this work, we investigated the solution structures of sequences containing two to eight GGCCTG repeats using nuclear magnetic resonance (NMR) spectroscopy. They were found to form diverse secondary structures, including hairpin, duplex and G-quadruplex (G4). Intriguingly, the hairpin structure was present in all the investigated sequences. The NMR solution structure of the hairpin formed by d(GGCCTG)2 was determined, disclosing an unprecedented CCTGGG hexanucleotide loop in which the first and sixth loop residues formed a Watson-Crick loop-closing base pair, the second and third loop residues stacked in the major groove, whereas the fourth and fifth loop residues formed a G·G mismatch. Apart from the hairpin, antiparallel G4 and palindromic duplex structures were found to form in d(GGCCTG)2 and d(GGCCTG)3–8, respectively. Results of this work provide new insights into the genetic instability of d(GGCCTG)n repeats and structure-based drug design for SCA36.

Thirugnana Sambandhar - A Mathematician

India has been the Land of notable poets whose exemplary works are world renowned. One such great poet is Thirugnana Sambandhar. He is a saint, poet, philosopher, composer who belongs to 7th Century. He was born in Seerkaazhi of Tamilnadu. He had coined many Special Geometrical poetic structures like Thiru ezhukkootrirukkai (poem with mathematical Triangular Pattern), Maalai Maatru (a poem with palindromic Structure), Mozhi Maatru (a poem in which the meaning of the poem can be observed by a systematic Chane of words), Gomuthri (Flow of the poem in such a way it forms a wave line), Chakramaatru (a poem which is constructed in a circular form ). By the above mentioned amazing structure He has no parallels in the worlds poetry Thirugnana Sambandhar is the epitome of Tamil Literature has penned down many such extraordinary poems. A Mathematician is one who uses an extensive knowledge of Mathematics in their work. Mathematicians are concerned with numbers, data, quantity, structure, space,models and change. Here in this poetic form Thiruezhukkootrirukkai Thirugnana Sambandhar had used numbers in a brilliant way to form a Triangle. This is called “Chitrakavi” in Tamil. By analyzing the whole poem we will get a geometrical structure. In this Thiruezhukkootrirukkai Thirugnana Sambandhar has constructed the words in such a way to form a symmetrical triangle. These triangle is arranged in a perfect mathematical calculation. This can be analysed through the law of binomial co- efficient. This is analysed and proved in this paper. Thirugnana Sambandhar belongs to 7th Century whereas the Scientist and Mathematician Pascal who discovered the law of Bi-nomial co-efficient belongs to 17th century. Other than this Mathematical diagram of triangle this poem has Palindromic numbers which add more beauty to this structure which is also a mathematical calculation. By constructing this amazing poetic structure Thirugnana Sambandhar proves beyond doubt that he is a “Mathematician” of India of the 7th Century itself who had applied the law of triangle earlier.

Genomic Sequence Analysis of Bombyx mori Nucleopolyhedrovirus Isolated from Yunnan Sericulture Region, China.

The blood pathogens of grasserie caused by Bombyx mori nucleopolyhedrovirus BmNPV have a serious impact on the sericulture industry. To understand the genetic status of BmNPV endemic strains in the Yunnan sericulture region, the structure and complete genome sequence of BmNPV isolated from Baoshan city of Yunnan Province were described and compared to known strains. The BmNPV-Baoshan isolate was a nucleopolyhedrovirus parasitized in silkworm larvae. Its genome has 128, 452bp with a G + C content of 40.4%. Phylogenetic analysis clustered the virus with China BmNPV isolates; BmNPV-Baoshan was closely related to BomaNPV-S1 (both strains originated from the same ancestor). BmNPV-Baoshan strain has bro-b gene deletion, hr1 missing 4 repeat units of 30-bp palindrome structure compared to BmNPV-T3 strain. The aim of this study was to elucidate the evolution of the virus further and provide insights for the protection of virus-induced hematologic sepsis.

Low-Rank Perturbation of Regular Matrix Pencils with Symmetry Structures

The generic change of the Weierstraß canonical form of regular complex structured matrix pencils under generic structure-preserving additive low-rank perturbations is studied. Several different symmetry structures are considered, and it is shown that for most of the structures, the generic change in the eigenvalues is analogous to the case of generic perturbations that ignore the structure. However, for some odd/even and palindromic structures, there is a different behavior for the eigenvalues 0 and \(\infty \), respectively, \(+1\) and \(-1\). The differences arise in those cases where the parity of the partial multiplicities in the perturbed matrix pencil provided by the generic behavior in the general structure-ignoring case is not in accordance with the restrictions imposed by the structure. The new results extend results for the rank-1 and rank-2 cases that were obtained in Batzke (Linear Algebra Appl 458:638–670, 2014, Oper Matrices 10:83–112, 2016) for the case of special structure-preserving perturbations. As the main tool, we use decompositions of matrix pencils with symmetry structure into sums of rank-1 matrix pencils, as those allow a parametrization of the set of matrix pencils with a given symmetry structure and a given rank.

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.

BackgroundDucks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques.ResultsA major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination.ConclusionsOur results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.